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Sample records for intronic enhancers control

  1. Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells.

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    López Rodríguez, Maykel; Kaminska, Dorota; Lappalainen, Kati; Pihlajamäki, Jussi; Kaikkonen, Minna U; Laakso, Markku

    2017-07-06

    Genome-wide association studies (GWAS) have identified more than 100 genetic loci associated with type 2 diabetes (T2D). However, the underlying biological mechanisms for many of these associations remain unknown. GWAS signals close to the glucokinase regulatory protein gene (GCKR) have been reported for lipid and glucose metabolism traits and the risk of T2D. We investigated the regulatory function of an intronic locus at GCKR represented by the lead single nucleotide polymorphism (SNP) rs780094. We used ENCODE project histone modification and transcription factor binding data to determine the regulatory features of a GCKR intronic locus formed by the high linkage disequilibrium rs780094(C/T), rs780095(G/A), and rs780096(G/C) SNPs. Characterization of the transcriptional activity of this region was assessed by luciferase reporter assays in HepG2 cells and mouse primary hepatocytes. ChIP-qPCR was used to determine the levels of haplotype specific transcription factor binding and histone marks. A CRISPR-dCas9 transcriptional activator system and qPCR were used to activate the locus and measure GCKR expression, respectively. Differential haplotype expression was measured from human liver biopsies. The ENCODE data suggest the existence of a liver-specific intragenic enhancer at the locus represented by s780094. We observed that FOXA2 increased the transcriptional activity of this region in a haplotype specific way (CGG > TAC; rs780094, rs780095, and rs780096). In addition, the CGG haplotype showed higher binding to FOXA2 and higher levels of the H3K27Ac histone mark. The epigenetic activation of this locus increased the expression of endogenous GCKR in HepG2 cells, confirming that GCKR is the direct target gene of the enhancer. Finally, we confirmed that the CGG haplotype exhibits higher levels of transcription in human liver. Our results demonstrate the existence of a liver-specific FOXA2-regulated transcriptional enhancer at an intronic T2D locus represented by

  2. Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer

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    Tai Phillip WL

    2011-07-01

    Full Text Available Abstract Background Hundreds of genes, including muscle creatine kinase (MCK, are differentially expressed in fast- and slow-twitch muscle fibers, but the fiber type-specific regulatory mechanisms are not well understood. Results Modulatory region 1 (MR1 is a 1-kb regulatory region within MCK intron 1 that is highly active in terminally differentiating skeletal myocytes in vitro. A MCK small intronic enhancer (MCK-SIE containing a paired E-box/myocyte enhancer factor 2 (MEF2 regulatory motif resides within MR1. The SIE's transcriptional activity equals that of the extensively characterized 206-bp MCK 5'-enhancer, but the MCK-SIE is flanked by regions that can repress its activity via the individual and combined effects of about 15 different but highly conserved 9- to 24-bp sequences. ChIP and ChIP-Seq analyses indicate that the SIE and the MCK 5'-enhancer are occupied by MyoD, myogenin and MEF2. Many other E-boxes located within or immediately adjacent to intron 1 are not occupied by MyoD or myogenin. Transgenic analysis of a 6.5-kb MCK genomic fragment containing the 5'-enhancer and proximal promoter plus the 3.2-kb intron 1, with and without MR1, indicates that MR1 is critical for MCK expression in slow- and intermediate-twitch muscle fibers (types I and IIa, respectively, but is not required for expression in fast-twitch muscle fibers (types IIb and IId. Conclusions In this study, we discovered that MR1 is critical for MCK expression in slow- and intermediate-twitch muscle fibers and that MR1's positive transcriptional activity depends on a paired E-box MEF2 site motif within a SIE. This is the first study to delineate the DNA controls for MCK expression in different skeletal muscle fiber types.

  3. Highly efficient expression of interleukin-2 under the control of rabbit β-globin intron II gene enhances protective immune responses of porcine reproductive and respiratory syndrome (PRRS DNA vaccine in pigs.

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    Yijun Du

    Full Text Available Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV had caused catastrophic losses in swine industry in China. The current inactivated vaccine provided only limited protection, and the attenuated live vaccine could protect piglets against the HP-PRRSV but there was a possibility that the attenuated virus returned to high virulence. In this study, the eukaryotic expression vector pVAX1© was modified under the control of rabbit β-globin intron II gene and the modified vector pMVAX1© was constructed. Porcine interleukin-2 (IL-2 and GP3-GP5 fusion protein of HP-PRRSV strain SD-JN were highly expressed by pMVAX1©. Mice inoculated with pMVAX1©-GP35 developed significantly higher PRRSV-specific antibody responses and T cell proliferation than those vaccinated with pVAX1©-GP35. pMVAX1©-GP35 was selected as PRRS DNA vaccine candidate and co-administrated with pVAX1©-IL-2 or pMVAX1©-IL-2 in pigs. pMVAX1©-IL-2+pMVAX1©-GP35 could provide enhanced PRRSV-specific antibody responses, T cell proliferation, Th1-type and Th2-type cytokine responses and CTL responses than pMVAX1©-GP35 and pVAX1©-IL-2+pMVAX1©-GP35. Following homologous challenge with HP-PRRSV strain SD-JN, similar with attenuated PRRS vaccine group, pigs inoculated with pMVAX1©-IL-2+pMVAX1©-GP35 showed no clinical signs, almost no lung lesions and no viremia, as compared to those in pMVAX1©-GP35 and pVAX1©-IL-2+pMVAX1©-GP35 groups. It indicated that pMVAX1©-IL-2 effectively increases humoral and cell mediated immune responses of pMVAX1©-GP35. Co-administration of pMVAX1©-IL-2 and pMVAX1©-GP35 might be attractive candidate vaccines for preventing HP-PRRSV infections.

  4. Highly efficient expression of interleukin-2 under the control of rabbit β-globin intron II gene enhances protective immune responses of porcine reproductive and respiratory syndrome (PRRS) DNA vaccine in pigs.

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    Du, Yijun; Lu, Yu; Wang, Xinglong; Qi, Jing; Liu, Jiyu; Hu, Yue; Li, Feng; Wu, Jiaqiang; Guo, Lihui; Liu, Junzhen; Tao, Haiying; Sun, Wenbo; Chen, Lei; Cong, Xiaoyan; Ren, Sufang; Shi, Jianli; Li, Jun; Wang, Jinbao; Huang, Baohua; Wan, Renzhong

    2014-01-01

    Highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV) had caused catastrophic losses in swine industry in China. The current inactivated vaccine provided only limited protection, and the attenuated live vaccine could protect piglets against the HP-PRRSV but there was a possibility that the attenuated virus returned to high virulence. In this study, the eukaryotic expression vector pVAX1© was modified under the control of rabbit β-globin intron II gene and the modified vector pMVAX1© was constructed. Porcine interleukin-2 (IL-2) and GP3-GP5 fusion protein of HP-PRRSV strain SD-JN were highly expressed by pMVAX1©. Mice inoculated with pMVAX1©-GP35 developed significantly higher PRRSV-specific antibody responses and T cell proliferation than those vaccinated with pVAX1©-GP35. pMVAX1©-GP35 was selected as PRRS DNA vaccine candidate and co-administrated with pVAX1©-IL-2 or pMVAX1©-IL-2 in pigs. pMVAX1©-IL-2+pMVAX1©-GP35 could provide enhanced PRRSV-specific antibody responses, T cell proliferation, Th1-type and Th2-type cytokine responses and CTL responses than pMVAX1©-GP35 and pVAX1©-IL-2+pMVAX1©-GP35. Following homologous challenge with HP-PRRSV strain SD-JN, similar with attenuated PRRS vaccine group, pigs inoculated with pMVAX1©-IL-2+pMVAX1©-GP35 showed no clinical signs, almost no lung lesions and no viremia, as compared to those in pMVAX1©-GP35 and pVAX1©-IL-2+pMVAX1©-GP35 groups. It indicated that pMVAX1©-IL-2 effectively increases humoral and cell mediated immune responses of pMVAX1©-GP35. Co-administration of pMVAX1©-IL-2 and pMVAX1©-GP35 might be attractive candidate vaccines for preventing HP-PRRSV infections.

  5. An intronic (A/U)GGG repeat enhances the splicing of an alternative intron of the chicken beta-tropomyosin pre-mRNA.

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    Sirand-Pugnet, P; Durosay, P; Brody, E; Marie, J

    1995-09-11

    Computer analysis of human intron sequences have revealed a 50 nucleotide (nt) GC-rich region downstream of the 5' splice site; the trinucleotide GGG occurs almost four times as frequently as it would in a random sequence. The 5' part of a beta-tropomyosin intron exhibits six repetitions of the motif (A/U)GGG. In order to test whether these motifs play a role in the splicing process we have mutated some or all of them. Mutated RNAs show a lower in vitro splicing efficiency when compared with the wild-type, especially when all six motifs are mutated (> 70% inhibition). Assembly of the spliceosome complex B and, to a lesser extent, of the pre-spliceosome complex A also appears to be strongly affected by this mutation. A 55 kDa protein within HeLa cell nuclear extract is efficiently cross-linked to the G-rich region. This protein is present in the splicing complexes and its cross-linking to the pre-mRNA requires the presence of one or several snRNP. Altogether our results suggest that the G-rich sequences present in the 5' part of introns may act as an enhancer of the splicing reaction at the level of spliceosome assembly.

  6. Antagonistic factors control the unproductive splicing of SC35 terminal intron.

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    Dreumont, Natacha; Hardy, Sara; Behm-Ansmant, Isabelle; Kister, Liliane; Branlant, Christiane; Stévenin, James; Bourgeois, Cyril F

    2010-03-01

    Alternative splicing is regulated in part by variations in the relative concentrations of a variety of factors, including serine/arginine-rich (SR) proteins. The SR protein SC35 self-regulates its expression by stimulating unproductive splicing events in the 3' untranslated region of its own pre-mRNA. Using various minigene constructs containing the terminal retained intron and flanking exons, we identified in the highly conserved last exon a number of exonic splicing enhancer elements responding specifically to SC35, and showed an inverse correlation between affinity of SC35 and enhancer strength. The enhancer region, which is included in a long stem loop, also contains repressor elements, and is recognized by other RNA-binding proteins, notably hnRNP H protein and TAR DNA binding protein (TDP-43). Finally, in vitro and in cellulo experiments indicated that hnRNP H and TDP-43 antagonize the binding of SC35 to the terminal exon and specifically repress the use of SC35 terminal 3' splice site. Our study provides new information about the molecular mechanisms of SC35-mediated splicing activation. It also highlights the existence of a complex network of self- and cross-regulatory mechanisms between splicing regulators, which controls their homeostasis and offers many ways of modulating their concentration in response to the cellular environment.

  7. The evolution of the macrophage-specific enhancer (Fms intronic regulatory element) within the CSF1R locus of vertebrates.

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    Hume, David A; Wollscheid-Lengeling, Evi; Rojo, Rocio; Pridans, Clare

    2017-12-07

    The Csf1r locus encodes the receptor for macrophage colony-stimulating factor, which controls the proliferation, differentiation and survival of macrophages. The 300 bp Fms intronic regulatory element (FIRE), within the second intron of Csf1r, is necessary and sufficient to direct macrophage-specific transcription. We have analysed the conservation and divergence of the FIRE DNA sequence in vertebrates. FIRE is present in the same location in the Csf1r locus in reptile, avian and mammalian genomes. Nearest neighbor analysis based upon this element alone largely recapitulates phylogenies inferred from much larger genomic sequence datasets. One core element, containing binding sites for AP1 family and the macrophage-specific transcription factor, PU.1, is conserved from lizards to humans. Around this element, the FIRE sequence is conserved within clades with the most conserved elements containing motifs for known myeloid-expressed transcription factors. Conversely, there is little alignment between clades outside the AP1/PU.1 element. The analysis favours a hybrid between "enhanceosome" and "smorgasbord" models of enhancer function, in which elements cooperate to bind components of the available transcription factor milieu.

  8. Antagonistic factors control the unproductive splicing of SC35 terminal intron

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    Dreumont, Natacha; Hardy, Sara; Behm-Ansmant, Isabelle; Kister, Liliane; Branlant, Christiane; St?venin, James; Bourgeois, Cyril F.

    2009-01-01

    Alternative splicing is regulated in part by variations in the relative concentrations of a variety of factors, including serine/arginine-rich (SR) proteins. The SR protein SC35 self-regulates its expression by stimulating unproductive splicing events in the 3? untranslated region of its own pre-mRNA. Using various minigene constructs containing the terminal retained intron and flanking exons, we identified in the highly conserved last exon a number of exonic splicing enhancer elements respon...

  9. Role of intron-mediated enhancement on accumulation of an Arabidopsis NB-LRR class R-protein that confers resistance to Cucumber mosaic virus.

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    Yukiyo Sato

    Full Text Available The accumulation of RCY1 protein, which is encoded by RESISTANCE TO CMV(Y (RCY1, a CC-NB-LRR class R-gene, is tightly correlated with the strength of the resistance to a yellow strain of Cucumber mosaic virus [CMV(Y] in Arabidopsis thaliana. In order to enhance resistance to CMV by overexpression of RCY1, A. thaliana was transformed with intron-less RCY1 cDNA construct under the control of strong CaMV35S promoter. Remarkably, a relative amount of RCY1 protein accumulation in the transformants was much lower than that in plants expressing genomic RCY1 under the control of its native promoter. To identify a regulatory element of RCY1 that could cause such differential levels of RCY1 accumulation, a series of RCY1 cDNA and genomic RCY1 constructs were transiently expressed in Nicotiana benthamiana leaves by the Agrobacterium-mediated infiltration method. Comparative analysis of the level of RCY1 accumulation in the leaf tissues transiently expressing each construct indicated that the intron located in the RCY1-coding region of genomic RCY1, but not the native RCY1 genomic promoter or the 5'-and 3'-untranslated regions of RCY1, was indispensable for high level RCY1 accumulation. The increased levels of RCY1 accelerated plant disease defense reactions. Interestingly, such intron-mediated enhancement of RCY1 accumulation depended neither on the abundance of the RCY1 transcript nor on the RCY1 specific-intron sequence. Taken together, intron-mediated RCY1 expression seems to play a key role in the expression of complete resistance to CMV(Y by maintaining RCY1 accumulation at high levels.

  10. AML1/ETO trans-activates c-KIT expression through the long range interaction between promoter and intronic enhancer.

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    Tian, Ying; Wang, Genjie; Hu, Qingzhu; Xiao, Xichun; Chen, Shuxia

    2018-04-01

    The AML1/ETO onco-fusion protein is crucial for the genesis of t(8;21) acute myeloid leukemia (AML) and is well documented as a transcriptional repressor through dominant-negative effect. However, little is known about the transactivation mechanism of AML1/ETO. Through large cohort of patient's expression level data analysis and a series of experimental validation, we report here that AML1/ETO transactivates c-KIT expression through directly binding to and mediating the long-range interaction between the promoter and intronic enhancer regions of c-KIT. Gene expression analyses verify that c-KIT expression is significantly high in t(8;21) AML. Further ChIP-seq analysis and motif scanning identify two regulatory regions located in the promoter and intronic enhancer region of c-KIT, respectively. Both regions are enriched by co-factors of AML1/ETO, such as AML1, CEBPe, c-Jun, and c-Fos. Further luciferase reporter assays show that AML1/ETO trans-activates c-KIT promoter activity through directly recognizing the AML1 motif and the co-existence of co-factors. The induction of c-KIT promoter activity is reinforced with the existence of intronic enhancer region. Furthermore, ChIP-3C-qPCR assays verify that AML1/ETO mediates the formation of DNA-looping between the c-KIT promoter and intronic enhancer region through the long-range interaction. Collectively, our data uncover a novel transcriptional activity mechanism of AML1/ETO and enrich our knowledge of the onco-fusion protein mediated transcription regulation. © 2017 Wiley Periodicals, Inc.

  11. Neomycin B inhibits splicing of the td intron indirectly by interfering with translation and enhances missplicing in vivo.

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    Waldsich, C; Semrad, K; Schroeder, R

    1998-12-01

    The aminoglycoside antibiotic neomycin B inhibits translation in prokaryotes and interferes with RNA-protein interactions in HIV both in vivo and in vitro. Hitherto, inhibition of ribozyme catalysis has only been observed in vitro. We therefore monitored the activity of neomycin B and several other aminoglycoside antibiotics on splicing of the T4 phage thymidylate synthase (td) intron in vivo. All antibiotics tested inhibited splicing, even chloramphenicol, which does not inhibit splicing in vitro. Splicing of the td intron in vivo requires translation for proper folding of the pre-mRNA. In the absence of translation, two interactions between sequences in the upstream exon and the 5' and 3' splice sites trap the pre-mRNA in splicing-incompetent conformations. Their disruption by mutations rendered splicing less dependent on translation and also less sensitive to neomycin B. Intron splicing was affected by neither neomycin B nor gentamicin in Escherichia coli strains carrying antibiotic-resistance genes that modify the ribosomal RNA. Taken together, this demonstrates that in vivo splicing of td intron is not directly inhibited by aminoglycosides, but rather indirectly by their interference with translation. This was further confirmed by assaying splicing of the Tetrahymena group I intron, which is inserted in the E. coli 23 S rRNA and, thus, not translated. Furthermore, neomycin B, paromomycin, and streptomycin enhanced missplicing in antibiotic-sensitive strains. Missplicing is caused by an alternative structural element containing a cryptic 5' splice site, which serves as a substrate for the ribozyme. Our results demonstrate that aminoglycoside antibiotics display different effects on ribozymes in vivo and in vitro.

  12. Recruitment of Staufen2 Enhances Dendritic Localization of an Intron-Containing CaMKIIα mRNA

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    Raúl Ortiz

    2017-07-01

    Full Text Available Regulation of mRNA localization is a conserved cellular process observed in many types of cells and organisms. Asymmetrical mRNA distribution plays a particularly important role in the nervous system, where local translation of localized mRNA represents a key mechanism in synaptic plasticity. CaMKIIα is a very abundant mRNA detected in neurites, consistent with its crucial role at glutamatergic synapses. Here, we report the presence of CaMKIIα mRNA isoforms that contain intron i16 in dendrites, RNA granules, and synaptoneurosomes from primary neurons and brain. This subpopulation of unspliced mRNA preferentially localizes to distal dendrites in a synaptic-activity-dependent manner. Staufen2, a well-established marker of RNA transport in dendrites, interacts with intron i16 sequences and enhances its distal dendritic localization, pointing to the existence of intron-mediated mechanisms in the molecular pathways that modulate dendritic transport and localization of synaptic mRNAs.

  13. Effects of promoter, intron and enhancer elements on transient gene expression in sugar-cane and carrot protoplasts.

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    Rathus, C; Bower, R; Birch, R G

    1993-11-01

    Various chimaeric promoter regions coupled to the uidA beta-glucuronidase gene were evaluated for transient expression strength following electroporation into sugar-cane (monocot) and carrot (dicot) protoplasts. Multiple enhancer elements increased expression in sugar-cane, by up to 400-fold for the artificial Emu promoter relative to the CaMV 35S promoter. The relative expression strengths of promoters varied substantially between the species. Sugar-cane also differed in some respects from previously tested species in the family Poaceae. For example, in sugar-cane the nopaline synthase and CaMV 35S promoters were of equivalent strength, and insertion of Adh1 intron 1 into the 5' transcribed region decreased expression strength.

  14. Sequence features responsible for intron retention in human

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    Sakabe Noboru

    2007-02-01

    Full Text Available Abstract Background One of the least common types of alternative splicing is the complete retention of an intron in a mature transcript. Intron retention (IR is believed to be the result of intron, rather than exon, definition associated with failure of the recognition of weak splice sites flanking short introns. Although studies on individual retained introns have been published, few systematic surveys of large amounts of data have been conducted on the mechanisms that lead to IR. Results TTo understand how sequence features are associated with or control IR, and to produce a generalized model that could reveal previously unknown signals that regulate this type of alternative splicing, we partitioned intron retention events observed in human cDNAs into two groups based on the relative abundance of both isoforms and compared relevant features. We found that a higher frequency of IR in human is associated with individual introns that have weaker splice sites, genes with shorter intron lengths, higher expression levels and lower density of both a set of exon splicing silencers (ESSs and the intronic splicing enhancer GGG. Both groups of retained introns presented events conserved in mouse, in which the retained introns were also short and presented weaker splice sites. Conclusion Although our results confirmed that weaker splice sites are associated with IR, they showed that this feature alone cannot explain a non-negligible fraction of events. Our analysis suggests that cis-regulatory elements are likely to play a crucial role in regulating IR and also reveals previously unknown features that seem to influence its occurrence. These results highlight the importance of considering the interplay among these features in the regulation of the relative frequency of IR.

  15. Identification of GATA2 and AP-1 activator elements within the enhancer VNTR occurring in intron 5 of the human SIRT3 gene

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    Human SIRT3 gene contains an intronic VNTR enhancer. A T > C transition occurring in the second repeat of each VNTR allele implies the presence/absence of a putative GATA binding motif. A partially overlapping AP-1 site, not affected by the transition, was also identified. Aims of the present study ...

  16. The Role of Transcription Factor PU.I in the Activity of the Intronic Enhancer of the Eosinophil-Derived Neurotoxin (RNS2) Gene

    NARCIS (Netherlands)

    Dijk, Thamar B. van; Caldenhoven, Eric; Raaijmakers, J.A.M.; Lammers, J.W.J.; Koenderman, L.; Groot, Rolf P. de

    1997-01-01

    Eosinophil-derived neurotoxin (EDN) found in the granules of human eosinophils is a cationic ribonuclease toxin. Expression of the EDN gene (RNS2) in eosinophils is dependent on proximal promoter sequences in combination with an enhancer located in the first intron. We further define here

  17. An Orchestrated Intron Retention Program in Meiosis Controls Timely Usage of Transcripts during Germ Cell Differentiation.

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    Naro, Chiara; Jolly, Ariane; Di Persio, Sara; Bielli, Pamela; Setterblad, Niclas; Alberdi, Antonio J; Vicini, Elena; Geremia, Raffaele; De la Grange, Pierre; Sette, Claudio

    2017-04-10

    Global transcriptome reprogramming during spermatogenesis ensures timely expression of factors in each phase of male germ cell differentiation. Spermatocytes and spermatids require particularly extensive reprogramming of gene expression to switch from mitosis to meiosis and to support gamete morphogenesis. Here, we uncovered an extensive alternative splicing program during this transmeiotic differentiation. Notably, intron retention was largely the most enriched pattern, with spermatocytes showing generally higher levels of retention compared with spermatids. Retained introns are characterized by weak splice sites and are enriched in genes with strong relevance for gamete function. Meiotic intron-retaining transcripts (IRTs) were exclusively localized in the nucleus. However, differently from other developmentally regulated IRTs, they are stable RNAs, showing longer half-life than properly spliced transcripts. Strikingly, fate-mapping experiments revealed that IRTs are recruited onto polyribosomes days after synthesis. These studies reveal an unexpected function for regulated intron retention in modulation of the timely expression of select transcripts during spermatogenesis. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  18. An evolutionarily conserved intronic region controls the spatiotemporal expression of the transcription factor Sox10

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    Pavan William J

    2008-10-01

    Full Text Available Abstract Background A major challenge lies in understanding the complexities of gene regulation. Mutation of the transcription factor SOX10 is associated with several human diseases. The disease phenotypes reflect the function of SOX10 in diverse tissues including the neural crest, central nervous system and otic vesicle. As expected, the SOX10 expression pattern is complex and highly dynamic, but little is known of the underlying mechanisms regulating its spatiotemporal pattern. SOX10 expression is highly conserved between all vertebrates characterised. Results We have combined in vivo testing of DNA fragments in zebrafish and computational comparative genomics to identify the first regulatory regions of the zebrafish sox10 gene. Both approaches converged on the 3' end of the conserved 1st intron as being critical for spatial patterning of sox10 in the embryo. Importantly, we have defined a minimal region crucial for this function. We show that this region contains numerous binding sites for transcription factors known to be essential in early neural crest induction, including Tcf/Lef, Sox and FoxD3. We show that the identity and relative position of these binding sites are conserved between zebrafish and mammals. A further region, partially required for oligodendrocyte expression, lies in the 5' region of the same intron and contains a putative CSL binding site, consistent with a role for Notch signalling in sox10 regulation. Furthermore, we show that β-catenin, Notch signalling and Sox9 can induce ectopic sox10 expression in early embryos, consistent with regulatory roles predicted from our transgenic and computational results. Conclusion We have thus identified two major sites of sox10 regulation in vertebrates and provided evidence supporting a role for at least three factors in driving sox10 expression in neural crest, otic epithelium and oligodendrocyte domains.

  19. Reenacting the birth of an intron

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    Hellsten, Uffe; Aspden, Julie L.; Rio, Donald C.; Rokhsar, Daniel S.

    2011-07-01

    An intron is an extended genomic feature whose function requires multiple constrained positions - donor and acceptor splice sites, a branch point, a polypyrimidine tract and suitable splicing enhancers - that may be distributed over hundreds or thousands of nucleotides. New introns are therefore unlikely to emerge by incremental accumulation of functional sub-elements. Here we demonstrate that a functional intron can be created de novo in a single step by a segmental genomic duplication. This experiment recapitulates in vivo the birth of an intron that arose in the ancestral jawed vertebrate lineage nearly half a billion years ago.

  20. Inferring Invasion History of Red Swamp Crayfish (Procambarus clarkii in China from Mitochondrial Control Region and Nuclear Intron Sequences

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    Yanhe Li

    2015-06-01

    Full Text Available Identifying the dispersal pathways of an invasive species is useful for adopting the appropriate strategies to prevent and control its spread. However, these processes are exceedingly complex. So, it is necessary to apply new technology and collect representative samples for analysis. This study used Approximate Bayesian Computation (ABC in combination with traditional genetic tools to examine extensive sample data and historical records to infer the invasion history of the red swamp crayfish, Procambarus clarkii, in China. The sequences of the mitochondrial control region and the proPOx intron in the nuclear genome of samples from 37 sites (35 in China and one each in Japan and the USA were analyzed. The results of combined scenarios testing and historical records revealed a much more complex invasion history in China than previously believed. P. clarkii was most likely originally introduced into China from Japan from an unsampled source, and the species then expanded its range primarily into the middle and lower reaches and, to a lesser extent, into the upper reaches of the Changjiang River in China. No transfer was observed from the upper reaches to the middle and lower reaches of the Changjiang River. Human-mediated jump dispersal was an important dispersal pathway for P. clarkii. The results provide a better understanding of the evolutionary scenarios involved in the rapid invasion of P. clarkii in China.

  1. Group I intron ribozymes

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    Nielsen, Henrik

    2012-01-01

    Group I intron ribozymes constitute one of the main classes of ribozymes and have been a particularly important model in the discovery of key concepts in RNA biology as well as in the development of new methods. Compared to other ribozyme classes, group I intron ribozymes display considerable...... variation both in their structure and the reactions they catalyze. The best described pathway is the splicing pathway that results in a spliced out intron and ligated exons. This is paralleled by the circularization pathway that leads to full-length circular intron and un-ligated exons. In addition......, the intronic products of these pathways have the potential to integrate into targets and to form various types of circular RNA molecules. Thus, group I intron ribozymes and associated elements found within group I introns is a rich source of biological phenomena. This chapter provides a strategy and protocols...

  2. Multiple single nucleotide polymorphisms in the first intron of the IL2RA gene affect transcription factor binding and enhancer activity.

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    Schwartz, Anton M; Demin, Denis E; Vorontsov, Ilya E; Kasyanov, Artem S; Putlyaeva, Lidia V; Tatosyan, Karina A; Kulakovskiy, Ivan V; Kuprash, Dmitry V

    2017-02-20

    IL2RA gene encodes the alpha subunit of a high-affinity receptor for interleukin-2 which is expressed by several distinct populations of lymphocytes involved in autoimmune processes. A large number of polymorphic alleles of the IL2RA locus are associated with the development of various autoimmune diseases. With bioinformatics analysis we the dissected the first intron of the IL2RA gene and selected several single nucleotide polymorphisms (SNPs) that may influence the regulation of the IL2RA gene in cell types relevant to autoimmune pathology. We described five enhancers containing the selected SNPs that stimulated activity of the IL2RA promoter in a cell-type specific manner, and tested the effect of specific SNP alleles on activity of the respective enhancers (E1 to E5, labeled according to the distance to the promoter). The E4 enhancer with minor T variant of rs61839660 SNP demonstrated reduced activity due to disrupted binding of MEF2A/C transcription factors (TFs). Neither rs706778 nor rs706779 SNPs, both associated with a number of autoimmune diseases, had any effect on the activity of the enhancer E2. However, rare variants of several SNPs (rs139767239, rs115133228, rs12722502, rs12722635) genetically linked to either rs706778 and/or rs706779 significantly influenced the activity of E1, E3 and E5 enhancers, presumably by disrupting EBF1, GABPA and ELF1 binding sites. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. The fission yeast RNA binding protein Mmi1 regulates meiotic genes by controlling intron specific splicing and polyadenylation coupled RNA turnover.

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    Huei-Mei Chen

    Full Text Available The polyA tails of mRNAs are monitored by the exosome as a quality control mechanism. We find that fission yeast, Schizosaccharomyces pombe, adopts this RNA quality control mechanism to regulate a group of 30 or more meiotic genes at the level of both splicing and RNA turnover. In vegetative cells the RNA binding protein Mmi1 binds to the primary transcripts of these genes. We find the novel motif U(U/C/GAAAC highly over-represented in targets of Mmi1. Mmi1 can specifically regulate the splicing of particular introns in a transcript: it inhibits the splicing of introns that are in the vicinity of putative Mmi1 binding sites, while allowing the splicing of other introns that are far from such sites. In addition, binding of Mmi1, particularly near the 3' end, alters 3' processing to promote extremely long polyA tails of up to a kilobase. The hyperadenylated transcripts are then targeted for degradation by the nuclear exonuclease Rrp6. The nuclear polyA binding protein Pab2 assists this hyperadenylation-mediated RNA decay. Rrp6 also targets other hyperadenylated transcripts, which become hyperadenylated in an unknown, but Mmi1-independent way. Thus, hyperadenylation may be a general signal for RNA degradation. In addition, binding of Mmi1 can affect the efficiency of 3' cleavage. Inactivation of Mmi1 in meiosis allows meiotic expression, through splicing and RNA stabilization, of at least 29 target genes, which are apparently constitutively transcribed.

  4. Origin of introns by 'intronization' of exonic sequences

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob Lewin; Penny, David

    2008-01-01

    The mechanisms of spliceosomal intron creation have proved elusive. Here we describe a new mechanism: the recruitment of internal exonic sequences ('intronization') in Caenorhabditis species. The numbers of intronization events and introns gained by other mechanisms are similar, suggesting that i...

  5. Intronic variation at the

    NARCIS (Netherlands)

    Trimbos, K.B.; Kentie, R.; van der Velde, M.; Hooijmeijer, J.C.E.W.; Poley, C.; Musters, C.J.M.; de Snoo, G.R.; Piersma, T.

    2013-01-01

    Recently, Schroeder etal. (2010, Ibis 152: 368-377) suggested that intronic variation in the CHD1-Z gene of Black-tailed Godwits breeding in southwest Friesland, The Netherlands, correlated with fitness components. Here we re-examine this surprising result using an expanded dataset (2088 birds

  6. The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms.

    Science.gov (United States)

    Mattick, J S; Gagen, M J

    2001-09-01

    Eukaryotic phenotypic diversity arises from multitasking of a core proteome of limited size. Multitasking is routine in computers, as well as in other sophisticated information systems, and requires multiple inputs and outputs to control and integrate network activity. Higher eukaryotes have a mosaic gene structure with a dual output, mRNA (protein-coding) sequences and introns, which are released from the pre-mRNA by posttranscriptional processing. Introns have been enormously successful as a class of sequences and comprise up to 95% of the primary transcripts of protein-coding genes in mammals. In addition, many other transcripts (perhaps more than half) do not encode proteins at all, but appear both to be developmentally regulated and to have genetic function. We suggest that these RNAs (eRNAs) have evolved to function as endogenous network control molecules which enable direct gene-gene communication and multitasking of eukaryotic genomes. Analysis of a range of complex genetic phenomena in which RNA is involved or implicated, including co-suppression, transgene silencing, RNA interference, imprinting, methylation, and transvection, suggests that a higher-order regulatory system based on RNA signals operates in the higher eukaryotes and involves chromatin remodeling as well as other RNA-DNA, RNA-RNA, and RNA-protein interactions. The evolution of densely connected gene networks would be expected to result in a relatively stable core proteome due to the multiple reuse of components, implying that cellular differentiation and phenotypic variation in the higher eukaryotes results primarily from variation in the control architecture. Thus, network integration and multitasking using trans-acting RNA molecules produced in parallel with protein-coding sequences may underpin both the evolution of developmentally sophisticated multicellular organisms and the rapid expansion of phenotypic complexity into uncontested environments such as those initiated in the Cambrian

  7. Intron retention as a component of regulated gene expression programs.

    Science.gov (United States)

    Jacob, Aishwarya G; Smith, Christopher W J

    2017-09-01

    Intron retention has long been an exemplar of regulated splicing with case studies of individual events serving as models that provided key mechanistic insights into the process of splicing control. In organisms such as plants and budding yeast, intron retention is well understood as a major mechanism of gene expression regulation. In contrast, in mammalian systems, the extent and functional significance of intron retention have, until recently, remained greatly underappreciated. Technical challenges to the global detection and quantitation of transcripts with retained introns have often led to intron retention being overlooked or dismissed as "noise". Now, however, with the wealth of information available from high-throughput deep sequencing, combined with focused computational and statistical analyses, we are able to distinguish clear intron retention patterns in various physiological and pathological contexts. Several recent studies have demonstrated intron retention as a central component of gene expression programs during normal development as well as in response to stress and disease. Furthermore, these studies revealed various ways in which intron retention regulates protein isoform production, RNA stability and translation efficiency, and rapid induction of expression via post-transcriptional splicing of retained introns. In this review, we highlight critical findings from these transcriptomic studies and discuss commonalties in the patterns prevalent in intron retention networks at the functional and regulatory levels.

  8. Functional characterisation of an intron retaining K+ transporter of barley reveals intron-mediated alternate splicing

    KAUST Repository

    Shahzad, K.

    2015-01-01

    Intron retention in transcripts and the presence of 5 and 3 splice sites within these introns mediate alternate splicing, which is widely observed in animals and plants. Here, functional characterisation of the K+ transporter, HvHKT2;1, with stably retained introns from barley (Hordeum vulgare) in yeast (Saccharomyces cerevisiae), and transcript profiling in yeast and transgenic tobacco (Nicotiana tabacum) is presented. Expression of intron-retaining HvHKT2;1 cDNA (HvHKT2;1-i) in trk1, trk2 yeast strain defective in K+ uptake restored growth in medium containing hygromycin in the presence of different concentrations of K+ and mediated hypersensitivity to Na+. HvHKT2;1-i produces multiple transcripts via alternate splicing of two regular introns and three exons in different compositions. HKT isoforms with retained introns and exon skipping variants were detected in relative expression analysis of (i) HvHKT2;1-i in barley under native conditions, (ii) in transgenic tobacco plants constitutively expressing HvHKT2;1-i, and (iii) in trk1, trk2 yeast expressing HvHKT2;1-i under control of an inducible promoter. Mixed proportions of three HKT transcripts: HvHKT2;1-e (first exon region), HvHKT2;1-i1 (first intron) and HvHKT2;1-i2 (second intron) were observed. The variation in transcript accumulation in response to changing K+ and Na+ concentrations was observed in both heterologous and plant systems. These findings suggest a link between intron-retaining transcripts and different splice variants to ion homeostasis, and their possible role in salt stress.

  9. Regulation of α-Smooth Muscle Actin Expression in Granulation Tissue Myofibroblasts Is Dependent on the Intronic CArG Element and the Transforming Growth Factor-β1 Control Element

    Science.gov (United States)

    Tomasek, James J.; McRae, Joel; Owens, Gary K.; Haaksma, Carol J.

    2005-01-01

    Myofibroblasts are specialized contractile fibroblasts that are critical in wound closure and tissue contracture. Generation of contractile force is correlated with the expression of α-smooth muscle actin (α-SMA); however, little is known regarding molecular mechanisms that control activation of α-SMA in myofibroblasts in granulation tissue. The aims of the present studies were to identify sufficient promoter regions required for α-SMA expression in myofibroblasts in vivo and to determine whether activation of α-SMA expression in myofibroblasts in vivo is dependent on an intronic CArG [CC(A/T)6GG] and a transforming growth factor-β1 control element (TCE) that are required for α-SMA expression in smooth muscle cells. A Lac Z transgene construct from −2600 through the first intron was expressed in myofibroblasts within granulation tissue of cutaneous wounds in a pattern that closely mimicked endogenous α-SMA expression. Mutation of either the intronic CArG element or the TCE completely inhibited transgene expression in myofibroblasts in granulation tissue and responsiveness to transforming growth factor-β1 in cultured transgenic fibroblasts. These same elements were also critical in regulating α-SMA expression during skeletal muscle repair but not during skeletal muscle development. Taken together, these results provide the first in vivo evidence for the importance of the intronic CArG and TCE cis-elements in the regulation of α-SMA expression in myofibroblasts in granulation tissue. PMID:15855636

  10. Intron V, not intron I of human thrombopoietin, improves expression in the milk of transgenic mice regulated by goat beta-casein promoter.

    Science.gov (United States)

    Li, Yan; Hao, Hu; Zhou, Mingqian; Zhou, Hongwei; Ye, Jianbin; Ning, Lijun; Ning, Yunshan

    2015-11-03

    Introns near 5' end of genes generally enhance gene expression because of an enhancer /a promoter within their sequence or as intron-mediated enhancement. Surprisingly, our previous experiments found that the vector containing the last intron (intron V) of human thromobopoietin (hTPO) expressed higher hTPO in cos-1 cell than the vector containing intron I regulated by cytomegalovirus promoter. Moreover, regulated by 1.0 kb rat whey acidic protein promoter, hTPO expression was higher in transgenic mice generated by intron V-TPOcDNA than in transgenic mice generated by TPOcDNA and TPOgDNA. However, it is unknown whether the enhancement of hTPO expression by intron I is decreased by uAUG7 at 5'-UTR of hTPO in vivo. Currently, we constructed vectors regulated by stronger 6.5 kb β-casein promoter, including pTPOGA (containing TPOcDNA), pTPOGB (containing TUR-TPOcDNA, TUR including exon1, intron I and non-coding exon2 of hTPO gene), pTPOGC (containing ΔTUR-TPOcDNA, nucleotides of TUR from uAUG7 to physiological AUG were deleted), pTPOGD (containing intron V-TPOcDNA) and pTPOGE (containing TPOgDNA), to evaluate the effect of intron I on hTPO expression and to further verify whether intron V enhances hTPO expression in the milk of transgenic mice. The results demonstrated that intron V, not intron I improved hTPO expression.

  11. An intronic single-nucleotide polymorphism (rs13217795) in FOXO3 is associated with asthma and allergic rhinitis: a case-case-control study.

    Science.gov (United States)

    Amarin, Justin Z; Naffa, Randa G; Suradi, Haya H; Alsaket, Yousof M; Obeidat, Nathir M; Mahafza, Tareq M; Zihlif, Malek A

    2017-11-15

    Asthma and allergic rhinitis are respiratory diseases with a significant global burden. Forkhead box O3 (FOXO3) is a gene involved in the etiology of a number of respiratory diseases. The objective of this study is to assess the association of rs13217795, an intronic FOXO3 single-nucleotide polymorphism, with asthma and allergic rhinitis. In this case-case-control genetic association study, genotyping was conducted using the PCR-RFLP method. Genotype-based associations were investigated under the general, recessive, and dominant models of disease penetrance using binomial logistic regression; and, allele-based associations were tested using Pearson's chi-squared test. The final study population consisted of 94 controls, 124 asthmatics, and 110 allergic rhinitis patients. The general and recessive models of disease penetrance were statistically significant for both case-control comparisons. Under the general model, the odds of the asthma phenotype were 1.46 (0.64 to 3.34) and 3.42 (1.37 to 8.57) times higher in heterozygotes and derived allele homozygotes, respectively, compared to ancestral allele homozygotes. The corresponding odds ratios for the allergic rhinitis phenotype were 1.05 (0.46 to 2.40) and 2.35 (0.96 to 5.73), respectively. The dominant model of disease penetrance was not statistically significant. The minor allele in all study groups was the ancestral allele, with a frequency of 0.49 in controls. There was no deviation from Hardy-Weinberg equilibrium in controls. Both case-control allele-based associations were statistically significant. Herein we present the first report of the association between rs13217795 and allergic rhinitis, and the first independent verification of the association between rs13217795 and asthma. Marker selection in future genetic association studies of asthma and allergic rhinitis should include functional polymorphisms in linkage disequilibrium with rs13217795.

  12. Functional Analysis of Deep Intronic SNP rs13438494 in Intron 24 of PCLO Gene

    Science.gov (United States)

    Seo, Seunghee; Takayama, Kanako; Uno, Kyosuke; Ohi, Kazutaka; Hashimoto, Ryota; Nishizawa, Daisuke; Ikeda, Kazutaka; Ozaki, Norio; Nabeshima, Toshitaka; Miyamoto, Yoshiaki; Nitta, Atsumi

    2013-01-01

    The single nucleotide polymorphism (SNP) rs13438494 in intron 24 of PCLO was significantly associated with bipolar disorder in a meta-analysis of genome-wide association studies. In this study, we performed functional minigene analysis and bioinformatics prediction of splicing regulatory sequences to characterize the deep intronic SNP rs13438494. We constructed minigenes with A and C alleles containing exon 24, intron 24, and exon 25 of PCLO to assess the genetic effect of rs13438494 on splicing. We found that the C allele of rs13438494 reduces the splicing efficiency of the PCLO minigene. In addition, prediction analysis of enhancer/silencer motifs using the Human Splice Finder web tool indicated that rs13438494 induces the abrogation or creation of such binding sites. Our results indicate that rs13438494 alters splicing efficiency by creating or disrupting a splicing motif, which functions by binding of splicing regulatory proteins, and may ultimately result in bipolar disorder in affected people. PMID:24167553

  13. Emergence and loss of spliceosomal twin introns

    OpenAIRE

    Flipphi, Michel; Ág, Norbert; Karaffa, Levente; Kavalecz, Napsugár; Cerqueira, Gustavo; Scazzocchio, Claudio; Fekete, Erzsébet

    2017-01-01

    Background In the primary transcript of nuclear genes, coding sequences—exons—usually alternate with non-coding sequences—introns. In the evolution of spliceosomal intron–exon structure, extant intron positions can be abandoned and new intron positions can be occupied. Spliceosomal twin introns (“stwintrons”) are unconventional intervening sequences where a standard “internal” intron interrupts a canonical splicing motif of a second, “external” intron. The availability of genome sequences of ...

  14. RNA-binding protein regulates plant DNA methylation by controlling mRNA processing at the intronic heterochromatin-containing gene IBM1.

    Science.gov (United States)

    Wang, Xingang; Duan, Cheng-Guo; Tang, Kai; Wang, Bangshing; Zhang, Huiming; Lei, Mingguang; Lu, Kun; Mangrauthia, Satendra K; Wang, Pengcheng; Zhu, Guohui; Zhao, Yang; Zhu, Jian-Kang

    2013-09-17

    DNA methylation-dependent heterochromatin formation is a conserved mechanism of epigenetic silencing of transposons and other repeat elements in many higher eukaryotes. Genes adjacent to repetitive elements are often also subjected to this epigenetic silencing. Consequently, plants have evolved antisilencing mechanisms such as active DNA demethylation mediated by the REPRESSOR OF SILENCING 1 (ROS1) family of 5-methylcytosine DNA glycosylases to protect these genes from silencing. Some transposons and other repeat elements have found residence in the introns of genes. It is unclear how these intronic repeat elements-containing genes are regulated. We report here the identification of ANTI-SILENCING 1 (ASI1), a bromo-adjacent homology domain and RNA recognition motif-containing protein, from a forward genetic screen for cellular antisilencing factors in Arabidopsis thaliana. ASI1 is required to prevent promoter DNA hypermethylation and transcriptional silencing of some transgenes. Genome-wide DNA methylation analysis reveals that ASI1 has a similar role to that of the histone H3K9 demethylase INCREASE IN BONSAI METHYLATION 1 (IBM1) in preventing CHG methylation in the bodies of thousands of genes. We found that ASI1 is an RNA-binding protein and ensures the proper expression of IBM1 full-length transcript by associating with an intronic heterochromatic repeat element of IBM1. Through mRNA sequencing, we identified many genes containing intronic transposon elements that require ASI1 for proper expression. Our results suggest that ASI1 associates with intronic heterochromatin and binds the gene transcripts to promote their 3' distal polyadenylation. The study thus reveals a unique mechanism by which higher eukaryotes deal with the collateral effect of silencing intronic repeat elements.

  15. YIDB: the Yeast Intron DataBase

    OpenAIRE

    Lopez, Pascal J.; Séraphin, Bertrand

    2000-01-01

    The Yeast Intron DataBase (YIDB) contains currently available information about all introns encoded in the nuclear and mitochondrial genomes of the yeast Saccharomyces cerevisiae. Introns are divided according to their mechanism of excision: group I and group II introns, pre-mRNA introns, tRNA introns and the HAC1 intron. Information about the host genome, the type of RNA in which they are inserted and their primary structure are provided together with references. For nuclear pre-mRNA introns...

  16. Identification of a family of group II introns encoding LAGLIDADG ORFs typical of group I introns.

    OpenAIRE

    Toor, Navtej; Zimmerly, Steven

    2002-01-01

    Group I and group II introns are unrelated classes of introns that each encode proteins that facilitate intron splicing and intron mobility. Here we describe a new subfamily of nine introns in fungi that are group II introns but encode LAGLIDADG ORFs typical of group I introns. The introns have fairly standard group IIB1 RNA structures and are inserted into three different sites in SSU and LSU rRNA genes. Therefore, introns should not be assumed to be group I introns based solely on the prese...

  17. The Biology of Intron Gain and Loss

    DEFF Research Database (Denmark)

    Jeffares, Daniel C; Mourier, Tobias; Penny, David

    2006-01-01

    eukaryote genomes during their evolution from an intron-poor ancestor. However, recent studies have shown that some eukaryotes lost many introns, whereas others accumulated and/or gained many introns. In this article, we discuss the growing evidence that these differences are subject to selection acting...... on introns depending on the biology of the organism and the gene involved....

  18. Why Selection Might Be Stronger When Populations Are Small: Intron Size and Density Predict within and between-Species Usage of Exonic Splice Associated cis-Motifs

    Science.gov (United States)

    Wu, XianMing; Hurst, Laurence D.

    2015-01-01

    The nearly neutral theory predicts that small effective population size provides the conditions for weakened selection. This is postulated to explain why our genome is more “bloated” than that of, for example, yeast, ours having large introns and large intergene spacer. If a bloated genome is also an error prone genome might it, however, be the case that selection for error-mitigating properties is stronger in our genome? We examine this notion using splicing as an exemplar, not least because large introns can predispose to noisy splicing. We thus ask whether, owing to genomic decay, selection for splice error-control mechanisms is stronger, not weaker, in species with large introns and small populations. In humans much information defining splice sites is in cis-exonic motifs, most notably exonic splice enhancers (ESEs). These act as splice-error control elements. Here then we ask whether within and between-species intron size is a predictor of the commonality of exonic cis-splicing motifs. We show that, as predicted, the proportion of synonymous sites that are ESE-associated and under selection in humans is weakly positively correlated with the size of the flanking intron. In a phylogenetically controlled framework, we observe, also as expected, that mean intron size is both predicted by Ne.μ and is a good predictor of cis-motif usage across species, this usage coevolving with splice site definition. Unexpectedly, however, across taxa intron density is a better predictor of cis-motif usage than intron size. We propose that selection for splice-related motifs is driven by a need to avoid decoy splice sites that will be more common in genes with many and large introns. That intron number and density predict ESE usage within human genes is consistent with this, as is the finding of intragenic heterogeneity in ESE density. As intronic content and splice site usage across species is also well predicted by Ne.μ, the result also suggests an unusual circumstance in

  19. Intron gain by tandem genomic duplication: a novel case in a potato gene encoding RNA-dependent RNA polymerase

    Directory of Open Access Journals (Sweden)

    Ming-Yue Ma

    2016-07-01

    Full Text Available The origin and subsequent accumulation of spliceosomal introns are prominent events in the evolution of eukaryotic gene structure. However, the mechanisms underlying intron gain remain unclear because there are few proven cases of recently gained introns. In an RNA-dependent RNA polymerase (RdRp gene, we found that a tandem duplication occurred after the divergence of potato and its wild relatives among other Solanum plants. The duplicated sequence crosses the intron-exon boundary of the first intron and the second exon. A new intron was detected at this duplicated region, and it includes a small previously exonic segment of the upstream copy of the duplicated sequence and the intronic segment of the downstream copy of the duplicated sequence. The donor site of this new intron was directly obtained from the small previously exonic segment. Most of the splicing signals were inherited directly from the parental intron/exon structure, including a putative branch site, the polypyrimidine tract, the 3′ splicing site, two putative exonic splicing enhancers, and the GC contents differed between the intron and exon. In the widely cited model of intron gain by tandem genomic duplication, the duplication of an AGGT-containing exonic segment provides the GT and AG splicing sites for the new intron. Our results illustrate that the tandem duplication model of intron gain should be diverse in terms of obtaining the proper splicing signals.

  20. A Leader Intron of a Soybean Elongation Factor 1A (eEF1A) Gene Interacts with Proximal Promoter Elements to Regulate Gene Expression in Synthetic Promoters.

    Science.gov (United States)

    Zhang, Ning; McHale, Leah K; Finer, John J

    2016-01-01

    Introns, especially the first intron in the 5' untranslated region (5'UTR), can significantly impact gene expression via intron-mediated enhancement (IME). In this study, we demonstrate the leader intron of a soybean elongation factor 1A (eEF1A) gene (GmScreamM8) was essential for the high activity of the native promoter. Furthermore, the interaction of the GmScreamM8 leader intron with regulatory element sequences from several soybean eEF1A promoters was studied using synthetic promoters, which consisted of element tetramers upstream of a core promoter used to regulate a green fluorescent protein (gfp) reporter gene. Element tetramers, placed upstream of a GmScreamM8 core promoter, showed very high activity using both transient expression in lima bean cotyledons and stable expression in soybean hairy roots, only if the native leader intron was included, suggesting an interaction between intronic sequences and promoter elements. Partial deletions of the leader intron showed that a 222 bp intronic sequence significantly contributed to very high levels of GFP expression. Generation of synthetic intron variants with a monomeric or trimeric repeat of the 222 bp intronic sequence, yielded almost two-fold higher expression compared to the original intron, while partial deletion of the 222 bp intronic repeated sequence significantly decreased gene expression, indicating that this intronic sequence was essential for the intron-element interaction enhancement.

  1. Intronic Alus influence alternative splicing.

    Directory of Open Access Journals (Sweden)

    Galit Lev-Maor

    2008-09-01

    Full Text Available Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA formation within the human transcriptome. Most of the editing sites are located in the primate-specific retrotransposed element called Alu. A large fraction of Alus are found in intronic sequences, implying extensive Alu-Alu dsRNA formation in mRNA precursors. Yet, the effect of these intronic Alus on splicing of the flanking exons is largely unknown. Here, we show that more Alus flank alternatively spliced exons than constitutively spliced ones; this is especially notable for those exons that have changed their mode of splicing from constitutive to alternative during human evolution. This implies that Alu insertions may change the mode of splicing of the flanking exons. Indeed, we demonstrate experimentally that two Alu elements that were inserted into an intron in opposite orientation undergo base-pairing, as evident by RNA editing, and affect the splicing patterns of a downstream exon, shifting it from constitutive to alternative. Our results indicate the importance of intronic Alus in influencing the splicing of flanking exons, further emphasizing the role of Alus in shaping of the human transcriptome.

  2. Origin and evolution of spliceosomal introns

    Directory of Open Access Journals (Sweden)

    Rogozin Igor B

    2012-04-01

    Full Text Available Abstract Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded ‘introns first’ held that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. The introns-late concept held that introns emerged only in eukaryotes and new introns have been accumulating continuously throughout eukaryotic evolution. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists, suggesting that many ancestral introns have persisted since the last eukaryotic common ancestor (LECA. Reconstructions of intron gain and loss using the growing collection of genomes of diverse eukaryotes and increasingly advanced probabilistic models convincingly show that the LECA and the ancestors of each eukaryotic supergroup had intron-rich genes, with intron densities comparable to those in the most intron-rich modern genomes such as those of vertebrates. The subsequent evolution in most lineages of eukaryotes involved primarily loss of introns, with only a few episodes of substantial intron gain that might have accompanied major evolutionary innovations such as the origin of metazoa. The original invasion of self-splicing Group II introns, presumably originating from the mitochondrial endosymbiont, into the genome of the emerging eukaryote might have been a key factor of eukaryogenesis that in particular triggered the origin of endomembranes and the nucleus. Conversely, splicing errors gave rise to alternative splicing, a major contribution to the biological complexity of multicellular eukaryotes. There is no indication that any prokaryote has

  3. Database for mobile group II introns

    OpenAIRE

    Dai, Lixin; Toor, Navtej; Olson, Robert; Keeping, Andrew; Zimmerly, Steven

    2003-01-01

    Group II introns are self-splicing RNAs and retroelements found in bacteria and lower eukaryotic organelles. During the past several years, they have been uncovered in surprising numbers in bacteria due to the genome sequencing projects; however, most of the newly sequenced introns are not correctly identified. We have initiated an ongoing web site database for mobile group II introns in order to provide correct information on the introns, particularly in bacteria. Information in the web site...

  4. 50/50 Expressional Odds of Retention Signifies the Distinction between Retained Introns and Constitutively Spliced Introns in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Rui Mao

    2017-10-01

    Full Text Available Intron retention, one of the most prevalent alternative splicing events in plants, can lead to introns retained in mature mRNAs. However, in comparison with constitutively spliced introns (CSIs, the relevantly distinguishable features for retained introns (RIs are still poorly understood. This work proposes a computational pipeline to discover novel RIs from multiple next-generation RNA sequencing (RNA-Seq datasets of Arabidopsis thaliana. Using this pipeline, we detected 3,472 novel RIs from 18 RNA-Seq datasets and re-confirmed 1,384 RIs which are currently annotated in the TAIR10 database. We also use the expression of intron-containing isoforms as a new feature in addition to the conventional features. Based on these features, RIs are highly distinguishable from CSIs by machine learning methods, especially when the expressional odds of retention (i.e., the expression ratio of the RI-containing isoforms relative to the isoforms without RIs for the same gene reaches to or larger than 50/50. In this case, the RIs and CSIs can be clearly separated by the Random Forest with an outstanding performance of 0.95 on AUC (the area under a receiver operating characteristics curve. The closely related characteristics to the RIs include the low strength of splice sites, high similarity with the flanking exon sequences, low occurrence percentage of YTRAY near the acceptor site, existence of putative intronic splicing silencers (ISSs, i.e., AG/GA-rich motifs and intronic splicing enhancers (ISEs, i.e., TTTT-containing motifs, and enrichment of Serine/Arginine-Rich (SR proteins and heterogeneous nuclear ribonucleoparticle proteins (hnRNPs.

  5. Epigenetic Regulation of Intronic Transgenes in Arabidopsis.

    Science.gov (United States)

    Osabe, Kenji; Harukawa, Yoshiko; Miura, Saori; Saze, Hidetoshi

    2017-03-24

    Defense mechanisms of plant genomes can epigenetically inactivate repetitive sequences and exogenous transgenes. Loss of mutant phenotypes in intronic T-DNA insertion lines by interaction with another T-DNA locus, termed T-DNA suppression, has been observed in Arabidopsis thaliana, although the molecular basis of establishment and maintenance of T-DNA suppression is poorly understood. Here we show that maintenance of T-DNA suppression requires heterochromatinisation of T-DNA sequences and the nuclear proteins, INCREASED IN BONSAI METHYLATION 2 (IBM2) and ENHANCED DOWNY MILDEW 2 (EDM2), which prevent ectopic 3' end processing of mRNA in atypically long introns containing T-DNA sequences. Initiation of T-DNA suppression is mediated by the canonical RdDM pathway after hybridisation of two T-DNA strains, accompanied by DNA hypermethylation of T-DNA sequences in the F1 generation. Our results reveal the presence of a genome surveillance mechanism through genome hybridisation that masks repetitive DNAs intruding into transcription units.

  6. Lenalidomide modulates gene expression in human ABC-DLBCL cells by regulating IKAROS interaction with an intronic control region of SPIB.

    Science.gov (United States)

    Solomon, Lauren A; Batista, Carolina R; DeKoter, Rodney P

    2017-12-01

    Activated B-cell diffuse large B-cell lymphoma (ABC-DLBCL) is associated with a poor prognosis compared with other DLBCL types and therefore represents a top priority for developing novel therapies. Lenalidomide, an immunomodulatory drug in trials for treatment of ABC-DLBCL, targets the transcription factor IKAROS for degradation by the cereblon E3 ubiquitin ligase complex. In this study, we investigated whether the gene encoding the transcription factor SPI-B is a target of IKAROS. Using cultured ABC-DLBCL cell lines, we found that high levels of SPI-B expression conferred resistance to lenalidomide. Lenalidomide treatment of ABC-DLBCL cells resulted in downregulation of SPIB at the level of transcription. SPIB was regulated directly by IKAROS through a binding site located in the first intron of the gene. Inhibition of IKAROS binding using CRISPR/Cas9-mediated transcriptional repression downregulated endogenous SPIB transcription. Finally, ectopic expression of IKAROS protected SPIB from downregulation. These results show that the mechanism of action of lenalidomide in ABC-DLBCL cells involves downregulation of SPIB transcription by cereblon-induced degradation of IKAROS. These results have implications for the design of synthetic lethal therapy for the treatment of ABC-DLBCL. Copyright © 2017 ISEH – Society for Hematology and Stem Cells. Published by Elsevier Inc. All rights reserved.

  7. Emergence and loss of spliceosomal twin introns.

    Science.gov (United States)

    Flipphi, Michel; Ág, Norbert; Karaffa, Levente; Kavalecz, Napsugár; Cerqueira, Gustavo; Scazzocchio, Claudio; Fekete, Erzsébet

    2017-01-01

    In the primary transcript of nuclear genes, coding sequences-exons-usually alternate with non-coding sequences-introns. In the evolution of spliceosomal intron-exon structure, extant intron positions can be abandoned and new intron positions can be occupied. Spliceosomal twin introns ("stwintrons") are unconventional intervening sequences where a standard "internal" intron interrupts a canonical splicing motif of a second, "external" intron. The availability of genome sequences of more than a thousand species of fungi provides a unique opportunity to study spliceosomal intron evolution throughout a whole kingdom by means of molecular phylogenetics. A new stwintron was encountered in Aspergillus nidulans and Aspergillus niger . It is present across three classes of Leotiomyceta in the transcript of a well-conserved gene encoding a putative lipase ( lipS ). It occupies the same position as a standard intron in the orthologue gene in species of the early divergent classes of the Pezizomycetes and the Orbiliomycetes, suggesting that an internal intron has appeared within a pre-extant intron. On the other hand, the stwintron has been lost from certain taxa in Leotiomycetes and Eurotiomycetes at several occasions, most likely by a mechanism involving reverse transcription and homologous recombination. Another ancient stwintron present across whole Pezizomycotina orders-in the transcript of the bifunctional biotin biosynthesis gene bioDA -occurs at the same position as a standard intron in many species of non-Dikarya. Nevertheless, also the bioDA stwintron has disappeared from certain lineages within the taxa where it occurs, i.e., Sordariomycetes and Botryosphaeriales. Intriguingly, only the internal intron was lost from the Sordariomycetes bioDA stwintron at all but one occasion, leaving a standard intron in the same position, while where the putative lipase stwintron was lost, no intronic sequences remain. Molecular phylogeny of the peptide product was used to monitor

  8. How complex an intron may be? The example of the first intron of the CTP synthase gene of Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Roberto Piergentili

    2013-02-01

    Full Text Available In eukaryotes, maturation of primary transcripts into mature messenger RNAs involves the elimination of parts of the gene called ‘introns’. The biological significance of introns is not yet completely understood. It has been demonstrated that introns may contain other genes, or regulatory sequences that may be involved in transcriptional control, or also being involved in alternative splicing mechanisms. However, these functions explain the role of only a small number of them, and it is very difficult to formulate any generalization. The CTP synthase gene of Drosophila melanogaster is characterized by the presence of a long first intron (approximately 7.2 kilobases whose role is currently unknown. In the present report we analyzed in silico the content of this intron, and found that it contains at least three interesting sub-sequences. Two of them are homologous to the CTP synthase itself and to a putative nucleotide pyrophosphatase, respectively. The third is a short stretch of DNA able to fold into a thermodynamically stable hairpin and showing homology with other 19 sequences from 21 genes inside the D. melanogaster genome. These findings suggest a complex yet very accurate way of controlling gene expression inside the fruit fly.

  9. The origin of introns and their role in eukaryogenesis: a compromise solution to the introns-early versus introns-late debate?

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2006-08-01

    Full Text Available Abstract Background Ever since the discovery of 'genes in pieces' and mRNA splicing in eukaryotes, origin and evolution of spliceosomal introns have been considered within the conceptual framework of the 'introns early' versus 'introns late' debate. The 'introns early' hypothesis, which is closely linked to the so-called exon theory of gene evolution, posits that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. Under this scenario, the absence of spliceosomal introns in prokaryotes is considered to be a result of "genome streamlining". The 'introns late' hypothesis counters that spliceosomal introns emerged only in eukaryotes, and moreover, have been inserted into protein-coding genes continuously throughout the evolution of eukaryotes. Beyond the formal dilemma, the more substantial side of this debate has to do with possible roles of introns in the evolution of eukaryotes. Results I argue that several lines of evidence now suggest a coherent solution to the introns-early versus introns-late debate, and the emerging picture of intron evolution integrates aspects of both views although, formally, there seems to be no support for the original version of introns-early. Firstly, there is growing evidence that spliceosomal introns evolved from group II self-splicing introns which are present, usually, in small numbers, in many bacteria, and probably, moved into the evolving eukaryotic genome from the α-proteobacterial progenitor of the mitochondria. Secondly, the concept of a primordial pool of 'virus-like' genetic elements implies that self-splicing introns are among the most ancient genetic entities. Thirdly, reconstructions of the ancestral state of eukaryotic genes suggest that the last common ancestor of extant eukaryotes had an intron

  10. A novel intronic peroxisome proliferator-activated receptor gamma enhancer in the uncoupling protein (UCP) 3 gene as a regulator of both UCP2 and -3 expression in adipocytes

    DEFF Research Database (Denmark)

    Bugge, Anne Skovsø; Siersbaek, Majken; Madsen, Maria S

    2010-01-01

    homologues function to facilitate mitochondrial fatty acid oxidation. UCP2 and -3 expression is activated by the peroxisome proliferator-activated receptors (PPARs), but so far no PPAR response element has been reported in the vicinity of the Ucp2 and Ucp3 genes. Using genome-wide profiling of PPARgamma...... in the Ucp2 and Ucp3 loci is located in intron 1 of the Ucp3 gene and is the only site that facilitates PPARgamma transactivation of a heterologous promoter. This site furthermore transactivates the endogenous Ucp3 promoter, and using chromatin conformation capture we show that it loops out to specifically...

  11. Did group II intron proliferation in an endosymbiont-bearing archaeon create eukaryotes?

    Directory of Open Access Journals (Sweden)

    Poole Anthony M

    2006-12-01

    Full Text Available Abstract Martin & Koonin recently proposed that the eukaryote nucleus evolved as a quality control mechanism to prevent ribosome readthrough into introns. In their scenario, the bacterial ancestor of mitochondria was resident in an archaeal cell, and group II introns (carried by the fledgling mitochondrion inserted into coding regions in the archaeal host genome. They suggest that if transcription and translation were coupled, and because splicing is expected to have been slower than translation, the effect of insertion would have been ribosome readthrough into introns, resulting in production of aberrant proteins. The emergence of the nuclear compartment would thus have served to separate transcription and splicing from translation, thereby alleviating this problem. In this article, I argue that Martin & Koonin's model is not compatible with current knowledge. The model requires that group II introns would spread aggressively through an archaeal genome. It is well known that selfish elements can spread through an outbreeding sexual population despite a substantial fitness cost to the host. The same is not true for asexual lineages however, where both theory and observation argue that such elements will be under pressure to reduce proliferation, and may be lost completely. The recent introduction of group II introns into archaea by horizontal transfer provides a natural test case with which to evaluate Martin & Koonin's model. The distribution and behaviour of these introns fits prior theoretical expectations, not the scenario of aggressive proliferation advocated by Martin & Koonin. I therefore conclude that the mitochondrial seed hypothesis for the origin of eukaryote introns, on which their model is based, better explains the early expansion of introns in eukaryotes. The mitochondrial seed hypothesis has the capacity to separate the origin of eukaryotes from the origin of introns, leaving open the possibility that the cell that engulfed the

  12. FGLamide Allatostatin genes in Arthropoda: introns early or late?

    Science.gov (United States)

    Martínez-Pérez, Francisco; Bendena, William G; Chang, Belinda S W; Tobe, Stephen S

    2009-07-01

    FGLamide allatostatins are invertebrate neuropeptides which inhibit juvenile hormone biosynthesis in Dictyoptera and related orders and also show myomodulatory activity. The FGLamide allatostatin (AST) gene structure in Dictyoptera is intronless within the ORF, whereas in 9 species of Diptera, the FGLamide AST ORF has one intron. To investigate the evolutionary history of AST intron structure, (intron early versus intron late hypothesis), all available Arthropoda FGLamide AST gene sequences were examined from genome databases with reference to intron presence and position/phase. Three types of FGLamide AST ORF organization were found: intronless in I. scapularis and P. humanus corporis; one intron in D. pulex, A. pisum, A. mellifera and five Drosophila sp.; two introns in N. vitripennis, B. mori strains, A. aegypti, A. gambiae and C. quinquefasciatus. The literature suggests that for the majority of genes examined, most introns exist between codons (phase 0) which may reflect an ancient function of introns to separate protein modules. 60% of the FGLamide AST ORFs introns were between the first and second base within a codon (phase 1), 28% were between the second and third nucleotides within a codon (phase two) and 12% were phase 0. As would be required for correct intron splicing consensus sequence, 84% of introns were in codons starting with guanine. The positioning of introns was a maximum of 9 codons from a dibasic cleavage site. Our results suggest that the introns in the analyzed species support the intron late model.

  13. Bilingualism and Musicianship Enhance Cognitive Control.

    Science.gov (United States)

    Schroeder, Scott R; Marian, Viorica; Shook, Anthony; Bartolotti, James

    2016-01-01

    Learning how to speak a second language (i.e., becoming a bilingual) and learning how to play a musical instrument (i.e., becoming a musician) are both thought to increase executive control through experience-dependent plasticity. However, evidence supporting this effect is mixed for bilingualism and limited for musicianship. In addition, the combined effects of bilingualism and musicianship on executive control are unknown. To determine whether bilingualism, musicianship, and combined bilingualism and musicianship improve executive control, we tested 219 young adults belonging to one of four groups (bilinguals, musicians, bilingual musicians, and controls) on a nonlinguistic, nonmusical, visual-spatial Simon task that measured the ability to ignore an irrelevant and misinformative cue. Results revealed that bilinguals, musicians, and bilingual musicians showed an enhanced ability to ignore a distracting cue relative to controls, with similar levels of superior performance among bilinguals, musicians, and bilingual musicians. These results indicate that bilingualism and musicianship improve executive control and have implications for educational and rehabilitation programs that use music and foreign language instruction to boost cognitive performance.

  14. Functional intron+ and intron- rDNA in the same macronucleus of the ciliate Tetrahymena pigmentosa

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Engberg, J

    1985-01-01

    alleles was followed in the total culture and in single cells during their vegetative segregation and it was observed that replication was non-preferential with respect to the two alleles. The diallelic clones were also used to demonstrate that intron-containing rDNA was transcribed and the transcript......Diallelic clones of Tetrahymena pigmentosa containing equal amounts of intron+ and intron- rDNA in the macronucleus were constructed. The macronucleus of the resulting strains divides amitotically during vegetative growth and the diallelic genotype is therefore unstable. The coexistence of the two...

  15. Intron size and genome size in plants.

    Science.gov (United States)

    J. Wendel; R. Cronn; I. Alvarez; B. Liu; R. Small; D. Senchina

    2002-01-01

    It has long been known that genomes vary over a remarkable range of sizes in both plants (Bennett, Cox, and Leitch 1997) and animals (Gregory 2001). It also has become evident that across the broad phylogenetic sweep, genome size may be correlated with intron size (Deutsch and Long 1999; Vinogradov 1999; McLysaght et al. 2000), suggesting that some component of genome...

  16. Evolution of the Exon-Intron Structure in Ciliate Genomes.

    Directory of Open Access Journals (Sweden)

    Vladyslav S Bondarenko

    Full Text Available A typical eukaryotic gene is comprised of alternating stretches of regions, exons and introns, retained in and spliced out a mature mRNA, respectively. Although the length of introns may vary substantially among organisms, a large fraction of genes contains short introns in many species. Notably, some Ciliates (Paramecium and Nyctotherus possess only ultra-short introns, around 25 bp long. In Paramecium, ultra-short introns with length divisible by three (3n are under strong evolutionary pressure and have a high frequency of in-frame stop codons, which, in the case of intron retention, cause premature termination of mRNA translation and consequent degradation of the mis-spliced mRNA by the nonsense-mediated decay mechanism. Here, we analyzed introns in five genera of Ciliates, Paramecium, Tetrahymena, Ichthyophthirius, Oxytricha, and Stylonychia. Introns can be classified into two length classes in Tetrahymena and Ichthyophthirius (with means 48 bp, 69 bp, and 55 bp, 64 bp, respectively, but, surprisingly, comprise three distinct length classes in Oxytricha and Stylonychia (with means 33-35 bp, 47-51 bp, and 78-80 bp. In most ranges of the intron lengths, 3n introns are underrepresented and have a high frequency of in-frame stop codons in all studied species. Introns of Paramecium, Tetrahymena, and Ichthyophthirius are preferentially located at the 5' and 3' ends of genes, whereas introns of Oxytricha and Stylonychia are strongly skewed towards the 5' end. Analysis of evolutionary conservation shows that, in each studied genome, a significant fraction of intron positions is conserved between the orthologs, but intron lengths are not correlated between the species. In summary, our study provides a detailed characterization of introns in several genera of Ciliates and highlights some of their distinctive properties, which, together, indicate that splicing spellchecking is a universal and evolutionarily conserved process in the biogenesis of short

  17. For Group II Introns, More Heat Means More Mobility

    OpenAIRE

    Mohr, Georg; Ghanem, Eman; Lambowitz, Alan M.

    2010-01-01

    Mobile group II introns, which are found in bacterial and organellar genomes, are site-specific retroelements hypothesized to be evolutionary ancestors of spliceosomal introns and retrotransposons in higher organisms. Most bacteria, however, contain no more than one or a few group II introns, making it unclear how introns could have proliferated to higher copy numbers in eukaryotic genomes. An exception is the thermophilic cyanobacterium Thermosynechococcus elongatus, which contains 28 closel...

  18. GRK5 intronic (CAn polymorphisms associated with type 2 diabetes in Chinese Hainan Island.

    Directory of Open Access Journals (Sweden)

    Zhenfang Xia

    Full Text Available A genome-wide association study had showed G-protein-coupled receptor kinase 5 (GRK5 rs10886471 was related to the risk of type 2 diabetes mellitus (T2DM through upregulated GRK5 mRNA expression. Rs10886471 is located in the intron region of GRK5. However, the mechanism by which intronic SNP affects gene expression remains unclear, whether the effect on gene expression depends on the intronic short tandem repeat (STR (CAn splicing regulator or not. Here we investigated the STR (CAn polymorphism in rs10886471 and further discussed its role in the T2DM risk of Chinese Hainan Island individuals. A total of 1164 subjects were recruited and classified into a normal fasting glucose (NFG group, an impaired fasting glucose (IFG group, an impaired glucose tolerance (IGT group, and a T2DM group. STR (CAn polymorphisms were detected through polymerase chain reaction and sequencing. Five intronic (CAn alleles, (CA15 to (CA19, were identified in GRK5 rs10886471. Only the (CA16 allele was significantly associated with increased prediabetes and T2DM risk [odds ratio (OR>1, P<0.05]. Conversely, multiple alleles without any (CA16 protected against prediabetes and T2DM (0intronic SNP causes GRK5 overexpression the subsequent risk of T2DM may be due to the rs10886471 intronic STR (CAn splicing enhancer. Further studies should focus on verifying these finding using a large sample size and analyzing the splicing mechanism of intronic (CAn in rs10886471.

  19. Analysis of ribosomal protein gene structures: implications for intron evolution.

    Directory of Open Access Journals (Sweden)

    2006-03-01

    Full Text Available Many spliceosomal introns exist in the eukaryotic nuclear genome. Despite much research, the evolution of spliceosomal introns remains poorly understood. In this paper, we tried to gain insights into intron evolution from a novel perspective by comparing the gene structures of cytoplasmic ribosomal proteins (CRPs and mitochondrial ribosomal proteins (MRPs, which are held to be of archaeal and bacterial origin, respectively. We analyzed 25 homologous pairs of CRP and MRP genes that together had a total of 527 intron positions. We found that all 12 of the intron positions shared by CRP and MRP genes resulted from parallel intron gains and none could be considered to be "conserved," i.e., descendants of the same ancestor. This was supported further by the high frequency of proto-splice sites at these shared positions; proto-splice sites are proposed to be sites for intron insertion. Although we could not definitively disprove that spliceosomal introns were already present in the last universal common ancestor, our results lend more support to the idea that introns were gained late. At least, our results show that MRP genes were intronless at the time of endosymbiosis. The parallel intron gains between CRP and MRP genes accounted for 2.3% of total intron positions, which should provide a reliable estimate for future inferences of intron evolution.

  20. Man-machine enhancements to existing FFTF control panels

    International Nuclear Information System (INIS)

    Miller, E.M.

    1984-01-01

    FFTF Project enhanced existing control panels with tape and labels to mitigate operator problems and to incorporate the guidance of NUREG-0700. The enhancements grouped displays and controls into meaningful units and labelled controls and displays to facilitate their identification and efficient use. The enhancements were inexpensive and well received by the facility's operations staff

  1. Noise-Enhanced Human Balance Control

    Science.gov (United States)

    Priplata, Attila; Niemi, James; Salen, Martin; Harry, Jason; Lipsitz, Lewis A.; Collins, J. J.

    2002-11-01

    Noise can enhance the detection and transmission of weak signals in certain nonlinear systems, via a mechanism known as stochastic resonance. Here we show that input noise can be used to improve motor control in humans. Specifically, we show that the postural sway of both young and elderly individuals during quiet standing can be significantly reduced by applying subsensory mechanical noise to the feet. We further demonstrate with input noise a trend towards the reduction of postural sway in elderly subjects to the level of young subjects. These results suggest that noise-based devices, such as randomly vibrating shoe inserts, may enable people to overcome functional difficulties due to age-related sensory loss.

  2. The ability to form full-length intron RNA circles is a general property of nuclear group I introns

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Fiskaa, Tonje; Birgisdottir, Asa Birna

    2003-01-01

    in which the intron terminal guanosine attacks the 5' splice site presented in a structure analogous to that of the first step of splicing. The products of the reactions are full-length circular intron and unligated exons. For this reason, the circularization reaction is to the benefit of the intron...

  3. OXYGEN ENHANCED COMBUSTION FOR NOx CONTROL

    Energy Technology Data Exchange (ETDEWEB)

    Lawrence E. Bool; Jack C. Chen; David R. Thompson

    2000-07-01

    Increased environmental regulations will require utility boilers to reduce NO{sub x} emissions to less than 0.15lb/MMBtu in the near term. Conventional technologies such as Selective Catalytic Reduction (SCR) and Selective Non-Catalytic Reduction (SNCR) are unable to achieve these lowered emission levels without substantially higher costs and major operating problems. Oxygen enhanced combustion is a novel technology that allows utilities to meet the NO{sub x} emission requirements without the operational problems that occur with SCR and SNCR. Furthermore, oxygen enhanced combustion can achieve these NO{sub x} limits at costs lower than conventional technologies. The objective of this program is to demonstrate the use of oxygen enhanced combustion as a technical and economical method of meeting the EPA State Implementation Plan for NO{sub x} reduction to less than 0.15lb/MMBtu for a wide range of boilers and coal. The oxygen enhanced coal combustion program (Task 1) focused this quarter on the specific objective of exploration of the impact of oxygen enrichment on NO{sub x} formation utilizing small-scale combustors for parametric testing. Research efforts toward understanding any limitations to the applicability of the technology to different burners and fuels such as different types of coal are underway. The objective of the oxygen transport membrane (OTM) materials development program (Task 2.1) is to ascertain a suitable material composition that can be fabricated into dense tubes capable of producing the target oxygen flux under the operating conditions. This requires that the material have sufficient oxygen permeation resulting from high oxygen ion conductivity, high electronic conductivity and high oxygen surface exchange rate. The OTM element development program (Task 2.2) objective is to develop, fabricate and characterize OTM elements for laboratory and pilot reactors utilizing quality control parameters to ensure reproducibility and superior performance

  4. Analysis of the intronic single nucleotide polymorphism rs#466452 of the nephrin gene in patients with diabetic nephropathy

    Directory of Open Access Journals (Sweden)

    RODRIGO GONZÁLEZ

    2009-01-01

    Full Text Available We present the analysis of an intronic polymorphism of the nephrin gene and its relationship to the development of diabetic nephropathy in a study of diabetes type 1 and type 2 patients. The frequency of the single nucleotide polymorphism rs#466452 in the nephrin gene was determined in 231 patients and control subjects. The C/T status of the polymorphism was assessed using restriction enzyme digestions and the nephrin transcript from a kidney biopsy was examined. Association between the polymorphism and clinical parameters was evaluated using multivaríate correspondence analysis. A bioinformatics analysis of the single nucleotide polymorphism rs#466452 suggested the appearance of a splicing enhancer sequence in intron 24 of the nephrin gene and a modification of proteins that bind to this sequence. However, no change in the splicing of a nephrin transcript from a renal biopsy was found. No association was found between the polymorphism and diabetes or degree of renal damage in diabetes type 1 or 2 patients. The single nucleotide polymorphism rs#466452 of the nephrin gene seems to be neutral in relation to diabetes and the development of diabetic nephropathy, and does not affect the splicing of a nephrin transcript, in spite of a splicing enhancer site.

  5. Ancient nature of alternative splicing and functions of introns

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Kemin; Salamov, Asaf; Kuo, Alan; Aerts, Andrea; Grigoriev, Igor

    2011-03-21

    Using four genomes: Chamydomonas reinhardtii, Agaricus bisporus, Aspergillus carbonarius, and Sporotricum thermophile with EST coverage of 2.9x, 8.9x, 29.5x, and 46.3x respectively, we identified 11 alternative splicing (AS) types that were dominated by intron retention (RI; biased toward short introns) and found 15, 35, 52, and 63percent AS of multiexon genes respectively. Genes with AS were more ancient, and number of AS correlated with number of exons, expression level, and maximum intron length of the gene. Introns with tendency to be retained had either stop codons or length of 3n+1 or 3n+2 presumably triggering nonsense-mediated mRNA decay (NMD), but introns retained in major isoforms (0.2-6percent of all introns) were biased toward 3n length and stop codon free. Stopless introns were biased toward phase 0, but 3n introns favored phase 1 that introduced more flexible and hydrophilic amino acids on both ends of introns which would be less disruptive to protein structure. We proposed a model in which minor RI intron could evolve into major RI that could facilitate intron loss through exonization.

  6. A high density of ancient spliceosomal introns in oxymonad excavates

    Directory of Open Access Journals (Sweden)

    Keeling Patrick J

    2006-04-01

    Full Text Available Abstract Background Certain eukaryotic genomes, such as those of the amitochondriate parasites Giardia and Trichomonas, have very low intron densities, so low that canonical spliceosomal introns have only recently been discovered through genome sequencing. These organisms were formerly thought to be ancient eukaryotes that diverged before introns originated, or at least became common. Now however, they are thought to be members of a supergroup known as excavates, whose members generally appear to have low densities of canonical introns. Here we have used environmental expressed sequence tag (EST sequencing to identify 17 genes from the uncultivable oxymonad Streblomastix strix, to survey intron densities in this most poorly studied excavate group. Results We find that Streblomastix genes contain an unexpectedly high intron density of about 1.1 introns per gene. Moreover, over 50% of these are at positions shared between a broad spectrum of eukaryotes, suggesting theyare very ancient introns, potentially present in the last common ancestor of eukaryotes. Conclusion The Streblomastix data show that the genome of the ancestor of excavates likely contained many introns and the subsequent evolution of introns has proceeded very differently in different excavate lineages: in Streblomastix there has been much stasis while in Trichomonas and Giardia most introns have been lost.

  7. OXYGEN ENHANCED COMBUSTION FOR NOx CONTROL

    Energy Technology Data Exchange (ETDEWEB)

    David R. Thompson; Lawrence E. Bool; Jack C. Chen

    2004-04-01

    Conventional wisdom says adding oxygen to a combustion system enhances product throughput, system efficiency, and, unless special care is taken, increases NOx emissions. This increase in NOx emissions is typically due to elevated flame temperatures associated with oxygen use leading to added thermal NOx formation. Innovative low flame temperature oxy-fuel burner designs have been developed and commercialized to minimize both thermal and fuel NOx formation for gas and oil fired industrial furnaces. To be effective these systems require close to 100% oxy-fuel combustion and the cost of oxygen is paid for by fuel savings and other benefits. For applications to coal-fired utility boilers at the current cost of oxygen, however, it is not economically feasible to use 100% oxygen for NOx control. In spite of this conventional wisdom, Praxair and its team members, in partnership with the US Department of Energy National Energy Technology Laboratory, have developed a novel way to use oxygen to reduce NOx emissions without resorting to complete oxy-fuel conversion. In this concept oxygen is added to the combustion process to enhance operation of a low NOx combustion system. Only a small fraction of combustion air is replaced with oxygen in the process. By selectively adding oxygen to a low NOx combustion system it is possible to reduce NOx emissions from nitrogen-containing fuels, including pulverized coal, while improving combustion characteristics such as unburned carbon. A combination of experimental work and modeling was used to define how well oxygen enhanced combustion could reduce NOx emissions. The results of this work suggest that small amounts of oxygen replacement can reduce the NOx emissions as compared to the air-alone system. NOx emissions significantly below 0.15 lbs/MMBtu were measured. Oxygen addition was also shown to reduce carbon in ash. Comparison of the costs of using oxygen for NOx control against competing technologies, such as SCR, show that this

  8. A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response.

    Science.gov (United States)

    Melo, C A; Léveillé, N; Rooijers, K; Wijchers, P J; Geeven, G; Tal, A; Melo, S A; de Laat, W; Agami, R

    2016-08-18

    Genome-wide chromatin studies identified the tumor suppressor p53 as both a promoter and an enhancer-binding transcription factor. As an enhancer factor, p53 can induce local production of enhancer RNAs, as well as transcriptional activation of distal neighboring genes. Beyond the regulation of protein-coding genes, p53 has the capacity to regulate long intergenic noncoding RNA molecules (lincRNAs); however, their importance to the p53 tumor suppressive function remains poorly characterized. Here, we identified and characterized a novel p53-bound intronic enhancer that controls the expression of its host, the lincRNA00475 (linc-475). We demonstrate the requirement of linc-475 for the proper induction of a p53-dependent cell cycle inhibitory response. We further confirm the functional importance of linc-475 in the maintenance of CDKN1A/p21 levels, a cell cycle inhibitor and a major p53 target gene, following p53 activation. Interestingly, loss of linc-475 reduced the binding of both p53 and RNA polymerase II (RNAPII) to the promoter of p21, attenuating its transcription rate following p53 activation. Altogether, our data suggest a direct role of p53-bound enhancer domains in the activation of lincRNAs required for an efficient p53 transcriptional response.

  9. Enhanced Controlled Transdermal Delivery of Torasemide Using ...

    African Journals Online (AJOL)

    Purpose: To develop an ethylene-vinyl acetate (EVA) matrix system containing a permeation enhancer for enhanced transdermal delivery of torasemide. Methods: The solubility of torasemide was studied at various volume fraction of polyethylene glycol (PEG) 400. The effect of drug concentration was tested at 1.0, 2.0 and ...

  10. Regulation of Retention of FosB Intron 4 by PTB

    OpenAIRE

    Marinescu, Victor; Loomis, Patricia A.; Ehmann, Svetlana; Beales, Mitchell; Potashkin, Judith A.

    2007-01-01

    One effect of stressors such as chronic drug administration is that sequence within the terminal exon of the transcription factor FosB is recognized as intronic and removed by alternative splicing. This results in an open-reading-frame shift that produces a translation stop codon and ultimately a truncated protein, termed DeltaFosB. In vitro splicing assays with control and mutated transcripts generated from a fosB mini-gene construct indicated a CU-rich sequence at the 3' end of intron 4 (I4...

  11. Patterns of intron gain and conservation in eukaryotic genes

    Directory of Open Access Journals (Sweden)

    Wolf Yuri I

    2007-10-01

    Full Text Available Abstract Background: The presence of introns in protein-coding genes is a universal feature of eukaryotic genome organization, and the genes of multicellular eukaryotes, typically, contain multiple introns, a substantial fraction of which share position in distant taxa, such as plants and animals. Depending on the methods and data sets used, researchers have reached opposite conclusions on the causes of the high fraction of shared introns in orthologous genes from distant eukaryotes. Some studies conclude that shared intron positions reflect, almost entirely, a remarkable evolutionary conservation, whereas others attribute it to parallel gain of introns. To resolve these contradictions, it is crucial to analyze the evolution of introns by using a model that minimally relies on arbitrary assumptions. Results: We developed a probabilistic model of evolution that allows for variability of intron gain and loss rates over branches of the phylogenetic tree, individual genes, and individual sites. Applying this model to an extended set of conserved eukaryotic genes, we find that parallel gain, on average, accounts for only ~8% of the shared intron positions. However, the distribution of parallel gains over the phylogenetic tree of eukaryotes is highly non-uniform. There are, practically, no parallel gains in closely related lineages, whereas for distant lineages, such as animals and plants, parallel gains appear to contribute up to 20% of the shared intron positions. In accord with these findings, we estimated that ancestral introns have a high probability to be retained in extant genomes, and conversely, that a substantial fraction of extant introns have retained their positions since the early stages of eukaryotic evolution. In addition, the density of sites that are available for intron insertion is estimated to be, approximately, one in seven basepairs. Conclusion: We obtained robust estimates of the contribution of parallel gain to the observed

  12. The evolution of an intron: Analysis of a long, deletion-prone intron in the human dystrophin gene

    Energy Technology Data Exchange (ETDEWEB)

    McNaughton, J.C.; Hughes, G.; Jones, W.A. [Univ. of Otago, Dunedin (New Zealand)] [and others

    1997-03-01

    The sequence of a 112-kb region of the human dystrophin (DMD/BMD) gene encompassing the deletion prone intron 7 (110 kb) and the much shorter intron 8 (1.1 kb) has been determined. Recognizable insertion sequences account for approximately 40% of intron 7. LINE-1 and THE-1/LTR sequences occur in intron 7 with significantly higher frequency than would be expected statistically while Alu sequences are underrepresented. Intron 7 also contains numerous mammalian-wide interspersed repeats, a diverse range of medium reiteration repeats of unknown origin, and a sequence derived from a mariner transposon. By contrast, the shorter intron 8 contains no detectable insertion sequences. Dating of the L1 and Alu sequences suggests that intron 7 has approximately doubled in size within the past 130 million years, and comparison with the corresponding intron from the pufferfish (Fugu rubripes) suggests that the intron has expanded some 44-fold over a period of 400 million years. The possible contribution of the insertion elements to the instability of intron 7 is discussed. 66 refs., 2 figs., 2 tabs.

  13. Detained introns are a novel, widespread class of post-transcriptionally spliced introns.

    Science.gov (United States)

    Boutz, Paul L; Bhutkar, Arjun; Sharp, Phillip A

    2015-01-01

    Deep sequencing of embryonic stem cell RNA revealed many specific internal introns that are significantly more abundant than the other introns within polyadenylated transcripts; we classified these as "detained" introns (DIs). We identified thousands of DIs, many of which are evolutionarily conserved, in human and mouse cell lines as well as the adult mouse liver. DIs can have half-lives of over an hour yet remain in the nucleus and are not subject to nonsense-mediated decay (NMD). Drug inhibition of Clk, a stress-responsive kinase, triggered rapid splicing changes for a specific subset of DIs; half showed increased splicing, and half showed increased intron detention, altering transcript pools of >300 genes. Srsf4, which undergoes a dramatic phosphorylation shift in response to Clk kinase inhibition, regulates the splicing of some DIs, particularly in genes encoding RNA processing and splicing factors. The splicing of some DIs-including those in Mdm4, a negative regulator of p53-was also altered following DNA damage. After 4 h of Clk inhibition, the expression of >400 genes changed significantly, and almost one-third of these are p53 transcriptional targets. These data suggest a widespread mechanism by which the rate of splicing of DIs contributes to the level of gene expression. © 2015 Boutz et al.; Published by Cold Spring Harbor Laboratory Press.

  14. Enhanced Controlled Transdermal Delivery of Torasemide Using ...

    African Journals Online (AJOL)

    To increase pore size and flexibility of the EVA matrix, plasticizers with citrate and phthalate groups were added to the matrix containing torasemide. To improve the ... The effects of the enhancers on the skin penetration were evaluated using Franz diffusion cell fitted with the intact excised rat skin. Results: Solubility and ...

  15. Enhanced Controlled Transdermal Delivery of Torasemide Using ...

    African Journals Online (AJOL)

    Erah

    intercellular lipids to enhance drug transport across the intact skin or to increase the driving force for drug permeation. One of the most controversial methods is ..... alter the thermodynamic activity of the drugs in the vehicle, which would in turn modify the driving force for diffusion. PGs may partition into the tissue, facilitating ...

  16. Effective suppression of dengue virus using a novel group-I intron that induces apoptotic cell death upon infection through conditional expression of the Bax C-terminal domain.

    Science.gov (United States)

    Carter, James R; Keith, James H; Fraser, Tresa S; Dawson, James L; Kucharski, Cheryl A; Horne, Kate M; Higgs, Stephen; Fraser, Malcolm J

    2014-06-13

    Approximately 100 million confirmed infections and 20,000 deaths are caused by Dengue virus (DENV) outbreaks annually. Global warming and rapid dispersal have resulted in DENV epidemics in formally non-endemic regions. Currently no consistently effective preventive measures for DENV exist, prompting development of transgenic and paratransgenic vector control approaches. Production of transgenic mosquitoes refractory for virus infection and/or transmission is contingent upon defining antiviral genes that have low probability for allowing escape mutations, and are equally effective against multiple serotypes. Previously we demonstrated the effectiveness of an anti-viral group I intron targeting U143 of the DENV genome in mediating trans-splicing and expression of a marker gene with the capsid coding domain. In this report we examine the effectiveness of coupling expression of ΔN Bax to trans-splicing U143 intron activity as a means of suppressing DENV infection of mosquito cells. Targeting the conserved DENV circularization sequence (CS) by U143 intron trans-splicing activity appends a 3' exon RNA encoding ΔN Bax to the capsid coding region of the genomic RNA, resulting in a chimeric protein that induces premature cell death upon infection. TCID50-IFA analyses demonstrate an enhancement of DENV suppression for all DENV serotypes tested over the identical group I intron coupled with the non-apoptotic inducing firefly luciferase as the 3' exon. These cumulative results confirm the increased effectiveness of this αDENV-U143-ΔN Bax group I intron as a sequence specific antiviral that should be useful for suppression of DENV in transgenic mosquitoes. Annexin V staining, caspase 3 assays, and DNA ladder observations confirm DCA-ΔN Bax fusion protein expression induces apoptotic cell death. This report confirms the relative effectiveness of an anti-DENV group I intron coupled to an apoptosis-inducing ΔN Bax 3' exon that trans-splices conserved sequences of the 5' CS

  17. Intronic alternative splicing regulators identified by comparative genomics in nematodes.

    Directory of Open Access Journals (Sweden)

    Jennifer L Kabat

    2006-07-01

    Full Text Available Many alternative splicing events are regulated by pentameric and hexameric intronic sequences that serve as binding sites for splicing regulatory factors. We hypothesized that intronic elements that regulate alternative splicing are under selective pressure for evolutionary conservation. Using a Wobble Aware Bulk Aligner genomic alignment of Caenorhabditis elegans and Caenorhabditis briggsae, we identified 147 alternatively spliced cassette exons that exhibit short regions of high nucleotide conservation in the introns flanking the alternative exon. In vivo experiments on the alternatively spliced let-2 gene confirm that these conserved regions can be important for alternative splicing regulation. Conserved intronic element sequences were collected into a dataset and the occurrence of each pentamer and hexamer motif was counted. We compared the frequency of pentamers and hexamers in the conserved intronic elements to a dataset of all C. elegans intron sequences in order to identify short intronic motifs that are more likely to be associated with alternative splicing. High-scoring motifs were examined for upstream or downstream preferences in introns surrounding alternative exons. Many of the high-scoring nematode pentamer and hexamer motifs correspond to known mammalian splicing regulatory sequences, such as (TGCATG, indicating that the mechanism of alternative splicing regulation is well conserved in metazoans. A comparison of the analysis of the conserved intronic elements, and analysis of the entire introns flanking these same exons, reveals that focusing on intronic conservation can increase the sensitivity of detecting putative splicing regulatory motifs. This approach also identified novel sequences whose role in splicing is under investigation and has allowed us to take a step forward in defining a catalog of splicing regulatory elements for an organism. In vivo experiments confirm that one novel high-scoring sequence from our analysis

  18. Stochastic Adaptive Control and Estimation Enhancement

    Science.gov (United States)

    1990-02-01

    multioutput ARMA system. The plant has constant but unknown parameters. The cautious controller with a one-step horizon and a new dual controller with a two...system is shown to be stable. Multiinput multioutput systems with unknown parameters are encoun- Remark 4.1: tered in many practical situations, and...dual (181 B. Witterunark, "An active suboptimal dual controller for systems with stochastic c irfsoluin applied t-a multiipvt multioutput model

  19. Enhanced droplet control by transition boiling.

    Science.gov (United States)

    Grounds, Alex; Still, Richard; Takashina, Kei

    2012-01-01

    A droplet of water on a heated surface can levitate over a film of gas produced by its own evaporation in the Leidenfrost effect. When the surface is prepared with ratchet-like saw-teeth topography, these droplets can self-propel and can even climb uphill. However, the extent to which the droplets can be controlled is limited by the physics of the Leidenfrost effect. Here, we show that transition boiling can be induced even at very high surface temperatures and provide additional control over the droplets. Ratchets with acute protrusions enable droplets to climb steeper inclines while ratchets with sub-structures enable their direction of motion to be controlled by varying the temperature of the surface. The droplets' departure from the Leidenfrost regime is assessed by analysing the sound produced by their boiling. We anticipate these techniques will enable the development of more sophisticated methods for controlling small droplets and heat transfer.

  20. Enhanced Ground Control for ISS Robotics Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This project will investigate and adapt aides which will increase the efficiency of ISS robotics ground control operations with the intent of creating more...

  1. Enhanced Sleep Mode MAC Control for EPON

    DEFF Research Database (Denmark)

    Yan, Ying; Dittmann, Lars

    2011-01-01

    This paper introduces sleep mode operations for EPON. New MAC control functions are proposed to schedule sleep periods. Traffic profiles are considered to optimize energy efficiency and network performances. Simulation results are analyzed in OPNET modeler.......This paper introduces sleep mode operations for EPON. New MAC control functions are proposed to schedule sleep periods. Traffic profiles are considered to optimize energy efficiency and network performances. Simulation results are analyzed in OPNET modeler....

  2. Identifying the mechanisms of intron gain: progress and trends

    Directory of Open Access Journals (Sweden)

    Yenerall Paul

    2012-09-01

    Full Text Available Abstract Continued improvements in Next-Generation DNA/RNA sequencing coupled with advances in gene annotation have provided researchers access to a plethora of annotated genomes. Subsequent analyses of orthologous gene structures have identified numerous intron gain and loss events that have occurred both recently and in the very distant past. This research has afforded exceptional insight into the temporal and lineage-specific rates of intron gain and loss among various species throughout evolution. Numerous studies have also attempted to identify the molecular mechanisms of intron gain and loss. However, even after considerable effort, very little is known about these processes. In particular, the mechanism(s of intron gain have proven exceptionally enigmatic and remain topics of considerable debate. Currently, there exists no definitive consensus as to what mechanism(s may generate introns. Because many introns are known to affect gene expression, it is necessary to understand the molecular process(es by which introns may be gained. Here we review the seven most commonly purported mechanisms of intron gain and, when possible, summarize molecular evidence for or against the occurrence of each of these mechanisms. Furthermore, we catalogue indirect evidence that supports the occurrence of each mechanism. Finally, because these proposed mechanisms fail to explain the mechanistic origin of many recently gained introns, we also look at trends that may aid researchers in identifying other potential mechanism(s of intron gain. Reviewers This article was reviewed by Eugene Koonin, Scott Roy (nominated by W. Ford Doolittle, and John Logsdon.

  3. Group I introns in the liverwort mitochondrial genome: the gene coding for subunit 1 of cytochrome oxidase shares five intron positions with its fungal counterparts.

    OpenAIRE

    Ohta, E; Oda, K; Yamato, K; Nakamura, Y; Takemura, M; Nozato, N; Akashi, K; Ohyama, K; Michel, F

    1993-01-01

    The complete nucleotide sequence of the mitochondrial DNA (mtDNA) from a liverwort, Marchantia polymorpha, contains thirty-two introns. Twenty-five of these introns possess the characteristic secondary structures and consensus sequences of group II introns. The remaining seven are group I introns, six of which happen to interrupt the gene coding for subunit 1 of cytochrome oxidase (cox1). Interestingly, the insertion sites of one group II and four group I introns in the cox1 gene coincide wit...

  4. Distribution of Conventional and Nonconventional Introns in Tubulin (α and β) Genes of Euglenids

    OpenAIRE

    Milanowski, Rafał; Karnkowska, Anna; Ishikawa, Takao; Zakryś, Bożena

    2013-01-01

    The nuclear genomes of euglenids contain three types of introns: conventional spliceosomal introns, nonconventional introns for which a splicing mechanism is unknown (variable noncanonical borders, RNA secondary structure bringing together intron ends), and so-called intermediate introns, which combine features of conventional and nonconventional introns. Analysis of two genes, tubA and tubB, from 20 species of euglenids reveals contrasting distribution patterns of conventional and nonconvent...

  5. Flowfield Mixing Enhancement and Noise Control Using Flexible Filaments

    National Research Council Canada - National Science Library

    Gutmark, Ephraim

    2000-01-01

    The subject research program sought to explore a novel method for achieving passive flow field control, with applications to mixing enhancement and noise reduction, through the interaction of the flow...

  6. Enhancing Safety at Airline Operations Control Centre

    Directory of Open Access Journals (Sweden)

    Lukáš Řasa

    2015-04-01

    Full Text Available In recent years a new term of Safety Management System (SMS has been introduced into aviation legislation. This system is being adopted by airline operators. One of the groundbased actors of everyday operations is Operations Control Centre (OCC. The goal of this article has been to identify and assess risks and dangers which occur at OCC and create a template for OCC implementation into SMS.

  7. Eccentric Exercise to Enhance Neuromuscular Control.

    Science.gov (United States)

    Lepley, Lindsey K; Lepley, Adam S; Onate, James A; Grooms, Dustin R

    Neuromuscular alterations are a major causal factor of primary and secondary injuries. Though injury prevention programs have experienced some success, rates of injuries have not declined, and after injury, individuals often return to activity with functionality below clinical recommendations. Considering alternative therapies to the conventional concentric exercise approach, such as one that can target neuromuscular injury risk and postinjury alterations, may provide for more effective injury prevention and rehabilitation protocols. Peer-reviewed sources available on the Web of Science and MEDLINE databases from 2000 through 2016 were gathered using searches associated with the keywords eccentric exercise, injury prevention, and neuromuscular control. Eccentric exercise will reduce injury risk by targeting specific neural and morphologic alterations that precipitate neuromuscular dysfunction. Clinical review. Level 4. Neuromuscular control is influenced by alterations in muscle morphology and neural activity. Eccentric exercise beneficially modifies several underlying factors of muscle morphology (fiber typing, cross-sectional area, working range, and pennation angle), and emerging evidence indicates that eccentric exercise is also beneficial to peripheral and central neural activity (alpha motorneuron recruitment/firing, sarcolemma activity, corticospinal excitability, and brain activation). There is mounting evidence that eccentric exercise is not only a therapeutic intervention influencing muscle morphology but also targets unique alterations in neuromuscular control, influencing injury risk.

  8. Method for enhanced control of welding processes

    Science.gov (United States)

    Sheaffer, Donald A.; Renzi, Ronald F.; Tung, David M.; Schroder, Kevin

    2000-01-01

    Method and system for producing high quality welds in welding processes, in general, and gas tungsten arc (GTA) welding, in particular by controlling weld penetration. Light emitted from a weld pool is collected from the backside of a workpiece by optical means during welding and transmitted to a digital video camera for further processing, after the emitted light is first passed through a short wavelength pass filter to remove infrared radiation. By filtering out the infrared component of the light emitted from the backside weld pool image, the present invention provides for the accurate determination of the weld pool boundary. Data from the digital camera is fed to an imaging board which focuses on a 100.times.100 pixel portion of the image. The board performs a thresholding operation and provides this information to a digital signal processor to compute the backside weld pool dimensions and area. This information is used by a control system, in a dynamic feedback mode, to automatically adjust appropriate parameters of a welding system, such as the welding current, to control weld penetration and thus, create a uniform weld bead and high quality weld.

  9. Controlling enhanced absorption in graphene metamaterial

    Science.gov (United States)

    Zhou, Qihui; Liu, Peiguo; Bian, Li-an; Liu, Hanqing; Liu, Chenxi; Chen, Genghui

    2018-04-01

    In this paper, a controllable terahertz (THz) metamaterial absorber (MA) is designed with the circuit analog method. Taking advantage of the patterned graphene on SiO2/doped Si/polyimide substrates with a gold reflector, the controllable MA achieves perfect absorption at 0.75 THz. The chemical potential of graphene is regulated by controlling the voltage between graphene and doped Si layers. As the chemical potential varies from 0 eV to 0.5 eV, the MA is changed from reflection (0.99). The distributions of surface current and electric field are illustrated to analyze the resonant characteristic of patterned graphene. According to the resonant characteristic, we introduce patterned graphene elements with different dimension in a unit cell, which effectively extends the effective absorption bandwidth (absorption > 0 . 9) from 0.67-0.93 THz to 0.52-0.95 THz. Moreover, replacing part of the graphene structure with gold, the switchable MA is turned into a frequency tunable MA. The absorption peak moves from 0.62 THz to 0.92 THz as the chemical potential increases from 0.1 eV to 0.5 eV. These designs overcome limitation of traditional absorbers and exhibit great potentials in many practical applications.

  10. Drosophila polytene chromosome bands formed by gene introns.

    Science.gov (United States)

    Zhimulev, I F; Boldyreva, L V; Demakova, O V; Poholkova, G V; Khoroshko, V A; Zykova, T Yu; Lavrov, S A; Belyaeva, E S

    2016-01-01

    Genetic organization of bands and interbands in polytene chromosomes has long remained a puzzle for geneticists. It has been recently demonstrated that interbands typically correspond to the 5'-ends of house-keeping genes, whereas adjacent loose bands tend to be composed of coding sequences of the genes. In the present work, we made one important step further and mapped two large introns of ubiquitously active genes on the polytene chromosome map. We show that alternative promoter regions of these genes map to interbands, whereas introns and coding sequences found between those promoters correspond to loose grey bands. Thus, a gene having its long intron "sandwiched" between to alternative promoters and a common coding sequence may occupy two interbands and one band in the context of polytene chromosomes. Loose, partially decompacted bands appear to host large introns.

  11. Intronic regulation of Aire expression by Jmjd6 for self-tolerance induction in the thymus.

    Science.gov (United States)

    Yanagihara, Toyoshi; Sanematsu, Fumiyuki; Sato, Tetsuya; Uruno, Takehito; Duan, Xuefeng; Tomino, Takahiro; Harada, Yosuke; Watanabe, Mayuki; Wang, Yuqing; Tanaka, Yoshihiko; Nakanishi, Yoichi; Suyama, Mikita; Yoshinori, Fukui

    2015-11-04

    The thymus has spatially distinct microenvironments, the cortex and the medulla, where the developing T-cells are selected to mature or die through the interaction with thymic stromal cells. To establish the immunological self in the thymus, medullary thymic epithelial cells (mTECs) express diverse sets of tissue-specific self-antigens (TSAs). This ectopic expression of TSAs largely depends on the transcriptional regulator Aire, yet the mechanism controlling Aire expression itself remains unknown. Here, we show that Jmjd6, a dioxygenase that catalyses lysyl hydroxylation of splicing regulatory proteins, is critical for Aire expression. Although Jmjd6 deficiency does not affect abundance of Aire transcript, the intron 2 of Aire gene is not effectively spliced out in the absence of Jmjd6, resulting in marked reduction of mature Aire protein in mTECs and spontaneous development of multi-organ autoimmunity in mice. These results highlight the importance of intronic regulation in controlling Aire protein expression.

  12. ADVANCED COMPRESSOR ENGINE CONTROLS TO ENHANCE OPERATION, RELIABILITY AND INTEGRITY

    Energy Technology Data Exchange (ETDEWEB)

    Gary D. Bourn; Jess W. Gingrich; Jack A. Smith

    2004-03-01

    This document is the final report for the ''Advanced Compressor Engine Controls to Enhance Operation, Reliability, and Integrity'' project. SwRI conducted this project for DOE in conjunction with Cooper Compression, under DOE contract number DE-FC26-03NT41859. This report addresses an investigation of engine controls for integral compressor engines and the development of control strategies that implement closed-loop NOX emissions feedback.

  13. Color and Contrast Enhancement by Controlled Piecewise Affine Histogram Equalization

    Directory of Open Access Journals (Sweden)

    Jose-Luis Lisani

    2012-10-01

    Full Text Available This paper presents a simple contrast enhancement algorithm based on histogram equalization (HE. The proposed algorithm performs a piecewise affine transform of the intensity levels of a digital image such that the new cumulative distribution function will be approximately uniform (as with HE, but where the stretching of the range is locally controlled to avoid brutal noise enhancement. We call this algorithm Piecewise Affine Equalization (PAE. Several experiments show that, in general, the new algorithm improves HE results.

  14. Alteration of introns in a hyaluronan synthase 1 (HAS1 minigene convert Pre-mRNA [corrected] splicing to the aberrant pattern in multiple myeloma (MM: MM patients harbor similar changes.

    Directory of Open Access Journals (Sweden)

    Jitra Kriangkum

    Full Text Available Aberrant pre-mRNA splice variants of hyaluronan synthase 1 (HAS1 have been identified in malignant cells from cancer patients. Bioinformatic analysis suggests that intronic sequence changes can underlie aberrant splicing. Deletions and mutations were introduced into HAS1 minigene constructs to identify regions that can influence aberrant intronic splicing, comparing the splicing pattern in transfectants with that in multiple myeloma (MM patients. Introduced genetic variations in introns 3 and 4 of HAS1 as shown here can promote aberrant splicing of the type detected in malignant cells from MM patients. HAS1Vd is a novel intronic splice variant first identified here. HAS1Vb, an intronic splice variant previously identified in patients, skips exon 4 and utilizes the same intron 4 alternative 3'splice site as HAS1Vd. For transfected constructs with unaltered introns 3 and 4, HAS1Vd transcripts are readily detectable, frequently to the exclusion of HAS1Vb. In contrast, in MM patients, HAS1Vb is more frequent than HAS1Vd. In the HAS1 minigene, combining deletion in intron 4 with mutations in intron 3 leads to a shift from HAS1Vd expression to HAS1Vb expression. The upregulation of aberrant splicing, exemplified here by the expression of HAS1Vb, is shown here to be influenced by multiple genetic changes in intronic sequences. For HAS1Vb, this includes enhanced exon 4 skipping and increased usage of alternative 3' splice sites. Thus, the combination of introduced mutations in HAS1 intron3 with introduced deletions in HAS1 intron 4 promoted a shift to an aberrant splicing pattern previously shown to be clinically significant. Most MM patients harbor genetic variations in intron 4, and as shown here, nearly half harbor recurrent mutations in HAS1 intron 3. Our work suggests that aberrant intronic HAS1 splicing in MM patients may rely on intronic HAS1 deletions and mutations that are frequent in MM patients but absent from healthy donors.

  15. Secondary Control for Voltage Quality Enhancement in Microgrids

    DEFF Research Database (Denmark)

    Savaghebi, Mehdi; Jalilian, Alireza; Vasquez, Juan Carlos

    2012-01-01

    In this paper, a hierarchical control scheme is proposed for enhancement of sensitive load bus (SLB) voltage quality in microgrids. The control structure consists of primary and secondary levels. The primary control level comprises distributed generators (DGs) local controllers. Each...... level is applied to manage the compensation of SLB voltage unbalance and harmonics by sending proper control signals to the primary level. DGs compensation efforts are controlled locally at the primary level. The system design procedure for selecting proper control parameters is discussed. Simulation...... of these controllers includes a selective virtual impedance loop which is considered to improve sharing of fundamental and harmonic components of load current among the DG units. The sharing improvement is provided at the expense of increasing voltage unbalance and harmonic distortion. Thus, the secondary control...

  16. Genomewide analysis of intronic microRNAs in rice and Arabidopsis

    Indian Academy of Sciences (India)

    Here we report a comprehensive computational analysis to characterize intronic miRNAs in rice and Arabidopsis. RT-PCR analysis confirmed that the identified intronic miRNAs were derived from the real introns of host genes. Interestingly, 13 intronic miRNAs in rice and two in Arabidopsis were located within seven clusters ...

  17. Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA

    Directory of Open Access Journals (Sweden)

    Simon Dawn M

    2005-11-01

    Full Text Available Abstract Background Group I introns have spread into over 90 different sites in nuclear ribosomal DNA (rDNA with greater than 1700 introns reported in these genes. These ribozymes generally spread through endonuclease-mediated intron homing. Another putative pathway is reverse splicing whereby a free group I intron inserts into a homologous or heterologous RNA through complementary base-pairing between the intron and exon RNA. Reverse-transcription of the RNA followed by general recombination results in intron spread. Here we used phylogenetics to test for reverse splicing spread in a taxonomically broadly sampled data set of fungal group I introns including 9 putatively ancient group I introns in the rDNA of the yeast-like symbiont Symbiotaphrina buchneri. Results Our analyses reveal a complex evolutionary history of the fungal introns with many cases of vertical inheritance (putatively for the 9 introns in S. buchneri and intron lateral transfer. There are several examples in which introns, many of which are still present in S. buchneri, may have spread through reverse splicing into heterologous rDNA sites. If the S. buchneri introns are ancient as we postulate, then group I intron loss was widespread in fungal rDNA evolution. Conclusion On the basis of these results, we suggest that the extensive distribution of fungal group I introns is at least partially explained by the reverse splicing movement of existing introns into ectopic rDNA sites.

  18. Enhanced pid vs model predictive control applied to bldc motor

    Science.gov (United States)

    Gaya, M. S.; Muhammad, Auwal; Aliyu Abdulkadir, Rabiu; Salim, S. N. S.; Madugu, I. S.; Tijjani, Aminu; Aminu Yusuf, Lukman; Dauda Umar, Ibrahim; Khairi, M. T. M.

    2018-01-01

    BrushLess Direct Current (BLDC) motor is a multivariable and highly complex nonlinear system. Variation of internal parameter values with environment or reference signal increases the difficulty in controlling the BLDC effectively. Advanced control strategies (like model predictive control) often have to be integrated to satisfy the control desires. Enhancing or proper tuning of a conventional algorithm results in achieving the desired performance. This paper presents a performance comparison of Enhanced PID and Model Predictive Control (MPC) applied to brushless direct current motor. The simulation results demonstrated that the PSO-PID is slightly better than the PID and MPC in tracking the trajectory of the reference signal. The proposed scheme could be useful algorithms for the system.

  19. PULSE MODULATION POWER AMPLIFIER WITH ENHANCED CASCADE CONTROL METHOD

    DEFF Research Database (Denmark)

    1998-01-01

    A digital switching power amplifier with Multivariable Enhanced Cascade Controlled (MECC) includes a modulator, a switching power stage and a low pass filter. In the first preferred embodiment an enhanced cascade control structure local to the switching power stage is added, characterised by havi...... and feedback path A to determine stable self-oscillating conditions. An implemented 250W example MECC digital power amplifier has proven superior performance in terms of audio performance (0.005 % distortion, 115 dB dynamic range) and efficiency (92 %)....

  20. Enhancing Raman signals with an interferometrically controlled AFM tip

    International Nuclear Information System (INIS)

    Oron-Carl, Matti; Krupke, Ralph

    2013-01-01

    We demonstrate the upgrade of a commercial confocal Raman microscope into a tip-enhanced Raman microscope/spectroscopy system (TERS) by integrating an interferometrically controlled atomic force microscope into the base of an existing upright microscope to provide near-field detection and thus signal enhancement. The feasibility of the system is demonstrated by measuring the Raman near-field enhancement on thin PEDOT:PSS films and on carbon nanotubes within a device geometry. An enhancement factor of 2–3 and of 5–6 is observed, respectively. Moreover, on a nanotube device we show local conductivity measurement and its correlation to Raman and topography recordings. Upgrading an existing upright confocal Raman microscope in the demonstrated way is significantly cheaper than purchasing a complete commercial TERS system. (paper)

  1. An intronic deletion in the PROM1 gene leads to autosomal recessive cone-rod dystrophy.

    Science.gov (United States)

    Eidinger, Osnat; Leibu, Rina; Newman, Hadas; Rizel, Leah; Perlman, Ido; Ben-Yosef, Tamar

    2015-01-01

    To investigate the genetic basis for autosomal recessive cone-rod dystrophy (CRD) in a consanguineous Israeli Jewish family. Patients underwent a detailed ophthalmic evaluation, including eye examination, visual field testing, optical coherence tomography (OCT), and electrophysiological tests, electroretinography (ERG) and visual evoked potential (VEP). Genome-wide homozygosity mapping using a single nucleotide polymorphism (SNP) array was performed to identify homozygous regions shared among two of the affected individuals. Mutation screening of the underlying gene was performed with direct sequencing. In silico and in vitro analyses were used to predict the effect of the identified mutation on splicing. The affected family members are three siblings who have various degrees of progressive visual deterioration, glare, color vision abnormalities, and night vision difficulties. Visual field tests revealed central scotomas of different extension. Cone and rod ERG responses were reduced, with cones more severely affected. Homozygosity mapping revealed several homozygous intervals shared among two of the affected individuals. One included the PROM1 gene. Sequence analysis of the 26 coding exons of PROM1 in one affected individual revealed no mutations in the coding sequence or in intronic splice sites. However, in intron 21, proximate to the intron-exon junction, we observed a homozygous 10 bp deletion between positions -26 and -17 (c.2281-26_-17del). The deletion was linked to a known SNP, c.2281-6C>G. The deletion cosegregated with the disease in the family, and was not detected in public databases or in 101 ethnically-matched control individuals. In silico analysis predicted that this deletion would lead to altered intron 21 splicing. Bioinformatic analysis predicted that a recognition site for the SRSF2 splicing factor is located within the deleted sequence. The in vitro splicing assay demonstrated that c.2281-26_-17del leads to complete exon 22 skipping. A novel

  2. Significant association of interleukin-4 gene intron 3 VNTR polymorphism with susceptibility to knee osteoarthritis.

    Science.gov (United States)

    Yigit, Serbulent; Inanir, Ahmet; Tekcan, Akın; Tural, Ercan; Ozturk, Gokhan Tuna; Kismali, Gorkem; Karakus, Nevin

    2014-03-01

    Interleukin-4 (IL-4) is a strong chondroprotective cytokine and polymorphisms within this gene may be a risk factor for osteoarthritis (OA). We aimed to investigate genotype and allele frequencies of IL-4 gene intron 3 variable number of tandem repeats (VNTR) polymorphism in patients with knee OA in a Turkish population. The study included 202 patients with knee OA and 180 healthy controls. Genomic DNA was isolated and IL-4 gene 70 bp VNTR polymorphism determined by using polymerase chain reaction (PCR) with specific primers followed by restriction fragment length polymorphism (RFLP) analysis. Our result show that there was statistically significant difference between knee OA patients and control group with respect to IL-4 genotype distribution and allele frequencies (p=0.000, OR: 0.20, 95% CI: 0.10-0.41, OR: 0.22, 95% CI: 0.12-0.42, respectively). Our findings suggest that there is an association of IL-4 gene intron 3 VNTR polymorphism with susceptibility of a person for development of knee OA. As a result, IL-4 gene intron 3 VNTR polymorphism could be a genetic marker in OA in a Turkish study population. This is the first association study that evaluates the associations between IL-4 gene VNTR polymorphism and knee OA. Crown Copyright © 2013. Published by Elsevier B.V. All rights reserved.

  3. A new strategy to enhance polysialic acid production by controlling ...

    African Journals Online (AJOL)

    STORAGESEVER

    2010-04-19

    Apr 19, 2010 ... Full Length Research Paper. A new strategy to enhance polysialic acid production by ... concentration higher than 40 g/L. A new strategy of controling sorbitol concentration in a range of 20 - 40 g/L in the broth during the ... embryogenesis, neural cell growth, differentiation, cell-cell mediating and membrane ...

  4. Optical waveguide mode control by nanoslit-enhanced terahertz field

    DEFF Research Database (Denmark)

    Novitsky, Andrey; Zalkovskij, Maksim; Malureanu, Radu

    2012-01-01

    In this Letter we propose a scheme providing control over an optical waveguide mode by a terahertz (THz) wave. The scheme is based on an optimization of the overlap between the optical waveguide mode and the THz field, with the THz field strength enhanced by the presence of a metallic nanoslit...

  5. Host Factors Influencing the Retrohoming Pathway of Group II Intron RmInt1, Which Has an Intron-Encoded Protein Naturally Devoid of Endonuclease Activity.

    Directory of Open Access Journals (Sweden)

    Rafael Nisa-Martínez

    Full Text Available Bacterial group II introns are self-splicing catalytic RNAs and mobile retroelements that have an open reading frame encoding an intron-encoded protein (IEP with reverse transcriptase (RT and RNA splicing or maturase activity. Some IEPs carry a DNA endonuclease (En domain, which is required to cleave the bottom strand downstream from the intron-insertion site for target DNA-primed reverse transcription (TPRT of the inserted intron RNA. Host factors complete the insertion of the intron. By contrast, the major retrohoming pathway of introns with IEPs naturally lacking endonuclease activity, like the Sinorhizobium meliloti intron RmInt1, is thought to involve insertion of the intron RNA into the template for lagging strand DNA synthesis ahead of the replication fork, with possible use of the nascent strand to prime reverse transcription of the intron RNA. The host factors influencing the retrohoming pathway of such introns have not yet been described. Here, we identify key candidates likely to be involved in early and late steps of RmInt1 retrohoming. Some of these host factors are common to En+ group II intron retrohoming, but some have different functions. Our results also suggest that the retrohoming process of RmInt1 may be less dependent on the intracellular free Mg2+ concentration than those of other group II introns.

  6. Tertiary architecture of the Oceanobacillus iheyensis group II intron

    Energy Technology Data Exchange (ETDEWEB)

    Toor, Navtej; Keating, Kevin S.; Fedorova, Olga; Rajashankar, Kanagalaghatta; Wang, Jimin; Pyle, Anna Marie (Yale); (Cornell)

    2010-05-03

    Group II introns are large ribozymes that act as self-splicing and retrotransposable RNA molecules. They are of great interest because of their potential evolutionary relationship to the eukaryotic spliceosome, their continued influence on the organization of many genomes in bacteria and eukaryotes, and their potential utility as tools for gene therapy and biotechnology. One of the most interesting features of group II introns is their relative lack of nucleobase conservation and covariation, which has long suggested that group II intron structures are stabilized by numerous unusual tertiary interactions and backbone-mediated contacts. Here, we provide a detailed description of the tertiary interaction networks within the Oceanobacillus iheyensis group IIC intron, for which a crystal structure was recently solved to 3.1 {angstrom} resolution. The structure can be described as a set of several intricately constructed tertiary interaction nodes, each of which contains a core of extended stacking networks and elaborate motifs. Many of these nodes are surrounded by a web of ribose zippers, which appear to further stabilize local structure. As predicted from biochemical and genetic studies, the group II intron provides a wealth of new information on strategies for RNA folding and tertiary structural organization.

  7. Intronic L1 retrotransposons and nested genes cause transcriptional interference by inducing intron retention, exonization and cryptic polyadenylation.

    Directory of Open Access Journals (Sweden)

    Kristel Kaer

    Full Text Available Transcriptional interference has been recently recognized as an unexpectedly complex and mostly negative regulation of genes. Despite a relatively few studies that emerged in recent years, it has been demonstrated that a readthrough transcription derived from one gene can influence the transcription of another overlapping or nested gene. However, the molecular effects resulting from this interaction are largely unknown.Using in silico chromosome walking, we searched for prematurely terminated transcripts bearing signatures of intron retention or exonization of intronic sequence at their 3' ends upstream to human L1 retrotransposons, protein-coding and noncoding nested genes. We demonstrate that transcriptional interference induced by intronic L1s (or other repeated DNAs and nested genes could be characterized by intron retention, forced exonization and cryptic polyadenylation. These molecular effects were revealed from the analysis of endogenous transcripts derived from different cell lines and tissues and confirmed by the expression of three minigenes in cell culture. While intron retention and exonization were comparably observed in introns upstream to L1s, forced exonization was preferentially detected in nested genes. Transcriptional interference induced by L1 or nested genes was dependent on the presence or absence of cryptic splice sites, affected the inclusion or exclusion of the upstream exon and the use of cryptic polyadenylation signals.Our results suggest that transcriptional interference induced by intronic L1s and nested genes could influence the transcription of the large number of genes in normal as well as in tumor tissues. Therefore, this type of interference could have a major impact on the regulation of the host gene expression.

  8. Video game training enhances cognitive control in older adults.

    Science.gov (United States)

    Anguera, J A; Boccanfuso, J; Rintoul, J L; Al-Hashimi, O; Faraji, F; Janowich, J; Kong, E; Larraburo, Y; Rolle, C; Johnston, E; Gazzaley, A

    2013-09-05

    Cognitive control is defined by a set of neural processes that allow us to interact with our complex environment in a goal-directed manner. Humans regularly challenge these control processes when attempting to simultaneously accomplish multiple goals (multitasking), generating interference as the result of fundamental information processing limitations. It is clear that multitasking behaviour has become ubiquitous in today's technologically dense world, and substantial evidence has accrued regarding multitasking difficulties and cognitive control deficits in our ageing population. Here we show that multitasking performance, as assessed with a custom-designed three-dimensional video game (NeuroRacer), exhibits a linear age-related decline from 20 to 79 years of age. By playing an adaptive version of NeuroRacer in multitasking training mode, older adults (60 to 85 years old) reduced multitasking costs compared to both an active control group and a no-contact control group, attaining levels beyond those achieved by untrained 20-year-old participants, with gains persisting for 6 months. Furthermore, age-related deficits in neural signatures of cognitive control, as measured with electroencephalography, were remediated by multitasking training (enhanced midline frontal theta power and frontal-posterior theta coherence). Critically, this training resulted in performance benefits that extended to untrained cognitive control abilities (enhanced sustained attention and working memory), with an increase in midline frontal theta power predicting the training-induced boost in sustained attention and preservation of multitasking improvement 6 months later. These findings highlight the robust plasticity of the prefrontal cognitive control system in the ageing brain, and provide the first evidence, to our knowledge, of how a custom-designed video game can be used to assess cognitive abilities across the lifespan, evaluate underlying neural mechanisms, and serve as a powerful tool

  9. Intronic TP53 Germline Sequence Variants Modify the Risk in German Breast/Ovarian Cancer Families

    Directory of Open Access Journals (Sweden)

    Liu Xuan

    2004-07-01

    Full Text Available Abstract To establish the contribution of TP53 germline mutations to familial breast/ovarian cancer in Germany we screened the complete coding region of the TP53 gene in a series of German breast/ovarian cancer families negative for mutations in the BRCA1 and BRCA2 genes. Two different intronic TP53 sequence variants were identified in 6/48 (12.5% breast/ovarian cancer families. A novel A to T nucleotide change at position 17708 in intron 10 segregating with the disease was detected in three breast cancer families (6.2%. One 17708 A>T-associated breast tumour showed loss of the wild-type allele. This variant was also found in 5/112 (4.5% healthy controls indicating that it is a polymorphism. A second sequence variant changing a G to C at position 13964 in intron 6 not segregating with the disease was found in two breast cancer families and one breast-ovarian cancer family (6.2%. This variant has previously been shown to occur at an elevated frequency in hereditary breast cancer patients from North America and to be of functional importance leading to inhibition of apoptosis and prolongation of cell survival after DNA-damage. Screening of 185 consecutive unselected German breast cancer patients revealed the 13964 G>C variant in four patients (2.2%. Immunohistochemical analysis of the TP53 protein showed negative immunoreactivity in normal and tumour tissues of one 17708 A>T and six 13964 G>C carriers. TP53 overexpression was detected in the tumour tissue of one sporadic breast cancer patient carrying the 13964 G>C variant. Our results show that intronic changes of the TP53 gene may act as or be associated with risk modifiers in familial breast cancer.

  10. Alternative splicing mechanisms orchestrating post-transcriptional gene expression: intron retention and the intron-rich genome of apicomplexan parasites.

    Science.gov (United States)

    Lunghi, Matteo; Spano, Furio; Magini, Alessandro; Emiliani, Carla; Carruthers, Vern B; Di Cristina, Manlio

    2016-02-01

    Apicomplexan parasites including Toxoplasma gondii and Plasmodium species have complex life cycles that include multiple hosts and differentiation through several morphologically distinct stages requiring marked changes in gene expression. This review highlights emerging evidence implicating regulation of mRNA splicing as a mechanism to prime these parasites for rapid gene expression upon differentiation. We summarize the most important insights in alternative splicing including its role in regulating gene expression by decreasing mRNA abundance via 'Regulated Unproductive Splicing and Translation'. As a related but less well-understood mechanism, we discuss also our recent work suggesting a role for intron retention for precluding translation of stage specific isoforms of T. gondii glycolytic enzymes. We additionally provide new evidence that intron retention might be a widespread mechanism during parasite differentiation. Supporting this notion, recent genome-wide analysis of Toxoplasma and Plasmodium suggests intron retention is more pervasive than heretofore thought. These findings parallel recent emergence of intron retention being more prevalent in mammals than previously believed, thereby adding to the established roles in plants, fungi and unicellular eukaryotes. Deeper mechanistic studies of intron retention will provide important insight into its role in regulating gene expression in apicomplexan parasites and more general in eukaryotic organisms.

  11. Lidar-Enhanced Wind Turbine Control: Past, Present, and Future

    Energy Technology Data Exchange (ETDEWEB)

    Scholbrock, Andrew; Fleming, Paul; Schlipf, David; Wright, Alan; Johnson, Kathryn; Wang, Na

    2016-08-01

    The main challenges in harvesting energy from the wind arise from the unknown incoming turbulent wind field. Balancing the competing interests of reduction in structural loads and increasing energy production is the goal of a wind turbine controller to reduce the cost of producing wind energy. Conventional wind turbines use feedback methods to optimize these goals, reacting to wind disturbances after they have already impacted the wind turbine. Lidar sensors offer a means to provide additional inputs to a wind turbine controller, enabling new techniques to improve control methods, allowing a controller to actuate a wind turbine in anticipation of an incoming wind disturbance. This paper will look at the development of lidar-enhanced controls and how they have been used for various turbine load reductions with pitch actuation, as well as increased energy production with improved yaw control. Ongoing work will also be discussed to show that combining pitch and torque control using feedforward nonlinear model predictive control can lead to both reduced loads and increased energy production. Future work is also proposed on extending individual wind turbine controls to the wind plant level and determining how lidars can be used for control methods to further lower the cost of wind energy by minimizing wake impacts in a wind farm.

  12. The association between Interleukin (IL)-4 gene intron 3 VNTR polymorphism and alopecia areata (AA) in Turkish population.

    Science.gov (United States)

    Kalkan, Göknur; Karakus, Nevin; Baş, Yalçın; Takçı, Zennure; Ozuğuz, Pınar; Ateş, Omer; Yigit, Serbulent

    2013-09-25

    Alopecia areata (AA) is hypothesized to be an organ-specific autoimmune disease of hair follicles mediated by T cells. As immunological and genetic factors have been implicated in the pathogenesis of AA, the purpose of the present study was to investigate possible associations between the functional Interleukin (IL)-4 gene intron 3 VNTR polymorphism and AA susceptibility and disease progression in Turkish population. The study group consisted of 116 unrelated patients with AA and 125 unrelated healthy controls. Genomic DNA was isolated and IL-4 gene 70 bp VNTR polymorphism determined by using polymerase chain reaction (PCR) with specific primers. No association was observed between AA patients and controls according to genotype distribution (p=0.051). The allele distribution of IL-4 gene intron 3 VNTR polymorphism was statistically different between AA patients and control group (p=0.026). The frequency of P1 allele in patients was significantly higher than that in the control group. When the P2P2 genotype was compared with P1P2+P1P1 genotypes, a statistically significant difference was observed between patients and controls (p=0.036). Intron 3 VNTR polymorphism in the IL-4 gene was found to be associated with AA susceptibility in Turkish population. The results suggest that IL-4 VNTR polymorphism in the intron 3 region may be a risk factor for the development of AA among Turkish population. This is the first to report that intron 3 VNTR polymorphism in the IL-4 gene is associated with AA susceptibility. © 2013.

  13. Accumulation of Stable Full-Length Circular Group I Intron RNAs during Heat-Shock

    DEFF Research Database (Denmark)

    Andersen, Kasper L.; Beckert, Bertrand; Masquida, Benoit

    2016-01-01

    Group I introns in nuclear ribosomal RNA of eukaryotic microorganisms are processed by splicing or circularization. The latter results in formation of full-length circular introns without ligation of the exons and has been proposed to be active in intron mobility. We applied qRT-PCR to estimate...... the copy number of circular intron RNA from the myxomycete Didymium iridis. In exponentially growing amoebae, the circular introns are nuclear and found in 70 copies per cell. During heat-shock, the circular form is up-regulated to more than 500 copies per cell. The intron harbours two ribozymes that have...

  14. Enhancing the intense field control of molecular fragmentation.

    Science.gov (United States)

    Anis, Fatima; Esry, B D

    2012-09-28

    We describe a pump-probe scheme with which the spatial asymmetry of dissociating molecular fragments-as controlled by the carrier-envelope phase of an intense few-cycle laser pulse-can be enhanced by an order of magnitude or more. We illustrate the scheme using extensive, full-dimensional calculations for dissociation of H(2)(+) and include the averaging necessary for comparison with experiment.

  15. Mental practice enhances surgical technical skills: a randomized controlled study.

    Science.gov (United States)

    Arora, Sonal; Aggarwal, Rajesh; Sirimanna, Pramudith; Moran, Aidan; Grantcharov, Teodor; Kneebone, Roger; Sevdalis, Nick; Darzi, Ara

    2011-02-01

    To assess the effects of mental practice on surgical performance. Increasing concerns for patient safety have highlighted a need for alternative training strategies outside the operating room. Mental practice (MP), "the cognitive rehearsal of a task before performance," has been successful in sport and music to enhance skill. This study investigates whether MP enhances performance in laparoscopic surgery. After baseline skills testing, 20 novice surgeons underwent training on an evidence-based virtual reality curriculum. After randomization using the closed envelope technique, all participants performed 5 Virtual Reality (VR) laparoscopic cholecystectomies (LC). Mental practice participants performed 30 minutes of MP before each LC; control participants viewed an online lecture. Technical performance was assessed using video Objective Structured Assessment of Technical Skills-based global ratings scale (scored from 7 to 35). Mental imagery was assessed using a previously validated Mental Imagery Questionnaire. Eighteen participants completed the study. There were no intergroup differences in baseline technical ability. Learning curves were demonstrated for both MP and control groups. Mental practice was superior to control (global ratings) for the first LC (median 20 vs 15, P = 0.005), second LC (20.5 vs 13.5, P = 0.001), third LC (24 vs 15.5, P enhances the quality of performance based on VR laparoscopic cholecystectomy. This may be a time- and cost-effective strategy to augment traditional training in the OR thus potentially improving patient care.

  16. Optimization of nonlinear controller with an enhanced biogeography approach

    Directory of Open Access Journals (Sweden)

    Mohammed Salem

    2014-07-01

    Full Text Available This paper is dedicated to the optimization of nonlinear controllers basing of an enhanced Biogeography Based Optimization (BBO approach. Indeed, The BBO is combined to a predator and prey model where several predators are used with introduction of a modified migration operator to increase the diversification along the optimization process so as to avoid local optima and reach the optimal solution quickly. The proposed approach is used in tuning the gains of PID controller for nonlinear systems. Simulations are carried out over a Mass spring damper and an inverted pendulum and has given remarkable results when compared to genetic algorithm and BBO.

  17. Use of probabilistic weights to enhance linear regression myoelectric control.

    Science.gov (United States)

    Smith, Lauren H; Kuiken, Todd A; Hargrove, Levi J

    2015-12-01

    Clinically available prostheses for transradial amputees do not allow simultaneous myoelectric control of degrees of freedom (DOFs). Linear regression methods can provide simultaneous myoelectric control, but frequently also result in difficulty with isolating individual DOFs when desired. This study evaluated the potential of using probabilistic estimates of categories of gross prosthesis movement, which are commonly used in classification-based myoelectric control, to enhance linear regression myoelectric control. Gaussian models were fit to electromyogram (EMG) feature distributions for three movement classes at each DOF (no movement, or movement in either direction) and used to weight the output of linear regression models by the probability that the user intended the movement. Eight able-bodied and two transradial amputee subjects worked in a virtual Fitts' law task to evaluate differences in controllability between linear regression and probability-weighted regression for an intramuscular EMG-based three-DOF wrist and hand system. Real-time and offline analyses in able-bodied subjects demonstrated that probability weighting improved performance during single-DOF tasks (p linear regression control. Use of probability weights can improve the ability to isolate individual during linear regression myoelectric control, while maintaining the ability to simultaneously control multiple DOFs.

  18. Intron evolution in Neurospora: the role of mutational bias and selection.

    Science.gov (United States)

    Sun, Yu; Whittle, Carrie A; Corcoran, Pádraic; Johannesson, Hanna

    2015-01-01

    We used comparative and population genomics to study intron evolutionary dynamics in the fungal model genus Neurospora. For our investigation, we used well-annotated genomes of N. crassa, N. discreta, and N. tetrasperma, and 92 resequenced genomes of N. tetrasperma from natural populations. By analyzing the four well-annotated genomes, we identified 9495 intron sites in 7619 orthologous genes. Our data supports nonhomologous end joining (NHEJ) and tandem duplication as mechanisms for intron gains in the genus and the RT-mRNA process as a mechanism for intron loss. We found a moderate intron gain rate (5.78-6.89 × 10(-13) intron gains per nucleotide site per year) and a high intron loss rate (7.53-13.76 × 10(-10) intron losses per intron sites per year) as compared to other eukaryotes. The derived intron gains and losses are skewed to high frequencies, relative to neutral SNPs, in natural populations of N. tetrasperma, suggesting that selection is involved in maintaining a high intron turnover. Furthermore, our analyses of the association between intron population-level frequency and genomic features suggest that selection is involved in shaping a 5' intron position bias and a low intron GC content. However, intron sequence analyses suggest that the gained introns were not exposed to recent selective sweeps. Taken together, this work contributes to our understanding of the importance of mutational bias and selection in shaping the intron distribution in eukaryotic genomes. © 2015 Sun et al.; Published by Cold Spring Harbor Laboratory Press.

  19. Frequent gain and loss of introns in fungal cytochrome b genes.

    Directory of Open Access Journals (Sweden)

    Liang-Fen Yin

    Full Text Available In this study, all available cytochrome b (Cyt b genes from the GOBASE database were compiled and the evolutionary dynamics of the Cyt b gene introns was assessed. Cyt b gene introns were frequently present in the fungal kingdom and some lower plants, but generally absent or rare in Chromista, Protozoa, and Animalia. Fungal Cyt b introns were found at 35 positions in Cyt b genes and the number of introns varied at individual positions from a single representative to 32 different introns at position 131, showing a wide and patchy distribution. Many homologous introns were present at the same position in distantly related species but absent in closely related species, suggesting that introns of the Cyt b genes were frequently lost. On the other hand, highly similar intron sequences were observed in some distantly related species rather than in closely related species, suggesting that these introns were gained independently, likely through lateral transfers. The intron loss-and-gain events could be mediated by transpositions that might have occurred between nuclear and mitochondria. Southern hybridization analysis confirmed that some introns contained repetitive sequences and might be transposable elements. An intron gain in Botryotinia fuckeliana prevented the development of QoI fungicide resistance, suggesting that intron loss-and-gain events were not necessarily beneficial to their host organisms.

  20. Frequent Gain and Loss of Introns in Fungal Cytochrome b Genes

    Science.gov (United States)

    Yin, Liang-Fen; Hu, Meng-Jun; Wang, Fei; Kuang, Hanhui; Zhang, Yu; Schnabel, Guido; Li, Guo-Qing; Luo, Chao-Xi

    2012-01-01

    In this study, all available cytochrome b (Cyt b) genes from the GOBASE database were compiled and the evolutionary dynamics of the Cyt b gene introns was assessed. Cyt b gene introns were frequently present in the fungal kingdom and some lower plants, but generally absent or rare in Chromista, Protozoa, and Animalia. Fungal Cyt b introns were found at 35 positions in Cyt b genes and the number of introns varied at individual positions from a single representative to 32 different introns at position 131, showing a wide and patchy distribution. Many homologous introns were present at the same position in distantly related species but absent in closely related species, suggesting that introns of the Cyt b genes were frequently lost. On the other hand, highly similar intron sequences were observed in some distantly related species rather than in closely related species, suggesting that these introns were gained independently, likely through lateral transfers. The intron loss-and-gain events could be mediated by transpositions that might have occurred between nuclear and mitochondria. Southern hybridization analysis confirmed that some introns contained repetitive sequences and might be transposable elements. An intron gain in Botryotinia fuckeliana prevented the development of QoI fungicide resistance, suggesting that intron loss-and-gain events were not necessarily beneficial to their host organisms. PMID:23145081

  1. Cognitive control in auditory working memory is enhanced in musicians.

    Science.gov (United States)

    Pallesen, Karen Johanne; Brattico, Elvira; Bailey, Christopher J; Korvenoja, Antti; Koivisto, Juha; Gjedde, Albert; Carlson, Synnöve

    2010-06-15

    Musical competence may confer cognitive advantages that extend beyond processing of familiar musical sounds. Behavioural evidence indicates a general enhancement of both working memory and attention in musicians. It is possible that musicians, due to their training, are better able to maintain focus on task-relevant stimuli, a skill which is crucial to working memory. We measured the blood oxygenation-level dependent (BOLD) activation signal in musicians and non-musicians during working memory of musical sounds to determine the relation among performance, musical competence and generally enhanced cognition. All participants easily distinguished the stimuli. We tested the hypothesis that musicians nonetheless would perform better, and that differential brain activity would mainly be present in cortical areas involved in cognitive control such as the lateral prefrontal cortex. The musicians performed better as reflected in reaction times and error rates. Musicians also had larger BOLD responses than non-musicians in neuronal networks that sustain attention and cognitive control, including regions of the lateral prefrontal cortex, lateral parietal cortex, insula, and putamen in the right hemisphere, and bilaterally in the posterior dorsal prefrontal cortex and anterior cingulate gyrus. The relationship between the task performance and the magnitude of the BOLD response was more positive in musicians than in non-musicians, particularly during the most difficult working memory task. The results confirm previous findings that neural activity increases during enhanced working memory performance. The results also suggest that superior working memory task performance in musicians rely on an enhanced ability to exert sustained cognitive control. This cognitive benefit in musicians may be a consequence of focused musical training.

  2. Cognitive control in auditory working memory is enhanced in musicians.

    Directory of Open Access Journals (Sweden)

    Karen Johanne Pallesen

    Full Text Available Musical competence may confer cognitive advantages that extend beyond processing of familiar musical sounds. Behavioural evidence indicates a general enhancement of both working memory and attention in musicians. It is possible that musicians, due to their training, are better able to maintain focus on task-relevant stimuli, a skill which is crucial to working memory. We measured the blood oxygenation-level dependent (BOLD activation signal in musicians and non-musicians during working memory of musical sounds to determine the relation among performance, musical competence and generally enhanced cognition. All participants easily distinguished the stimuli. We tested the hypothesis that musicians nonetheless would perform better, and that differential brain activity would mainly be present in cortical areas involved in cognitive control such as the lateral prefrontal cortex. The musicians performed better as reflected in reaction times and error rates. Musicians also had larger BOLD responses than non-musicians in neuronal networks that sustain attention and cognitive control, including regions of the lateral prefrontal cortex, lateral parietal cortex, insula, and putamen in the right hemisphere, and bilaterally in the posterior dorsal prefrontal cortex and anterior cingulate gyrus. The relationship between the task performance and the magnitude of the BOLD response was more positive in musicians than in non-musicians, particularly during the most difficult working memory task. The results confirm previous findings that neural activity increases during enhanced working memory performance. The results also suggest that superior working memory task performance in musicians rely on an enhanced ability to exert sustained cognitive control. This cognitive benefit in musicians may be a consequence of focused musical training.

  3. Limited MHC class I intron 2 repertoire variation in bonobos.

    Science.gov (United States)

    de Groot, Natasja G; Heijmans, Corrine M C; Helsen, Philippe; Otting, Nel; Pereboom, Zjef; Stevens, Jeroen M G; Bontrop, Ronald E

    2017-10-01

    Common chimpanzees (Pan troglodytes) experienced a selective sweep, probably caused by a SIV-like virus, which targeted their MHC class I repertoire. Based on MHC class I intron 2 data analyses, this selective sweep took place about 2-3 million years ago. As a consequence, common chimpanzees have a skewed MHC class I repertoire that is enriched for allotypes that are able to recognise conserved regions of the SIV proteome. The bonobo (Pan paniscus) shared an ancestor with common chimpanzees approximately 1.5 to 2 million years ago. To investigate whether the signature of this selective sweep is also detectable in bonobos, the MHC class I gene repertoire of two bonobo panels comprising in total 29 animals was investigated by Sanger sequencing. We identified 14 Papa-A, 20 Papa-B and 11 Papa-C alleles, of which eight, five and eight alleles, respectively, have not been reported previously. Within this pool of MHC class I variation, we recovered only 2 Papa-A, 3 Papa-B and 6 Papa-C intron 2 sequences. As compared to humans, bonobos appear to have an even more diminished MHC class I intron 2 lineage repertoire than common chimpanzees. This supports the notion that the selective sweep may have predated the speciation of common chimpanzees and bonobos. The further reduction of the MHC class I intron 2 lineage repertoire observed in bonobos as compared to the common chimpanzee may be explained by a founding effect or other subsequent selective processes.

  4. Identification of novel intronic BRCA1 variants of uncertain ...

    Indian Academy of Sciences (India)

    2011-08-19

    Aug 19, 2011 ... [Ratanaphan A., Panomwan P., Canyuk B. and Maipang T. 2011 Identification of novel intronic BRCA1 variants of uncertain significance in a Thai hereditary ... DNA structures, possibly through a slipped strand mispairing mechanism during .... have been related to inherited human disease as in genetic.

  5. Identification of novel intronic BRCA1 variants of uncertain ...

    Indian Academy of Sciences (India)

    2011-08-19

    Aug 19, 2011 ... with an asterisk. proband was transmitted to the proband's unaffected daugh- ter. In order to confirm these genetic variations, the exon– intron 7 boundary sequences of the remaining breast cancer patients were amplified, screened by SSCP and subsequently sequenced. Five oligonucleotide primer pairs ...

  6. Naturally occuring nucleosome positioning signals in human exons and introns

    DEFF Research Database (Denmark)

    Baldi, Pierre; Brunak, Søren; Chauvin, Yves

    1996-01-01

    We describe the structural implications of a periodic pattern found in human exons and introns by hidden Markov models. We show that exons (besides the reading frame) have a specific sequential structure in the form of a pattern with triplet consensus non-T(A/T)G, and a minimal periodicity...

  7. Identification of novel intronic BRCA1 variants of uncertain ...

    Indian Academy of Sciences (India)

    in a Thai hereditary breast cancer family. Adisorn Ratanaphan, Pornpen Panomwan, Bhutorn Canyuk and Tanaphon Maipang. J. Genet. 90, 327–331. Table 1. Oligodeoxyribonucleotide primers used for PCR amplification of BRCA1 exon–intron 7 boundary sequences. Primers. Nucleotide position. Primer sequence (5 –3 ).

  8. HLA-DQA1 introns 2 and 3 sequencing: DQA1 sequencing-based typing and characterization of a highly polymorphic microsatellite at intron 3 of DQA1*0505.

    Science.gov (United States)

    Balas, Antonio; Aviles, Maria J; Alonso-Nieto, Manuela; Zarapuz, Loreto; Blanco, Lydia; García-Sánchez, Felix; Vicario, Jose L

    2005-08-01

    DQA1 class II gene encodes the alpha-chain of the human leukocyte antigen (HLA)-DQ heterodimer. Sequencing-based typing (SBT) for HLA genes is the most powerful methodology described. However, most of the SBT procedures reported for HLA class II genes are not able to define complete exon 2 region. For that purpose, we have characterized introns 2 and 3 from most DQA1 alleles to design amplification procedures that were able to obtain complete exon 2 and 3 sequences from DQA1 genes. This coding information allowed us to reduce the number of ambiguities for DQA1 typing. DQA1 intron 2 and 3 characterization demonstrated the presence of two polymorphisms for alleles with the same exons 2 and 3 sequence from DQA1*05 group. Different samples including the DQA1*050101 alleles showed a single nucleotide polymorphism at position 53 of intron 2 (G53T). Additional haplotypic analysis showed the possible association of T53 allele with the Ax-Cw5-B18-DR17-DQ2 extended haplotype. On the other hand, DQA1*0505 sequencing from different control samples noticed the existence of a microsatellite (TTTC/AAAG)n located at position 126 of intron 3. Fragment length analysis demonstrated a high polymorphism for this short tandem repeat system (0505STR), defining alleles that ranged from 8 to 20 repetitions in our population.

  9. Enhancement of mercury control in flue-gas cleanup systems

    Energy Technology Data Exchange (ETDEWEB)

    Livengood, C.D.; Huang, Hann S.; Mendelsohn, M.H.; Wu, Jiann M.

    1996-07-01

    This paper summarizes research at Argonne National Laboratory which is focused on techniques to enhance the capture of elemental mercury and integrate its control into existing flue-gas cleanup (FGC) systems. Both laboratory and field tests have shown that very little elemental mercury is captured in a wet scrubber system due to the low solubility of that species. To enhance the ability of wet scrubbers to capture mercury, Argonne has studied improved mass transfer through both mechanical and chemical means, as well as the conversion of elemental mercury into a more soluble species that can be easily absorbed. Current research is investigating the roles of several halogen species either alone or in combination with typical flue-gas components such as sulfur dioxide and nitric oxide in the oxidation of mercury to form compounds that are easily scrubbed from the flue gas.

  10. Enhanced Control for Local Helicity Injection on the Pegasus ST

    Science.gov (United States)

    Pierren, C.; Bongard, M. W.; Fonck, R. J.; Lewicki, B. T.; Perry, J. M.

    2017-10-01

    Local helicity injection (LHI) experiments on Pegasus rely upon programmable control of a 250 MVA modular power supply system that drives the electromagnets and helicity injection systems. Precise control of the central solenoid is critical to experimental campaigns that test the LHI Taylor relaxation limit and the coupling efficiency of LHI-produced plasmas to Ohmic current drive. Enhancement and expansion of the present control system is underway using field programmable gate array (FPGA) technology for digital logic and control, coupled to new 10 MHz optical-to-digital transceivers for semiconductor level device communication. The system accepts optical command signals from existing analog feedback controllers, transmits them to multiple devices in parallel H-bridges, and aggregates their status signals for fault detection. Present device-level multiplexing/de-multiplexing and protection logic is extended to include bridge-level protections with the FPGA. An input command filter protects against erroneous and/or spurious noise generated commands that could otherwise cause device failures. Fault registration and response times with the FPGA system are 25 ns. Initial system testing indicates an increased immunity to power supply induced noise, enabling plasma operations at higher working capacitor bank voltage. This can increase the applied helicity injection drive voltage, enable longer pulse lengths and improve Ohmic loop voltage control. Work supported by US DOE Grant DE-FG02-96ER54375.

  11. Semantically Enhanced Online Configuration of Feedback Control Schemes.

    Science.gov (United States)

    Milis, Georgios M; Panayiotou, Christos G; Polycarpou, Marios M

    2018-03-01

    Recent progress toward the realization of the "Internet of Things" has improved the ability of physical and soft/cyber entities to operate effectively within large-scale, heterogeneous systems. It is important that such capacity be accompanied by feedback control capabilities sufficient to ensure that the overall systems behave according to their specifications and meet their functional objectives. To achieve this, such systems require new architectures that facilitate the online deployment, composition, interoperability, and scalability of control system components. Most current control systems lack scalability and interoperability because their design is based on a fixed configuration of specific components, with knowledge of their individual characteristics only implicitly passed through the design. This paper addresses the need for flexibility when replacing components or installing new components, which might occur when an existing component is upgraded or when a new application requires a new component, without the need to readjust or redesign the overall system. A semantically enhanced feedback control architecture is introduced for a class of systems, aimed at accommodating new components into a closed-loop control framework by exploiting the semantic inference capabilities of an ontology-based knowledge model. This architecture supports continuous operation of the control system, a crucial property for large-scale systems for which interruptions have negative impact on key performance metrics that may include human comfort and welfare or economy costs. A case-study example from the smart buildings domain is used to illustrate the proposed architecture and semantic inference mechanisms.

  12. Multiple gains of spliceosomal introns in a superfamily of vertebrate protease inhibitor genes

    Directory of Open Access Journals (Sweden)

    Frese Marc-André

    2009-08-01

    Full Text Available Abstract Background Intron gains reportedly are very rare during evolution of vertebrates, and the mechanisms underlying their creation are largely unknown. Previous investigations have shown that, during metazoan radiation, the exon-intron patterns of serpin superfamily genes were subject to massive changes, in contrast to many other genes. Results Here we investigated intron dynamics in the serpin superfamily in lineages pre- and postdating the split of vertebrates. Multiple intron gains were detected in a group of ray-finned fishes, once the canonical groups of vertebrate serpins had been established. In two genes, co-occurrence of non-standard introns was observed, implying that intron gains in vertebrates may even happen concomitantly or in a rapidly consecutive manner. DNA breakage/repair processes associated with genome compaction are introduced as a novel factor potentially favoring intron gain, since all non-canonical introns were found in a lineage of ray-finned fishes that experienced genomic downsizing. Conclusion Multiple intron acquisitions were identified in serpin genes of a lineage of ray-finned fishes, but not in any other vertebrates, suggesting that insertion rates for introns may be episodically increased. The co-occurrence of non-standard introns within the same gene discloses the possibility that introns may be gained simultaneously. The sequences flanking the intron insertion points correspond to the proto-splice site consensus sequence MAG↑N, previously proposed to serve as intron insertion site. The association of intron gains in the serpin superfamily with a group of fishes that underwent genome compaction may indicate that DNA breakage/repair processes might foster intron birth.

  13. Mitochondrial group I and group II introns in the sponge orders Agelasida and Axinellida

    OpenAIRE

    Huchon, Doroth?e; Szitenberg, Amir; Shefer, Sigal; Ilan, Micha; Feldstein, Tamar

    2015-01-01

    Background Self-splicing introns are present in the mitochondria of members of most eukaryotic lineages. They are divided into Group I and Group II introns, according to their secondary structure and splicing mechanism. Being rare in animals, self-splicing introns were only described in a few sponges, cnidarians, placozoans and one annelid species. In sponges, three types of mitochondrial Group I introns were previously described in two demosponge families (Tetillidae, and Aplysinellidae) and...

  14. Enhanced Maritime Safety through Diagnosis and Fault Tolerant Control

    DEFF Research Database (Denmark)

    Blanke, Mogens

    2001-01-01

    Faults in steering, navigation instruments or propulsion machinery are serious on a marine vessel since the consequence could be loss of maneuvering ability, and imply risk of damage to vessel personnel or environment. Early diagnosis and accomodation of faults could enhance safety. Fault......-tolerant control is a methodology to help prevent that faults develop into failure. The means include on-line fault diagnosis, automatic condition assessment and calculation of remedial action to avoid hazards. This paper gives an overview of methods to obtain fault-tolerance: fault diagnosis; analysis...

  15. Molecular characterization of a new member of the lariat capping twin-ribozyme introns

    DEFF Research Database (Denmark)

    Tang, Yunjia; Nielsen, Henrik; Masquida, Benoît

    2014-01-01

    BACKGROUND: Twin-ribozyme introns represent a complex class of mobile group I introns that harbour a lariat capping (LC) ribozyme and a homing endonuclease gene embedded in a conventional self-splicing group I ribozyme (GIR2). Twin-ribozyme introns have so far been confined to nucleolar DNA in Na...

  16. Inheritance of the group I rDNA intron in Tetrahymena pigmentosa

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Simon, E M; Engberg, J

    1992-01-01

    We have previously argued from phylogenetic sequence data that the group I intron in the rRNA genes of Tetrahymena was acquired by different Tetrahymena species at different times during evolution. We have now approached the question of intron mobility experimentally by crossing intron+ and intro...

  17. Use of probabilistic weights to enhance linear regression myoelectric control

    Science.gov (United States)

    Smith, Lauren H.; Kuiken, Todd A.; Hargrove, Levi J.

    2015-12-01

    Objective. Clinically available prostheses for transradial amputees do not allow simultaneous myoelectric control of degrees of freedom (DOFs). Linear regression methods can provide simultaneous myoelectric control, but frequently also result in difficulty with isolating individual DOFs when desired. This study evaluated the potential of using probabilistic estimates of categories of gross prosthesis movement, which are commonly used in classification-based myoelectric control, to enhance linear regression myoelectric control. Approach. Gaussian models were fit to electromyogram (EMG) feature distributions for three movement classes at each DOF (no movement, or movement in either direction) and used to weight the output of linear regression models by the probability that the user intended the movement. Eight able-bodied and two transradial amputee subjects worked in a virtual Fitts’ law task to evaluate differences in controllability between linear regression and probability-weighted regression for an intramuscular EMG-based three-DOF wrist and hand system. Main results. Real-time and offline analyses in able-bodied subjects demonstrated that probability weighting improved performance during single-DOF tasks (p < 0.05) by preventing extraneous movement at additional DOFs. Similar results were seen in experiments with two transradial amputees. Though goodness-of-fit evaluations suggested that the EMG feature distributions showed some deviations from the Gaussian, equal-covariance assumptions used in this experiment, the assumptions were sufficiently met to provide improved performance compared to linear regression control. Significance. Use of probability weights can improve the ability to isolate individual during linear regression myoelectric control, while maintaining the ability to simultaneously control multiple DOFs.

  18. Electrical stimulation enhances sensory recovery: a randomized controlled trial.

    Science.gov (United States)

    Wong, Joshua N; Olson, Jaret L; Morhart, Michael J; Chan, K Ming

    2015-06-01

    Brief postsurgical electrical stimulation (ES) has been shown to enhance peripheral nerve regeneration in animal models following axotomy and crush injury. However, whether this treatment is beneficial in humans with sensory nerve injury has not been tested. The goal of this study was to test the hypothesis that ES would enhance sensory nerve regeneration following digital nerve transection compared to surgery alone. Patients with complete digital nerve transection underwent epineurial nerve repair. After coaptation of the severed nerve ends, fine wire electrodes were implanted before skin closure. Postoperatively, patients were randomized to receiving either 1 hour of 20Hz continuous ES or sham stimulation in a double-blinded manner. Patients were followed monthly for 6 months by a blinded evaluator to monitor physiological recovery of spatial discrimination, pressure threshold, and quantitative small fiber sensory testing. Functional disability was measured using the Disability of Arm, Shoulder, and Hand questionnaire. A total of 36 patients were recruited, with 18 in each group. Those in the ES group showed consistently greater improvements in all sensory modalities by 5 to 6 months postoperatively compared to the controls. Although there was a trend of greater functional improvements in the ES group, it was not statistically significant (p > 0.01). Postsurgical ES enhanced sensory reinnervation in patients who sustained complete digital nerve transection. The conferred benefits apply to a wide range of sensory functions. © 2015 American Neurological Association.

  19. Electrical, control and information systems in the Enhanced CANDU 6

    Energy Technology Data Exchange (ETDEWEB)

    De Grosbois, J.; Raiskums, G.; Soulard, M. [Atomic Energy of Canada Limited, Mississauga, Ontario (Canada)

    2011-07-01

    This paper describes the electrical, control, and information system (EC and I) design feature improvements of the Enhanced CANDU 6 (EC6). These additional features are carefully integrated into the EC6 design platform, and are engineered with consideration of operational feedback, human factors, and leveraging the advantages of digital instrumentation and control (I and C) technology to create a coherent I and C architecture in support of safe and high performance operation. The design drivers for the selection of advanced features are also discussed. The EC6 nuclear power plant is a mid-sized Pressurized Heavy Water Reactor design, based on the highly successful CANDU 6 family of power plants, and upgraded to meet today's Canadian and international safety requirements and to satisfy Generation 3 design expectations. (author)

  20. Control of climatics environments to enhance reliability of electronics systems

    International Nuclear Information System (INIS)

    Sekhon, K.S.

    1979-01-01

    The techniques to control temperature and humidity to reduce failures in semiconductor devices are presented. The maximum operating junction temperature affects the electronic system reliability, and the equation for the junction temperature of the device shows that internal and external thermal resistances affect component life. Junction temperature reductions up to 60 C were achieved by the development of heat pipes for microcircuits, which will enhance electronics life by 32 times. Humidity control by improved sealing and use of heaters to prevent moisture condensation proved difficult and costly, and high pressure dehydrators were heavy and expensive. Therefore, low pressure dehydrator was developed which is smaller, lighter, and less expensive. The development of low pressure dehumidifying system including test data is presented

  1. Robust RNAi-mediated resistance to infection of seven potyvirids in soybean expressing an intron hairpin NIb RNA.

    Science.gov (United States)

    Yang, Xiangdong; Niu, Lu; Zhang, Wei; He, Hongli; Yang, Jing; Xing, Guojie; Guo, Dongquan; Du, Qian; Qian, Xueyan; Yao, Yao; Li, Qiyun; Dong, Yingshan

    2017-10-01

    Viral pathogens, such as soybean mosaic virus (SMV), are a major constraint in soybean production and often cause significant yield loss and quality deterioration. Engineering resistance by RNAi-mediated gene silencing is a powerful strategy for controlling viral diseases. In this study, a 248-bp inverted repeat of the replicase (nuclear inclusion b, NIb) gene was isolated from the SMV SC3 strain, driven by the leaf-specific rbcS2 promoter from Phaseolus vulgaris, and introduced into soybean. The transgenic lines had significantly lower average disease indices (ranging from 2.14 to 12.35) than did the non-transformed (NT) control plants in three consecutive generations, exhibiting a stable and significantly enhanced resistance to the SMV SC3 strain under field conditions. Furthermore, seed mottling did not occur in transgenic seeds, whereas the NT plants produced ~90% mottled seeds. Virus resistance spectrum screening showed that the greenhouse-grown transgenic lines exhibited robust resistance to five SMV strains (SC3, SC7, SC15, SC18, and a recombinant SMV), bean common mosaic virus, and watermelon mosaic virus. Nevertheless, no significantly enhanced resistance to bean pod mottle virus (BPMV, Comovirus) was observed in the transgenic lines relative to their NT counterparts. Consistent with the results of resistance evaluation, the accumulation of each potyvirid (but not of BPMV) was significantly inhibited in the transgenic plants relative to the NT controls as confirmed by quantitative real-time (qRT-PCR) and double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA). These results demonstrate that robust RNAi-mediated resistance to multiple potyvirids in soybean was conferred by expressing an intron hairpin SMV NIb RNA.

  2. Sleep enhances inhibitory behavioral control in discrimination learning in rats.

    Science.gov (United States)

    Borquez, Margarita; Born, Jan; Navarro, Victor; Betancourt, Ronald; Inostroza, Marion

    2014-05-01

    Sleep supports the consolidation of memory, and it has been proposed that this enhancing effect of sleep pertains in particular to memories which are encoded under control of prefrontal-hippocampal circuitry into an episodic memory system. Furthermore, repeated reactivation and transformation of such memories during sleep are thought to promote the de-contextualization of these memories. Here, we aimed to establish a behavioral model for the study of such sleep-dependent system consolidation in rats, using a go/nogo conditional discrimination learning task known to essentially depend on prefrontal-hippocampal function. Different groups of rats were trained to criterion on this task and, then, subjected to 80-min retention intervals filled with spontaneous morning sleep, sleep deprivation, or spontaneous evening wakefulness. In a subsequent test phase, the speed of relearning of the discrimination task was examined as indicator of memory, whereby rats were either tested in the same context as during training or in a different context. Sleep promoted relearning of the conditional discrimination task, and this effect was similar for testing memory in the same or different context (p sleep and wakefulness during the retention interval, animals showed faster relearning when tested in the same context as during learning, compared with testing in a different context (p sleep on discrimination learning was primarily due to an enhancing effect on response suppression during the nogo stimulus. We infer from these results that sleep enhances memory for inhibitory behavioral control in a generalized context-independent manner and thereby might eventually also contribute to the abstraction of schema-like representations.

  3. Control of Phosphorus Transient Enhanced Diffusion using Co-implantation

    Science.gov (United States)

    Vanderpool, Aaron; Budrevich, Andre; Taylor, Mitch

    2006-11-01

    The production of Ultra Shallow Junctions (USJ) in silicon devices requires controlling the Transient Enhanced Diffusion (TED) of electrical dopants. USJ development has focused on boron because hole mobility is lower than electron mobility in silicon and because arsenic has such excellent diffusion properties. However, the advent of strain enhanced mobility in P-type silicon has created the need to study higher solubility N-type dopants like phosphorus and find methods to control their diffusion. Co-implants have proven effective in controlling the interstitial diffusion mechanisms of boron TED. In this work the effectiveness of some co-implants on phosphorus to form high performance USJ is reported. It has been found that carbon and fluorine co-implants reduce phosphorus diffusion. As work with boron has shown, this is due to the carbon Kick-out mechanism and Fluorine-Vacancy clusters, both of which consume the interstitials driving TED. It has also been found that record levels of phosphorus diffusion control can be obtained if boron and carbon are co-implanted. In this junction diffusion control increases as the boron implant energy decreases; even as low as 0.5 KeV. However, this may be activating Uphill diffusion. The data also shows that the carbon implant energy has very little effect on phosphorus diffusion. The boron and carbon co-implants also produce the steepest phosphorus USJ yet reported at 2.5nm/decade with a solubility >1.0E21 atoms/cm3. Counter intuitively it has been found that the boron and carbon USJ is shallower with a higher solubility if the phosphorus implant energy is increased from 2 to 3 KeV. These boron and carbon co-implant findings are quite novel even if they are not technologically useful. They strongly support the widely held model that phosphorus TED occurs via an interstitial diffusion mechanism and that techniques to block this mechanism can control it. The boron implanted below the phosphorus is probably consuming interstitials

  4. Cyanobacterial ribosomal RNA genes with multiple, endonuclease-encoding group I introns

    Directory of Open Access Journals (Sweden)

    Turner Seán

    2007-09-01

    Full Text Available Abstract Background Group I introns are one of the four major classes of introns as defined by their distinct splicing mechanisms. Because they catalyze their own removal from precursor transcripts, group I introns are referred to as autocatalytic introns. Group I introns are common in fungal and protist nuclear ribosomal RNA genes and in organellar genomes. In contrast, they are rare in all other organisms and genomes, including bacteria. Results Here we report five group I introns, each containing a LAGLIDADG homing endonuclease gene (HEG, in large subunit (LSU rRNA genes of cyanobacteria. Three of the introns are located in the LSU gene of Synechococcus sp. C9, and the other two are in the LSU gene of Synechococcus lividus strain C1. Phylogenetic analyses show that these introns and their HEGs are closely related to introns and HEGs located at homologous insertion sites in organellar and bacterial rDNA genes. We also present a compilation of group I introns with homing endonuclease genes in bacteria. Conclusion We have discovered multiple HEG-containing group I introns in a single bacterial gene. To our knowledge, these are the first cases of multiple group I introns in the same bacterial gene (multiple group I introns have been reported in at least one phage gene and one prophage gene. The HEGs each contain one copy of the LAGLIDADG motif and presumably function as homodimers. Phylogenetic analysis, in conjunction with their patchy taxonomic distribution, suggests that these intron-HEG elements have been transferred horizontally among organelles and bacteria. However, the mode of transfer and the nature of the biological connections among the intron-containing organisms are unknown.

  5. The Tgif2 gene contains a retained intron within the coding sequence

    Directory of Open Access Journals (Sweden)

    Wotton David

    2006-01-01

    Full Text Available Abstract Background TGIF and TGIF2 are homeodomain proteins, which act as TGFβ specific Smad transcriptional corepressors. TGIF recruits general repressors including mSin3 and CtBP. The related TGIF2 protein functions in a similar manner, but does not bind CtBP. In addition to repressing TGFβ activated gene expression, TGIF and TGIF2 repress gene expression by binding directly to DNA. TGIF and TGIF2 share two major blocks of similarity, encompassing the homeodomain, and a conserved carboxyl terminal repression domain. Here we characterize two splice variants of the Tgif2 gene from mouse and demonstrate that the Tgif2 gene contains a retained intron. Results By PCR from mouse cDNA, we identified two alternate splice forms of the Tgif2 gene. One splice variant encodes the full length 237 amino acid Tgif2, whereas the shorter form results in the removal of 39 codons from the centre of the coding region. The generation of this alternate splice form occurs with the mouse RNA, but not the human, and both splice forms are present in all mouse tissues analyzed. Human and mouse Tgif2 coding sequences contain a retained intron, which in mouse Tgif2 is removed by splicing from around 25–50% of RNAs, as assessed by RT-PCR. This splicing event is dependent on sequences within the mouse Tgif2 coding sequence. Both splice forms of mouse Tgif2 encode proteins which are active transcriptional repressors, and can repress both TGFβ dependent and independent transcription. In addition, we show that human and mouse Tgif2 interact with the transcriptional corepressor mSin3. Conclusion These data demonstrate that the Tgif2 gene contains a retained intron, within the second coding exon. This retained intron is not removed from the human mRNA at a detectable level, but is spliced out in a significant proportion of mouse RNAs. This alternate splicing is dependent entirely on sequences within the mouse Tgif2 coding sequence, suggesting the presence of an exonic

  6. Maximizing Drilling Performance through Enhanced Solid Control System

    Science.gov (United States)

    Irawan, S.; Kinif, B. I.; Bayuaji, R.

    2017-11-01

    High solid content in drilling mud may affect its properties and result in uncertainties at downhole condition. It eventually contributes to poor rig operation performance and operating cost. This research focus on developing solid control system that is suit for drilling 12.25-inch hole. The first part discussed the performance of Rate of Penetration (ROP), Equivalent Circulating Density (ECD) and drill string drag while the second part of the research discussed about the effect of solid control system performance to mud properties Plastic Viscosity (PV), Yield Point (YP) and Low-Gravity Solid (LGS). The input parameters were gathered from two different set up of solid control systems that were used in Well A and Well B. The result is mainly based on the performance of original solid control system new design versus old design. Installation of distributor tank and channel the mud to respective shale shakers significantly enhanced the system and operational performance. The ROP at 12.25-inch drilling were improved by 20%. New design improved average the ECD margin by reducing additional pressure exerted using original mud from 4.9% to 2.9%. High ECD margin is not recommended because it can break the weak formation. Mud properties while drilling the 12.25-inch hole section; PV, YP and LGS values were improved by 14 %, 17 % and 25 % respectively. Proper mud flow control and routing system at new develop design of solid control system effectively removed the solid in the drilling fluid. This improvement minimizes the tendency of frequent mud flow, screen mesh plugging and tool wear issue. Mud properties such PV, YP and LGS were maintained with an acceptable mud design envelope.

  7. Enhanced Voltage Control of VSC-HVDC Connected Offshore Wind Farms Based on Model Predictive Control

    OpenAIRE

    Guo, Yifei; Gao, Houlei; Wu, Qiuwei; Zhao, Haoran; Østergaard, Jacob; Shahidehpour, Mohammad

    2018-01-01

    This paper proposes an enhanced voltage control strategy (EVCS) based on model predictive control (MPC) for voltage source converter based high voltage direct current (VSCHVDC) connected offshore wind farms (OWFs). In the proposed MPC based EVCS, all wind turbine generators (WTGs) as well as the wind farm side VSC are optimally coordinated to keep voltages within the feasible range and reduce system power losses. Considering the high ratio of the OWF collector system, the effects of active po...

  8. Both size and GC-content of minimal introns are selected in human populations.

    Directory of Open Access Journals (Sweden)

    Dapeng Wang

    Full Text Available BACKGROUND: We previously have studied the insertion and deletion polymorphism by sequencing no more than one hundred introns in a mixed human population and found that the minimal introns tended to maintain length at an optimal size. Here we analyzed re-sequenced 179 individual genomes (from African, European, and Asian populations from the data released by the 1000 Genome Project to study the size dynamics of minimal introns. PRINCIPAL FINDINGS: We not only confirmed that minimal introns in human populations are selected but also found two major effects in minimal intron evolution: (i Size-effect: minimal introns longer than an optimal size (87 nt tend to have a higher ratio of deletion to insertion than those that are shorter than the optimal size; (ii GC-effect: minimal introns with lower GC content tend to be more frequently deleted than those with higher GC content. The GC-effect results in a higher GC content in minimal introns than their flanking exons as opposed to larger introns (≥125 nt that always have a lower GC content than that of their flanking exons. We also observed that the two effects are distinguishable but not completely separable within and between populations. CONCLUSIONS: We validated the unique mutation dynamics of minimal introns in keeping their near-optimal size and GC content, and our observations suggest potentially important functions of human minimal introns in transcript processing and gene regulation.

  9. Universal PCR primers for ribosomal protein gene introns of fish

    Directory of Open Access Journals (Sweden)

    Seinen Chow

    2016-01-01

    Full Text Available Abstract Human ribosomal protein (RP gene sequences with respect to intron/exon structures and corresponding cDNA or genomic data of fish species were obtained from the GenBank database. Based on conserved exon sequences, 128 primer pairs for 41 genes were designed for exon-primed intron-crossing (EPIC polymerase chain reaction (PCR. In reference to the draft genome sequences of the Pacific bluefin tuna (Thunnus orientalis, 12 primer pairs expected to amplify introns of the bluefin tuna with lengths of 500–1000 bp were selected and applied to six distantly related fish species belonging to the Orders Clupeiformes, Tetraodontiformes, Pleuronectiformes, Perciformes, Scorpaeniformes, and Anguilliformes. PCR amplification was observed for at least four species in each primer pair, and all fragments were larger than those expected for intronless amplification. Single fragment amplification was observed for at least seven primer pairs per species. Fragment sizes of the bluefin tuna for nine primer pairs corresponded to those expected from the genomic data. Thus, our primer pairs are potentially applicable to a wide variety of fish species and serve as an initial step for isolating single-copy nuclear DNA sequences.

  10. Online naphazoline quality control by micellar-enhanced spectrofluorimetry.

    Science.gov (United States)

    Peralta, Cecilia Mariana; Silva, Raúl Alejandro; Fernández, Liliana Patricia; Masi, Adriana Noemí

    2011-01-01

    The aim of this study was to develop a method for online spectrofluorimetric quality control of naphazoline (NPZ) in pharmaceuticals and raw drugs. A combination of a flow-injection analysis (FIA) system with micellar-enhanced fluorescence detection is presented as a powerful alternative for the rapid and sensitive analysis of naphazoline. Since NPZ shows low native fluorescence, the use of an anionic surfactant, such as sodium dodecyl sulphate (SDS), provides a considerable enhancement of fluorescence intensity and the nature of the technique allows a possible and easy adaptation to a FIA system. Using λ(exc) = 280 nm and λ(em) = 326 nm, a good linear relationship (LOL) was obtained in the range 0.003-10 µg mL(-1) with a detection limit (LOD) of 3 × 10(-4) µg mL(-1) (s/n = 3). Parameters related to the nature of the analytical signal and to the FIA manifold were optimized. Satisfactory recoveries were obtained in the analysis of commercial pharmaceutical formulations. The proposed method is simple, accurate and allows for high-speed sampling and considerably shorter analysis times. In addition, it requires inexpensive equipment and reagents and has easy operational conditions and no side effects, thus avoiding environmental pollution through toxic waste. Copyright © 2011 John Wiley & Sons, Ltd.

  11. ASSESSMENT OF A WIND TURBINE INTELLIGENT CONTROLLER FOR ENHANCED ENERGY PRODUCTION AND POLLUTION REDUCTION

    Science.gov (United States)

    This study assessed the enhanced energy production which is possible when variable-speed wind turbines are electronically controlled by an intelligent controller for efficiency optimization and performance improvement. The control system consists of three fuzzy- logic controllers...

  12. Diversity of sponge mitochondrial introns revealed by cox 1 sequences of Tetillidae

    Directory of Open Access Journals (Sweden)

    Rot Chagai

    2010-09-01

    Full Text Available Abstract Background Animal mitochondrial introns are rare. In sponges and cnidarians they have been found in the cox 1 gene of some spirophorid and homosclerophorid sponges, as well as in the cox 1 and nad 5 genes of some Hexacorallia. Their sporadic distribution has raised a debate as to whether these mobile elements have been vertically or horizontally transmitted among their hosts. The first sponge found to possess a mitochondrial intron was a spirophorid sponge from the Tetillidae family. To better understand the mode of transmission of mitochondrial introns in sponges, we studied cox 1 intron distribution among representatives of this family. Results Seventeen tetillid cox 1 sequences were examined. Among these sequences only six were found to possess group I introns. Remarkably, three different forms of introns were found, named introns 714, 723 and 870 based on their different positions in the cox 1 alignment. These introns had distinct secondary structures and encoded LAGLIDADG ORFs belonging to three different lineages. Interestingly, sponges harboring the same intron form did not always form monophyletic groups, suggesting that their introns might have been transferred horizontally. To evaluate whether the introns were vertically or horizontally transmitted in sponges and cnidarians we used a host parasite approach. We tested for co-speciation between introns 723 (the introns with the highest number of sponge representatives and their nesting cox 1 sequences. Reciprocal AU tests indicated that the intron and cox 1 tree are significantly different, while a likelihood ratio test was not significant. A global test of co-phylogeny had significant results; however, when cnidarian sequences were analyzed separately the results were not significant. Conclusions The co-speciation analyses thus suggest that a vertical transmission of introns in the ancestor of sponges and cnidarians, followed by numerous independent losses, cannot solely

  13. A Bifunctional Intronic Element Regulates the Expression of the Arginine/Lysine Transporter Cat-1 via Mechanisms Involving the Purine-rich Element Binding Protein A (Purα)*

    Science.gov (United States)

    Huang, Charlie C.; Chiribau, Calin-Bogdan; Majumder, Mithu; Chiang, Cheng-Ming; Wek, Ronald C.; Kelm, Robert J.; Khalili, Kamel; Snider, Martin D.; Hatzoglou, Maria

    2009-01-01

    Expression of the arginine/lysine transporter Cat-1 is highly induced in proliferating and stressed cells via mechanisms that include transcriptional activation. A bifunctional INE (intronic element) within the first intron of the Cat-1 gene was identified and characterized in this study. The INE had high sequence homology to an amino acid response element and was shown to act as a transcriptional enhancer in unstressed cells by binding the transcription factor, purine-rich element binding protein A (Purα). During endoplasmic reticulum stress, binding of Purα to the INE decreased; the element acted as a positive regulator in early stress by binding of the transcription factor ATF4 and as a negative regulator in prolonged stress by binding the stress-induced C/EBP family member, CHOP. We conclude that transcriptional control of the Cat-1 gene is tightly controlled by multiple cis-DNA elements, contributing to regulation of cationic amino acid transport for cell growth and proliferation. In addition, we propose that genes may use stress-response elements such as the INE to support basal expression in the absence of stress. PMID:19720825

  14. Single nucleotide polymorphisms in intron 1 and intron 2 of Larimichthys crocea growth hormone gene are correlated with growth traits

    Science.gov (United States)

    Ni, Jing; You, Feng; Xu, Jianhe; Xu, Dongdong; Wen, Aiyun; Wu, Zhihao; Xu, Yongli; Zhang, Peijun

    2012-03-01

    The growth hormone gene ( GH) affects animal growth and is a potential target for genetic studies of variation related to growth traits. In this study, we analyzed single nucleotide polymorphisms (SNPs) in GH intron regions and their associations with growth traits in large yellow croaker, Larimichthys crocea, from Zhejiang and Fujian stocks. The results of PCR-single strand conformation polymorphism showed two haplotypes of intron 1, named AA and AB genotypes, in Zhejiang stock. AB exhibited an SNP at position 196 (G→A) that was negatively correlated with body height and positively correlated with standard length/body height ( P≤0.05). Two different genotypes, CC and CD, were identified in intron 2 in Fujian stock, with CD showing an SNP at position 692 (T→C). The CD genotype had a significantly positive correlation with both weight and total length ( P≤0.01). These basic data highlight the potential for using GH as a genetic marker of fish growth in marker assisted selection.

  15. Carbon Nanotube Materials for Substrate Enhanced Control of Catalytic Activity

    Energy Technology Data Exchange (ETDEWEB)

    Heben, M.; Dillon, A. C.; Engtrakul, C.; Lee, S.-H.; Kelley, R. D.; Kini, A. M.

    2007-05-01

    Carbon SWNTs are attractive materials for supporting electrocatalysts. The properties of SWNTs are highly tunable and controlled by the nanotube's circumferential periodicity and their surface chemistry. These unique characteristics suggest that architectures constructed from these types of carbon support materials would exhibit interesting and useful properties. Here, we expect that the structure of the carbon nanotube support will play a major role in stabilizing metal electrocatalysts under extreme operating conditions and suppress both catalyst and support degradation. Furthermore, the chemical modification of the carbon nanotube surfaces can be expected to alter the interface between the catalyst and support, thus, enhancing the activity and utilization of the electrocatalysts. We plan to incorporate discrete reaction sites into the carbon nanotube lattice to create intimate electrical contacts with the catalyst particles to increase the metal catalyst activity and utilization. The work involves materials synthesis, design of electrode architectures on the nanoscale, control of the electronic, ionic, and mass fluxes, and use of advanced optical spectroscopy techniques.

  16. Enhanced Voltage Control of VSC-HVDC Connected Offshore Wind Farms Based on Model Predictive Control

    DEFF Research Database (Denmark)

    Guo, Yifei; Gao, Houlei; Wu, Qiuwei

    2018-01-01

    This paper proposes an enhanced voltage control strategy (EVCS) based on model predictive control (MPC) for voltage source converter based high voltage direct current (VSCHVDC) connected offshore wind farms (OWFs). In the proposed MPC based EVCS, all wind turbine generators (WTGs) as well...... as the wind farm side VSC are optimally coordinated to keep voltages within the feasible range and reduce system power losses. Considering the high ratio of the OWF collector system, the effects of active power outputs of WTGs on voltage control are also taken into consideration. The predictive model of VSC...... with a typical cascaded control structure is derived in details. The sensitivity coefficients are calculated by an analytical method to improve the computational efficiency. A VSC-HVDC connected OWF with 64 WTGs was used to validate the proposed voltage control strategy....

  17. Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

    Directory of Open Access Journals (Sweden)

    Maayan Amit

    2012-05-01

    Full Text Available During evolution segments of homeothermic genomes underwent a GC content increase. Our analyses reveal that two exon-intron architectures have evolved from an ancestral state of low GC content exons flanked by short introns with a lower GC content. One group underwent a GC content elevation that abolished the differential exon-intron GC content, with introns remaining short. The other group retained the overall low GC content as well as the differential exon-intron GC content, and is associated with longer introns. We show that differential exon-intron GC content regulates exon inclusion level in this group, in which disease-associated mutations often lead to exon skipping. This group's exons also display higher nucleosome occupancy compared to flanking introns and exons of the other group, thus “marking” them for spliceosomal recognition. Collectively, our results reveal that differential exon-intron GC content is a previously unidentified determinant of exon selection and argue that the two GC content architectures reflect the two mechanisms by which splicing signals are recognized: exon definition and intron definition.

  18. Discovery of group I introns in the nuclear small subunit ribosomal RNA genes of Acanthamoeba.

    Science.gov (United States)

    Gast, R J; Fuerst, P A; Byers, T J

    1994-01-01

    The discovery of group I introns in small subunit nuclear rDNA (nsrDNA) is becoming more common as the effort to generate phylogenies based upon nsrDNA sequences grows. In this paper we describe the discovery of the first two group I introns in the nsrDNA from the genus Acanthamoeba. The introns are in different locations in the genes, and have no significant primary sequence similarity to each other. They are identified as group I introns by the conserved P, Q, R and S sequences (1), and the ability to fit the sequences to a consensus secondary structure model for the group I introns (1, 2). Both introns are absent from the mature srRNA. A BLAST search (3) of nucleic acid sequences present in GenBank and EMBL revealed that the A. griffini intron was most similar to the nsrDNA group I intron of the green alga Dunaliella parva. A similar search found that the A. lenticulata intron was not similar to any of the other reported group I introns. Images PMID:8127708

  19. Structural and functional characterization of ribosomal protein gene introns in sponges.

    Science.gov (United States)

    Perina, Drago; Korolija, Marina; Mikoč, Andreja; Roller, Maša; Pleše, Bruna; Imešek, Mirna; Morrow, Christine; Batel, Renato; Ćetković, Helena

    2012-01-01

    Ribosomal protein genes (RPGs) are a powerful tool for studying intron evolution. They exist in all three domains of life and are much conserved. Accumulating genomic data suggest that RPG introns in many organisms abound with non-protein-coding-RNAs (ncRNAs). These ancient ncRNAs are small nucleolar RNAs (snoRNAs) essential for ribosome assembly. They are also mobile genetic elements and therefore probably important in diversification and enrichment of transcriptomes through various mechanisms such as intron/exon gain/loss. snoRNAs in basal metazoans are poorly characterized. We examined 449 RPG introns, in total, from four demosponges: Amphimedon queenslandica, Suberites domuncula, Suberites ficus and Suberites pagurorum and showed that RPG introns from A. queenslandica share position conservancy and some structural similarity with "higher" metazoans. Moreover, our study indicates that mobile element insertions play an important role in the evolution of their size. In four sponges 51 snoRNAs were identified. The analysis showed discrepancies between the snoRNA pools of orthologous RPG introns between S. domuncula and A. queenslandica. Furthermore, these two sponges show as much conservancy of RPG intron positions between each other as between themselves and human. Sponges from the Suberites genus show consistency in RPG intron position conservation. However, significant differences in some of the orthologous RPG introns of closely related sponges were observed. This indicates that RPG introns are dynamic even on these shorter evolutionary time scales.

  20. Isolation and characterization of functional tripartite group II introns using a Tn5-based genetic screen.

    Directory of Open Access Journals (Sweden)

    Christine Ritlop

    Full Text Available BACKGROUND: Group II introns are RNA enzymes that splice themselves from pre-mRNA transcripts. Most bacterial group II introns harbour an open reading frame (ORF, coding for a protein with reverse transcriptase, maturase and occasionally DNA binding and endonuclease activities. Some ORF-containing group II introns were shown to be mobile retroelements that invade new DNA target sites. From an evolutionary perspective, group II introns are hypothesized to be the ancestors of the spliceosome-dependent nuclear introns and the small nuclear RNAs (snRNAs--U1, U2, U4, U5 and U6 that are important functional elements of the spliceosome machinery. The ability of some group II introns fragmented in two or three pieces to assemble and undergo splicing in trans supports the theory that spliceosomal snRNAs evolved from portions of group II introns. METHODOLOGY/PRINCIPAL FINDINGS: We used a transposon-based genetic screen to explore the ability of the Ll.LtrB group II intron from the Gram-positive bacterium Lactococcus lactis to be fragmented into three pieces in vivo. Trans-splicing tripartite variants of Ll.LtrB were selected using a highly efficient and sensitive trans-splicing/conjugation screen. We report that numerous fragmentation sites located throughout Ll.LtrB support tripartite trans-splicing, showing that this intron is remarkably tolerant to fragmentation. CONCLUSIONS/SIGNIFICANCE: This work unveils the great versatility of group II intron fragments to assemble and accurately trans-splice their flanking exons in vivo. The selected introns represent the first evidence of functional tripartite group II introns in bacteria and provide experimental support for the proposed evolutionary relationship between group II introns and snRNAs.

  1. Evidence for the late origin of introns in chloroplast genes from an evolutionary analysis of the genus Euglena.

    Science.gov (United States)

    Thompson, M D; Copertino, D W; Thompson, E; Favreau, M R; Hallick, R B

    1995-01-01

    The origin of present day introns is a subject of spirited debate. Any intron evolution theory must account for not only nuclear spliceosomal introns but also their antecedents. The evolution of group II introns is fundamental to this debate, since group II introns are the proposed progenitors of nuclear spliceosomal introns and are found in ancient genes from modern organisms. We have studied the evolution of chloroplast introns and twintrons (introns within introns) in the genus Euglena. Our hypothesis is that Euglena chloroplast introns arose late in the evolution of this lineage and that twintrons were formed by the insertion of one or more introns into existing introns. In the present study we find that 22 out of 26 introns surveyed in six different photosynthesis-related genes from the plastid DNA of Euglena gracilis are not present in one or more basally branching Euglena spp. These results are supportive of a late origin for Euglena chloroplast group II introns. The psbT gene in Euglena viridis, a basally branching Euglena species, contains a single intron in the identical position to a psbT twintron from E.gracilis, a derived species. The E.viridis intron, when compared with 99 other Euglena group II introns, is most similar to the external intron of the E.gracilis psbT twintron. Based on these data, the addition of introns to the ancestral psbT intron in the common ancester of E.viridis and E.gracilis gave rise to the psbT twintron in E.gracilis. Images PMID:8532514

  2. An intronic ABCA3 mutation that is responsible for respiratory disease.

    Science.gov (United States)

    Agrawal, Amit; Hamvas, Aaron; Cole, F Sessions; Wambach, Jennifer A; Wegner, Daniel; Coghill, Carl; Harrison, Keith; Nogee, Lawrence M

    2012-06-01

    Member A3 of the ATP-binding cassette family of transporters (ABCA3) is essential for surfactant metabolism. Nonsense, missense, frameshift, and splice-site mutations in the ABCA3 gene (ABCA3) have been reported as causes of neonatal respiratory failure (NRF) and interstitial lung disease. We tested the hypothesis that mutations in noncoding regions of ABCA3 may cause lung disease. ABCA3-specific cDNA was generated and sequenced from frozen lung tissue from a child with fatal lung disease with only one identified ABCA3 mutation. ABCA3 was sequenced from genomic DNA prepared from blood samples obtained from the proband, parents, and other children with NRF. ABCA3 cDNA from the proband contained sequences derived from intron 25 that would be predicted to alter the structure and function of the ABCA3 protein. Genomic DNA sequencing revealed a heterozygous C>T transition in intron 25 trans to the known mutation, creating a new donor splice site. Seven additional infants with an ABCA3-deficient phenotype and inconclusive genetic findings had this same variant, which was not found in 2,132 control chromosomes. These findings support that this variant is a disease-causing mutation that may account for additional cases of ABCA3 deficiency with negative genetic studies.

  3. Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: Introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes

    OpenAIRE

    Landthaler, Markus; Shub, David A.

    1999-01-01

    Analysis of RNA that can be labeled with GTP indicates the existence of group I introns in genes of at least three transcriptional classes in the genome of Staphylococcus aureus bacteriophage Twort. A single ORF of 142 amino acids (Orf142) is interrupted by three self-splicing group I introns, providing the first example of a phage gene with multiple intron insertions. Twort Orf142 is encoded in a message that is abundant 15–20 min after infection and is highly similar to a late gene product ...

  4. Enhanced methodology of focus control and monitoring on scanner tool

    Science.gov (United States)

    Chen, Yen-Jen; Kim, Young Ki; Hao, Xueli; Gomez, Juan-Manuel; Tian, Ye; Kamalizadeh, Ferhad; Hanson, Justin K.

    2017-03-01

    As the demand of the technology node shrinks from 14nm to 7nm, the reliability of tool monitoring techniques in advanced semiconductor fabs to achieve high yield and quality becomes more critical. Tool health monitoring methods involve periodic sampling of moderately processed test wafers to detect for particles, defects, and tool stability in order to ensure proper tool health. For lithography TWINSCAN scanner tools, the requirements for overlay stability and focus control are very strict. Current scanner tool health monitoring methods include running BaseLiner to ensure proper tool stability on a periodic basis. The focus measurement on YIELDSTAR by real-time or library-based reconstruction of critical dimensions (CD) and side wall angle (SWA) has been demonstrated as an accurate metrology input to the control loop. The high accuracy and repeatability of the YIELDSTAR focus measurement provides a common reference of scanner setup and user process. In order to further improve the metrology and matching performance, Diffraction Based Focus (DBF) metrology enabling accurate, fast, and non-destructive focus acquisition, has been successfully utilized for focus monitoring/control of TWINSCAN NXT immersion scanners. The optimal DBF target was determined to have minimized dose crosstalk, dynamic precision, set-get residual, and lens aberration sensitivity. By exploiting this new measurement target design, 80% improvement in tool-to-tool matching, >16% improvement in run-to-run mean focus stability, and >32% improvement in focus uniformity have been demonstrated compared to the previous BaseLiner methodology. Matching <2.4 nm across multiple NXT immersion scanners has been achieved with the new methodology of set baseline reference. This baseline technique, with either conventional BaseLiner low numerical aperture (NA=1.20) mode or advanced illumination high NA mode (NA=1.35), has also been evaluated to have consistent performance. This enhanced methodology of focus

  5. Cloud-Enhanced Robotic System for Smart City Crowd Control

    Directory of Open Access Journals (Sweden)

    Akhlaqur Rahman

    2016-12-01

    Full Text Available Cloud robotics in smart cities is an emerging paradigm that enables autonomous robotic agents to communicate and collaborate with a cloud computing infrastructure. It complements the Internet of Things (IoT by creating an expanded network where robots offload data-intensive computation to the ubiquitous cloud to ensure quality of service (QoS. However, offloading for robots is significantly complex due to their unique characteristics of mobility, skill-learning, data collection, and decision-making capabilities. In this paper, a generic cloud robotics framework is proposed to realize smart city vision while taking into consideration its various complexities. Specifically, we present an integrated framework for a crowd control system where cloud-enhanced robots are deployed to perform necessary tasks. The task offloading is formulated as a constrained optimization problem capable of handling any task flow that can be characterized by a Direct Acyclic Graph (DAG. We consider two scenarios of minimizing energy and time, respectively, and develop a genetic algorithm (GA-based approach to identify the optimal task offloading decisions. The performance comparison with two benchmarks shows that our GA scheme achieves desired energy and time performance. We also show the adaptability of our algorithm by varying the values for bandwidth and movement. The results suggest their impact on offloading. Finally, we present a multi-task flow optimal path sequence problem that highlights how the robot can plan its task completion via movements that expend the minimum energy. This integrates path planning with offloading for robotics. To the best of our knowledge, this is the first attempt to evaluate cloud-based task offloading for a smart city crowd control system.

  6. Electrical control and enhancement of boiling heat transfer during quenching

    Science.gov (United States)

    Shahriari, Arjang; Hermes, Mark; Bahadur, Vaibhav

    2016-02-01

    Heat transfer associated with boiling degrades at elevated temperatures due to the formation of an insulating vapor layer at the solid-liquid interface (Leidenfrost effect). Interfacial electrowetting (EW) fields can disrupt this vapor layer to promote liquid-surface wetting. We experimentally analyze EW-induced disruption of the vapor layer and measure the resulting enhanced cooling during the process of quenching. Imaging is employed to visualize the fluid-surface interactions and understand boiling patterns in the presence of an electrical voltage. It is seen that EW fields fundamentally change the boiling pattern, wherein a stable vapor layer is replaced by intermittent wetting of the surface. Heat conduction across the vapor gap is thus replaced with transient convection. This fundamental switch in the heat transfer mode significantly accelerates cooling during quenching. An order of magnitude increase in the cooling rate is observed, with the heat transfer seen approaching saturation at higher voltages. An analytical model is developed to extract voltage dependent heat transfer rates from the measured cooling curve. The results show that electric fields can alter and tune the traditional cooling curve. Overall, this study presents an ultralow power consumption concept to control the mechanical properties and metallurgy, by electrically tuning the cooling rate during quenching.

  7. Parallel loss of plastid introns and their maturase in the genus Cuscuta.

    Directory of Open Access Journals (Sweden)

    Joel R McNeal

    2009-06-01

    Full Text Available Plastid genome content and arrangement are highly conserved across most land plants and their closest relatives, streptophyte algae, with nearly all plastid introns having invaded the genome in their common ancestor at least 450 million years ago. One such intron, within the transfer RNA trnK-UUU, contains a large open reading frame that encodes a presumed intron maturase, matK. This gene is missing from the plastid genomes of two species in the parasitic plant genus Cuscuta but is found in all other published land plant and streptophyte algal plastid genomes, including that of the nonphotosynthetic angiosperm Epifagus virginiana and two other species of Cuscuta. By examining matK and plastid intron distribution in Cuscuta, we add support to the hypothesis that its normal role is in splicing seven of the eight group IIA introns in the genome. We also analyze matK nucleotide sequences from Cuscuta species and relatives that retain matK to test whether changes in selective pressure in the maturase are associated with intron deletion. Stepwise loss of most group IIA introns from the plastid genome results in substantial change in selective pressure within the hypothetical RNA-binding domain of matK in both Cuscuta and Epifagus, either through evolution from a generalist to a specialist intron splicer or due to loss of a particular intron responsible for most of the constraint on the binding region. The possibility of intron-specific specialization in the X-domain is implicated by evidence of positive selection on the lineage leading to C. nitida in association with the loss of six of seven introns putatively spliced by matK. Moreover, transfer RNA gene deletion facilitated by parasitism combined with an unusually high rate of intron loss from remaining functional plastid genes created a unique circumstance on the lineage leading to Cuscuta subgenus Grammica that allowed elimination of matK in the most species-rich lineage of Cuscuta.

  8. Characteristic differences between the promoters of intron-containing and intronless ribosomal protein genes in yeast

    Directory of Open Access Journals (Sweden)

    Vingron Martin

    2008-10-01

    Full Text Available Abstract Background More than two thirds of the highly expressed ribosomal protein (RP genes in Saccharomyces cerevisiae contain introns, which is in sharp contrast to the genome-wide five percent intron-containing genes. It is well established that introns carry regulatory sequences and that the transcription of RP genes is extensively and coordinately regulated. Here we test the hypotheses that introns are innately associated with heavily transcribed genes and that introns of RP genes contribute regulatory TF binding sequences. Moreover, we investigate whether promoter features are significantly different between intron-containing and intronless RP genes. Results We find that directly measured transcription rates tend to be lower for intron-containing compared to intronless RP genes. We do not observe any specifically enriched sequence motifs in the introns of RP genes other than those of the branch point and the two splice sites. Comparing the promoters of intron-containing and intronless RP genes, we detect differences in number and position of Rap1-binding and IFHL motifs. Moreover, the analysis of the length distribution and the folding free energies suggest that, at least in a sub-population of RP genes, the 5' untranslated sequences are optimized for regulatory function. Conclusion Our results argue against the direct involvement of introns in the regulation of transcription of highly expressed genes. Moreover, systematic differences in motif distributions suggest that RP transcription factors may act differently on intron-containing and intronless gene promoters. Thus, our findings contribute to the decoding of the RP promoter architecture and may fuel the discussion on the evolution of introns.

  9. Diversity, mobility, and structural and functional evolution of group II introns carrying an unusual 3' extension

    OpenAIRE

    Tourasse, Nicolas J; Stabell, Fredrik B; Kolstø, Anne-Brit

    2011-01-01

    Background Group II introns are widespread genetic elements endowed with a dual functionality. They are catalytic RNAs (ribozymes) that are able of self-splicing and they are also mobile retroelements that can invade genomic DNA. The group II intron RNA secondary structure is typically made up of six domains. However, a number of unusual group II introns carrying a unique extension of 53-56 nucleotides at the 3' end have been identified previously in bacteria of the Bacillu...

  10. Variation in intron length in caffeic acid O-methyltransferase (COMT) in Vanilla species (Orchidaceae).

    Science.gov (United States)

    Besse, Pascale; Da Silva, Denis; Bory, Séverine; Noirot, Michel; Grisoni, Michel

    2009-04-01

    Variation in intron length in caffeic acid O-methyltransferase (COMT) in Vanilla was studied and demonstrated that COMT genes in Vanilla are organized with four exons and three introns. At least two to four different versions (either allelic or paralogous) of the COMT multigenic family in the genus Vanilla (in terms of intron sizes) were detected. The three introns were differentially variable, with intron-1 being the most length-polymorphic. Patterns of variations were in accordance with known phylogenetic relationships in the genus obtained with neutral markers. In particular, the genus displayed a strong Old World versus New World differentiation with American fragrant species being characterized by a specific 99bp intron-1 size-variant and a unique 226bp intron-3 variant. Conversely, leafless species of the genus displayed unexpected variations in intron lengths. Due to their role in primary (lignin) and secondary (phenolics, e.g., vanillin, alkaloids) metabolisms, COMT genes might not be neutral markers, and represent candidate functional markers for resistance, aromatic or medicinal properties of Vanilla species. Investigating the orthologous/paralogous status of the different genes revealed (in terms of intron size) will allow the evolution of the COMT genes to be studied. Copyright © 2009 Elsevier Ireland Ltd. All rights reserved.

  11. An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes

    Directory of Open Access Journals (Sweden)

    Wernersson Rasmus

    2006-10-01

    Full Text Available Abstract Background A knowledge of the positions of introns in eukaryotic genes is important for understanding the evolution of introns. Despite this, there has been relatively little focus on the distribution of intron positions in genes. Results In proteins with signal peptides, there is an overabundance of phase 1 introns around the region of the signal peptide cleavage site. This has been described before. But in proteins without signal peptides, a novel phenomenon is observed: There is a sharp peak of phase 0 intron positions immediately following the start codon, i.e. between codons 1 and 2. This effect is seen in a wide range of eukaryotes: Vertebrates, arthropods, fungi, and flowering plants. Proteins carrying this start codon intron are found to comprise a special class of relatively short, lysine-rich and conserved proteins with an overrepresentation of ribosomal proteins. In addition, there is a peak of phase 0 introns at position 5 in Drosophila genes with signal peptides, predominantly representing cuticle proteins. Conclusion There is an overabundance of phase 0 introns immediately after the start codon in eukaryotic genes, which has been described before only for human ribosomal proteins. We give a detailed description of these start codon introns and the proteins that contain them.

  12. An overabundance of phase 0 introns immediately after the start codon in eukaryotic genes.

    Science.gov (United States)

    Nielsen, Henrik; Wernersson, Rasmus

    2006-10-11

    A knowledge of the positions of introns in eukaryotic genes is important for understanding the evolution of introns. Despite this, there has been relatively little focus on the distribution of intron positions in genes. In proteins with signal peptides, there is an overabundance of phase 1 introns around the region of the signal peptide cleavage site. This has been described before. But in proteins without signal peptides, a novel phenomenon is observed: There is a sharp peak of phase 0 intron positions immediately following the start codon, i.e. between codons 1 and 2. This effect is seen in a wide range of eukaryotes: Vertebrates, arthropods, fungi, and flowering plants. Proteins carrying this start codon intron are found to comprise a special class of relatively short, lysine-rich and conserved proteins with an overrepresentation of ribosomal proteins. In addition, there is a peak of phase 0 introns at position 5 in Drosophila genes with signal peptides, predominantly representing cuticle proteins. There is an overabundance of phase 0 introns immediately after the start codon in eukaryotic genes, which has been described before only for human ribosomal proteins. We give a detailed description of these start codon introns and the proteins that contain them.

  13. The Chloroplast Genome of Euglena mutabilis-Cluster Arrangement, Intron Analysis, and Intrageneric Trends.

    Science.gov (United States)

    Dabbagh, Nadja; Preisfeld, Angelika

    2017-01-01

    A comparative analysis of the chloroplast genome of Euglena mutabilis underlined a high diversity in the evolution of plastids in euglenids. Gene clusters in more derived Euglenales increased in complexity with only a few, but remarkable changes in the genus Euglena. Euglena mutabilis differed from other Euglena species in a mirror-inverted arrangement of 12 from 15 identified clusters, making it very likely that the emergence at the base of the genus Euglena, which has been considered a long branch artifact, is truly a probable position. This was corroborated by many similarities in gene arrangement and orientation with Strombomonas and Monomorphina, rendering the genome organization of E. mutabilis in certain clusters as plesiomorphic feature. By RNA analysis exact exon-intron boundaries and the type of the 77 introns identified were mostly determined unambiguously. A detailed intron study of psbC pointed at two important issues: First, the number of introns varied even between species, and no trend from few to many introns could be observed. Second, mat1 was localized in Eutreptiales exclusively in intron 1, and mat2 was not identified. With the emergence of Euglenaceae in most species, a new intron containing mat2 inserted in front of the previous intron 1 and thereby became intron 2 with mat1. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

  14. A maturase-encoding group IIA intron of yeast mitochondria self-splices in vitro.

    OpenAIRE

    Hebbar, S K; Belcher, S M; Perlman, P S

    1992-01-01

    Intron 1 of the coxI gene of yeast mitochondrial DNA (aI1) is a group IIA intron that encodes a maturase function required for its splicing in vivo. It is shown here to self-splice in vitro under some reaction conditions reported earlier to yield efficient self-splicing of group IIB introns of yeast mtDNA that do not encode maturase functions. Unlike the group IIB introns, aI1 is inactive in 10 mM Mg2+ (including spermidine) and requires much higher levels of Mg2+ and added salts (1M NH4Cl or...

  15. A new class of energy based control laws for revolute robot arms - Tracking control, robustness enhancement and adaptive control

    Science.gov (United States)

    Wen, John T.; Kreutz, Kenneth; Bayard, David S.

    1988-01-01

    A class of joint-level control laws for all-revolute robot arms is introduced. The analysis is similar to the recently proposed energy Liapunov function approach except that the closed-loop potential function is shaped in accordance with the underlying joint space topology. By using energy Liapunov functions with the modified potential energy, a much simpler analysis can be used to show closed-loop global asymptotic stability and local exponential stability. When Coulomb and viscous friction and model parameter errors are present, a sliding-mode-like modification of the control law is proposed to add a robustness-enhancing outer loop. Adaptive control is also addressed within the same framework. A linear-in-the-parameters formulation is adopted, and globally asymptotically stable adaptive control laws are derived by replacing the model parameters in the nonadaptive control laws by their estimates.

  16. An intronic microRNA links Rb/E2F and EGFR signaling.

    Directory of Open Access Journals (Sweden)

    Mary Truscott

    2014-07-01

    Full Text Available The importance of microRNAs in the regulation of various aspects of biology and disease is well recognized. However, what remains largely unappreciated is that a significant number of miRNAs are embedded within and are often co-expressed with protein-coding host genes. Such a configuration raises the possibility of a functional interaction between a miRNA and the gene it resides in. This is exemplified by the Drosophila melanogaster dE2f1 gene that harbors two miRNAs, mir-11 and mir-998, within its last intron. miR-11 was demonstrated to limit the proapoptotic function of dE2F1 by repressing cell death genes that are directly regulated by dE2F1, however the biological role of miR-998 was unknown. Here we show that one of the functions of miR-998 is to suppress dE2F1-dependent cell death specifically in rbf mutants by elevating EGFR signaling. Mechanistically, miR-998 operates by repressing dCbl, a negative regulator of EGFR signaling. Significantly, dCbl is a critical target of miR-998 since dCbl phenocopies the effects of miR-998 on dE2f1-dependent apoptosis in rbf mutants. Importantly, this regulation is conserved, as the miR-998 seed family member miR-29 repressed c-Cbl, and enhanced MAPK activity and wound healing in mammalian cells. Therefore, the two intronic miRNAs embedded in the dE2f1 gene limit the apoptotic function of dE2f1, but operate in different contexts and act through distinct mechanisms. These results also illustrate that examining an intronic miRNA in the context of its host's function can be valuable in elucidating the biological function of the miRNA, and provide new information about the regulation of the host gene itself.

  17. Enhanced Reliability of Photovoltaic Systems with Energy Storage and Controls

    Energy Technology Data Exchange (ETDEWEB)

    Manz, D.; Schelenz, O.; Chandra, R.; Bose, S.; de Rooij, M.; Bebic, J.

    2008-02-01

    This report summarizes efforts to reconfigure loads during outages to allow individual customers the opportunity to enhance the reliability of their electric service through the management of their loads, photovoltaics, and energy storage devices.

  18. Group-II intron splicing factors in higher-plants mitochondria

    Directory of Open Access Journals (Sweden)

    Gregory G. Brown

    2014-02-01

    Full Text Available Group-II introns are large catalytic RNAs (ribozymes which are found in bacteria and organellar genomes of several lower eukaryotes, but are particularly prevalent within the mitochondrial genomes (mtDNA in plants, where they reside in numerous critical genes. Their excision is therefore essential for mitochondria biogenesis and respiratory functions, and is facilitated in vivo by various protein cofactors. Typical group-II introns are classified as mobile genetic elements, consisting of the self-splicing ribozyme and its intron-encoded maturase protein. A hallmark of maturases is that they are intron specific, acting as cofactors which bind their own cognate containing pre-mRNAs to facilitate splicing. However, the plant organellar introns have diverged considerably from their bacterial ancestors, such as they lack many regions which are necessary for splicing and also lost their evolutionary related maturase ORFs. In fact, only a single maturase has retained in the mtDNA of angiosperms: matR encoded in the fourth intron of the NADH-dehydrogenase subunit 1 (nad1 intron 4. Their degeneracy and the absence of cognate ORFs suggest that the splicing of plant mitochondria introns is assisted by trans-acting cofactors. Interestingly, in addition to MatR, the nuclear genomes of angiosperms also harbor four genes (nMat 1-4, which are closely related to maturases and contain N-terminal mitochondrial localization signals. Recently, we established the roles of two of these paralogs in Arabidopsis, nMAT1 and nMAT2, in the splicing of mitochondrial introns. In addition to the nMATs, genetic screens led to the identification of other genes encoding various factors, which are required for the splicing and processing of mitochondrial introns in plants. In this review we will summarize recent data on the splicing and processing of mitochondrial introns and their implication in plant development and physiology, with a focus on maturases and their accessory

  19. Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea.

    Science.gov (United States)

    Srivastava, Rishi; Bajaj, Deepak; Sayal, Yogesh K; Meher, Prabina K; Upadhyaya, Hari D; Kumar, Rajendra; Tripathi, Shailesh; Bharadwaj, Chellapilla; Rao, Atmakuri R; Parida, Swarup K

    2016-11-01

    The discovery and large-scale genotyping of informative gene-based markers is essential for rapid delineation of genes/QTLs governing stress tolerance and yield component traits in order to drive genetic enhancement in chickpea. A genome-wide 119169 and 110491 ISM (intron-spanning markers) from 23129 desi and 20386 kabuli protein-coding genes and 7454 in silico InDel (insertion-deletion) (1-45-bp)-based ILP (intron-length polymorphism) markers from 3283 genes were developed that were structurally and functionally annotated on eight chromosomes and unanchored scaffolds of chickpea. A much higher amplification efficiency (83%) and intra-specific polymorphic potential (86%) detected by these markers than that of other sequence-based genetic markers among desi and kabuli chickpea accessions was apparent even by a cost-effective agarose gel-based assay. The genome-wide physically mapped 1718 ILP markers assayed a wider level of functional genetic diversity (19-81%) and well-defined phylogenetics among domesticated chickpea accessions. The gene-derived 1424 ILP markers were anchored on a high-density (inter-marker distance: 0.65cM) desi intra-specific genetic linkage map/functional transcript map (ICC 4958×ICC 2263) of chickpea. This reference genetic map identified six major genomic regions harbouring six robust QTLs mapped on five chromosomes, which explained 11-23% seed weight trait variation (7.6-10.5 LOD) in chickpea. The integration of high-resolution QTL mapping with differential expression profiling detected six including one potential serine carboxypeptidase gene with ILP markers (linked tightly to the major seed weight QTLs) exhibiting seed-specific expression as well as pronounced up-regulation especially in seeds of high (ICC 4958) as compared to low (ICC 2263) seed weight mapping parental accessions. The marker information generated in the present study was made publicly accessible through a user-friendly web-resource, "Chickpea ISM-ILP Marker Database

  20. Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor α-Bound Enhancers.

    Science.gov (United States)

    Carleton, Julia B; Berrett, Kristofer C; Gertz, Jason

    2017-10-25

    Multiple regulatory regions have the potential to regulate a single gene, yet how these elements combine to affect gene expression remains unclear. To uncover the combinatorial relationships between enhancers, we developed Enhancer-interference (Enhancer-i), a CRISPR interference-based approach that uses 2 different repressive domains, KRAB and SID, to prevent enhancer activation simultaneously at multiple regulatory regions. We applied Enhancer-i to promoter-distal estrogen receptor α binding sites (ERBS), which cluster around estradiol-responsive genes and therefore may collaborate to regulate gene expression. Targeting individual sites revealed predominant ERBS that are completely required for the transcriptional response, indicating a lack of redundancy. Simultaneous interference of different ERBS combinations identified supportive ERBS that contribute only when predominant sites are active. Using mathematical modeling, we find strong evidence for collaboration between predominant and supportive ERBS. Overall, our findings expose a complex functional hierarchy of enhancers, where multiple loci bound by the same transcription factor combine to fine-tune the expression of target genes. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Multilayer robust control for safety enhancement of reactor operations

    International Nuclear Information System (INIS)

    Edwards, R.M.; Lee, K.Y.; Ray, A.

    1991-01-01

    A novel concept of reactor power and temperature control has been recently reported in which a conventional output feedback controller is embedded within a state feedback setting. The embedded output feedback controller at the inner layer largely compensates for plant modeling uncertainties and external disturbances, and the outer layer generates an optimal control signal via feedback of the estimated plant states. A major advantage of this embedded architecture is the robustness of the control system relative to parametric and nonparametric uncertainties and thus the opportunity for designing fault-accommodating control algorithms to improve reactor operations and plant safety. The paper illustrates the architecture of the state-feedback-assisted classical (SFAC) control, which utilizes an embedded output feedback controller designed via classical techniques. It demonstrates the difference between the performance of conventional state feedback control and SFAC by examining the sensitivity of the dominant eigenvalues of the individual closed-loop systems

  2. Genomewide analysis of intronic microRNAs in rice and Arabidopsis

    Indian Academy of Sciences (India)

    Keywords. rice; Arabidopsis; intronic miRNA; host gene; bioinformatics; function. Abstract. MicroRNAs (miRNAs) are potent regulators of gene transcription and posttranscriptional processes. The majority of miRNAs are localized within intronic regions of protein-coding genes (host genes) and have diverse functions in ...

  3. Two CRM protein subfamilies cooperate in the splicing of group IIB introns in chloroplasts.

    Science.gov (United States)

    Asakura, Yukari; Bayraktar, Omer Ali; Barkan, Alice

    2008-11-01

    Chloroplast genomes in angiosperms encode approximately 20 group II introns, approximately half of which are classified as subgroup IIB. The splicing of all but one of the subgroup IIB introns requires a heterodimer containing the peptidyl-tRNA hydrolase homolog CRS2 and one of two closely related proteins, CAF1 or CAF2, that harbor a recently recognized RNA binding domain called the CRM domain. Two CRS2/CAF-dependent introns require, in addition, a CRM domain protein called CFM2 that is only distantly related to CAF1 and CAF2. Here, we show that CFM3, a close relative of CFM2, associates in vivo with those CRS2/CAF-dependent introns that are not CFM2 ligands. Mutant phenotypes in rice and Arabidopsis support a role for CFM3 in the splicing of most of the introns with which it associates. These results show that either CAF1 or CAF2 and either CFM2 or CFM3 simultaneously bind most chloroplast subgroup IIB introns in vivo, and that the CAF and CFM subunits play nonredundant roles in splicing. These results suggest that the expansion of the CRM protein family in plants resulted in two subfamilies that play different roles in group II intron splicing, with further diversification within a subfamily to accommodate multiple intron ligands.

  4. U12 type introns were lost at multiple occasions during evolution

    Directory of Open Access Journals (Sweden)

    Bartschat Sebastian

    2010-02-01

    Full Text Available Abstract Background Two categories of introns are known, a common U2 type and a rare U12 type. These two types of introns are removed by distinct spliceosomes. The phylogenetic distribution of spliceosomal RNAs that are characteristic of the U12 spliceosome, i.e. the U11, U12, U4atac and U6atac RNAs, suggest that U12 spliceosomes were lost in many phylogenetic groups. We have now examined the distribution of U2 and U12 introns in many of these groups. Results U2 and U12 introns were predicted by making use of available EST and genomic sequences. The results show that in species or branches where U12 spliceosomal components are missing, also U12 type of introns are lacking. Examples are the choanoflagellate Monosiga brevicollis, Entamoeba histolytica, green algae, diatoms, and the fungal lineage Basidiomycota. Furthermore, whereas U12 splicing does not occur in Caenorhabditis elegans, U12 introns as well as U12 snRNAs are present in Trichinella spiralis, which is deeply branching in the nematode tree. A comparison of homologous genes in T. spiralis and C. elegans revealed different mechanisms whereby U12 introns were lost. Conclusions The phylogenetic distribution of U12 introns and spliceosomal RNAs give further support to an early origin of U12 dependent splicing. In addition, this distribution identifies a large number of instances during eukaryotic evolution where such splicing was lost.

  5. The strength of intron donor splice sites in human genes displays a bell-shaped pattern

    DEFF Research Database (Denmark)

    Wang, Kai; Wernersson, Rasmus; Brunak, Søren

    2011-01-01

    introns. Interestingly, when analysing the intron containing gene pool from mouse consisting of >15 000 genes, we found the convex pattern to be conserved despite >75 million years of evolutionary divergence between the two organisms. We also analysed an interesting, novel class of chimeric genes which...

  6. Insertion of a self-splicing intron into the mtDNA of atriploblastic animal

    Energy Technology Data Exchange (ETDEWEB)

    Valles, Y.; Halanych, K.; Boore, J.L.

    2006-04-14

    Nephtys longosetosa is a carnivorous polychaete worm that lives in the intertidal and subtidal zones with worldwide distribution (pleijel&rouse2001). Its mitochondrial genome has the characteristics typical of most metazoans: 37 genes; circular molecule; almost no intergenic sequence; and no significant gene rearrangements when compared to other annelid mtDNAs (booremoritz19981995). Ubiquitous features as small intergenic regions and lack of introns suggested that metazoan mtDNAs are under strong selective pressures to reduce their genome size allowing for faster replication requirements (booremoritz19981995Lynch2005). Yet, in 1996 two type I introns were found in the mtDNA of the basal metazoan Metridium senile (FigureX). Breaking a long-standing rule (absence of introns in metazoan mtDNA), this finding was later supported by the further presence of group I introns in other cnidarians. Interestingly, only the class Anthozoa within cnidarians seems to harbor such introns. Although several hundreds of triploblastic metazoan mtDNAs have been sequenced, this study is the first evidence of mitochondrial introns in triploblastic metazoans. The cox1 gene of N. longosetosa has an intron of almost 2 kbs in length. This finding represents as well the first instance of a group II intron (anthozoans harbor group I introns) in all metazoan lineages. Opposite trends are observed within plants, fungi and protist mtDNAs, where introns (both group I and II) and other non-coding sequences are widespread. Plant, fungal and protist mtDNA structure and organization differ enormously from that of metazoan mtDNA. Both, plant and fungal mtDNA are dynamic molecules that undergo high rates of recombination, contain long intergenic spacer regions and harbor both group I and group II introns. However, as metazoans they have a conserved gene content. Protists, on the other hand have a striking variation of gene content and introns that account for the genome size variation. In contrast to

  7. Deterministic learning enhanced neutral network control of unmanned helicopter

    Directory of Open Access Journals (Sweden)

    Yiming Jiang

    2016-11-01

    Full Text Available In this article, a neural network–based tracking controller is developed for an unmanned helicopter system with guaranteed global stability in the presence of uncertain system dynamics. Due to the coupling and modeling uncertainties of the helicopter systems, neutral networks approximation techniques are employed to compensate the unknown dynamics of each subsystem. In order to extend the semiglobal stability achieved by conventional neural control to global stability, a switching mechanism is also integrated into the control design, such that the resulted neural controller is always valid without any concern on either initial conditions or range of state variables. In addition, deterministic learning is applied to the neutral network learning control, such that the adaptive neutral networks are able to store the learned knowledge that could be reused to construct neutral network controller with improved control performance. Simulation studies are carried out on a helicopter model to illustrate the effectiveness of the proposed control design.

  8. Crosstalk between pathways enhances the controllability of signalling networks.

    Science.gov (United States)

    Wang, Dingjie; Jin, Suoqin; Zou, Xiufen

    2016-02-01

    The control of complex networks is one of the most challenging problems in the fields of biology and engineering. In this study, the authors explored the controllability and control energy of several signalling networks, which consisted of many interconnected pathways, including networks with a bow-tie architecture. On the basis of the theory of structure controllability, they revealed that biological mechanisms, such as cross-pathway interactions, compartmentalisation and so on make the networks easier to fully control. Furthermore, using numerical simulations for two realistic examples, they demonstrated that the control energy of normal networks with crosstalk is lower than in networks without crosstalk. These results indicate that the biological networks are optimally designed to achieve their normal functions from the viewpoint of the control theory. The authors' work provides a comprehensive understanding of the impact of network structures and properties on controllability.

  9. Attributes Enhanced Role-Based Access Control Model

    DEFF Research Database (Denmark)

    Mahmood Rajpoot, Qasim; Jensen, Christian D.; Krishnan, Ram

    2015-01-01

    as an important area of research. In this paper, we propose an access control model that combines the two models in a novel way in order to unify their benefits. Our approach provides a fine-grained access control mechanism that not only takes contextual information into account while making the access control...

  10. Enhancing SOEC system lifetime by controlling inlet gas composition

    DEFF Research Database (Denmark)

    2015-01-01

    In a method for enhancing the lifetime of a solid oxide electrolysis cell system by counteracting nitridation of the threads of the in-line electrical heaters of the system, the start-up, shut-down and trip operations are done in a humidified nitrogen atmosphere on the fuel side to achieve a dew...

  11. The Function of the Conserved Regulatory Element within the Second Intron of the Mammalian Csf1r Locus

    Science.gov (United States)

    O’Neal, Julie; Sester, David P.; Tagoh, Hiromi; Ingram, Richard M.; Pridans, Clare; Bonifer, Constanze; Hume, David A.

    2013-01-01

    The gene encoding the receptor for macrophage colony-stimulating factor (CSF-1R) is expressed exclusively in cells of the myeloid lineages as well as trophoblasts. A conserved element in the second intron, Fms-Intronic Regulatory Element (FIRE), is essential for macrophage-specific transcription of the gene. However, the molecular details of how FIRE activity is regulated and how it impacts the Csf1r promoter have not been characterised. Here we show that agents that down-modulate Csf1r mRNA transcription regulated promoter activity altered the occupancy of key FIRE cis-acting elements including RUNX1, AP1, and Sp1 binding sites. We demonstrate that FIRE acts as an anti-sense promoter in macrophages and reversal of FIRE orientation within its native context greatly reduced enhancer activity in macrophages. Mutation of transcription initiation sites within FIRE also reduced transcription. These results demonstrate that FIRE is an orientation-specific transcribed enhancer element. PMID:23383005

  12. Stress-induced endogenous siRNAs targeting regulatory intron sequences in Brachypodium.

    Science.gov (United States)

    Wang, Hsiao-Lin V; Dinwiddie, Brandon L; Lee, Herman; Chekanova, Julia A

    2015-02-01

    Exposure to abiotic stresses triggers global changes in the expression of thousands of eukaryotic genes at the transcriptional and post-transcriptional levels. Small RNA (smRNA) pathways and splicing both function as crucial mechanisms regulating stress-responsive gene expression. However, examples of smRNAs regulating gene expression remain largely limited to effects on mRNA stability, translation, and epigenetic regulation. Also, our understanding of the networks controlling plant gene expression in response to environmental changes, and examples of these regulatory pathways intersecting, remains limited. Here, to investigate the role of smRNAs in stress responses we examined smRNA transcriptomes of Brachypodium distachyon plants subjected to various abiotic stresses. We found that exposure to different abiotic stresses specifically induced a group of novel, endogenous small interfering RNAs (stress-induced, UTR-derived siRNAs, or sutr-siRNAs) that originate from the 3' UTRs of a subset of coding genes. Our bioinformatics analyses predicted that sutr-siRNAs have potential regulatory functions and that over 90% of sutr-siRNAs target intronic regions of many mRNAs in trans. Importantly, a subgroup of these sutr-siRNAs target the important intron regulatory regions, such as branch point sequences, that could affect splicing. Our study indicates that in Brachypodium, sutr-siRNAs may affect splicing by masking or changing accessibility of specific cis-elements through base-pairing interactions to mediate gene expression in response to stresses. We hypothesize that this mode of regulation of gene expression may also serve as a general mechanism for regulation of gene expression in plants and potentially in other eukaryotes. © 2015 Wang et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  13. Prognostics Enhanced Reconfigurable Control of Electro-Mechanical Actuators

    Data.gov (United States)

    National Aeronautics and Space Administration — Actuator systems are employed widely in aerospace, transportation and industrial processes to provide power to critical loads, such as aircraft control surfaces....

  14. Cognitive control in auditory working memory is enhanced in musicians

    OpenAIRE

    Pallesen, K.J.; Brattico, E.; Bailey, C.J.; Korvenoja, A.; Koivisto, J.; Gjedde, A.; Carlson, Synnöve

    2010-01-01

    Musical competence may confer cognitive advantages that extend beyond processing of familiar musical sounds. Behavioural evidence indicates a general enhancement of both working memory and attention in musicians. It is possible that musicians, due to their training, are better able to maintain focus on task-relevant stimuli, a skill which is crucial to working memory. We measured the blood oxygenation-level dependent (BOLD) activation signal in musicians and non-musicians during working memor...

  15. Algorithm Design and Validation for Adaptive Nonlinear Control Enhancement (ADVANCE) Technology Development for Resilient Flight Control, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — SSCI proposes to develop and test a framework referred to as the ADVANCE (Algorithm Design and Validation for Adaptive Nonlinear Control Enhancement), within which...

  16. Phylogenetic distribution of intron positions in alpha-amylase genes of bilateria suggests numerous gains and losses.

    Directory of Open Access Journals (Sweden)

    Jean-Luc Da Lage

    Full Text Available Most eukaryotes have at least some genes interrupted by introns. While it is well accepted that introns were already present at moderate density in the last eukaryote common ancestor, the conspicuous diversity of intron density among genomes suggests a complex evolutionary history, with marked differences between phyla. The question of the rates of intron gains and loss in the course of evolution and factors influencing them remains controversial. We have investigated a single gene family, alpha-amylase, in 55 species covering a variety of animal phyla. Comparison of intron positions across phyla suggests a complex history, with a likely ancestral intronless gene undergoing frequent intron loss and gain, leading to extant intron/exon structures that are highly variable, even among species from the same phylum. Because introns are known to play no regulatory role in this gene and there is no alternative splicing, the structural differences may be interpreted more easily: intron positions, sizes, losses or gains may be more likely related to factors linked to splicing mechanisms and requirements, and to recognition of introns and exons, or to more extrinsic factors, such as life cycle and population size. We have shown that intron losses outnumbered gains in recent periods, but that "resets" of intron positions occurred at the origin of several phyla, including vertebrates. Rates of gain and loss appear to be positively correlated. No phase preference was found. We also found evidence for parallel gains and for intron sliding. Presence of introns at given positions was correlated to a strong protosplice consensus sequence AG/G, which was much weaker in the absence of intron. In contrast, recent intron insertions were not associated with a specific sequence. In animal Amy genes, population size and generation time seem to have played only minor roles in shaping gene structures.

  17. Phylogenetic Distribution of Intron Positions in Alpha-Amylase Genes of Bilateria Suggests Numerous Gains and Losses

    Science.gov (United States)

    Da Lage, Jean-Luc; Maczkowiak, Frédérique; Cariou, Marie-Louise

    2011-01-01

    Most eukaryotes have at least some genes interrupted by introns. While it is well accepted that introns were already present at moderate density in the last eukaryote common ancestor, the conspicuous diversity of intron density among genomes suggests a complex evolutionary history, with marked differences between phyla. The question of the rates of intron gains and loss in the course of evolution and factors influencing them remains controversial. We have investigated a single gene family, alpha-amylase, in 55 species covering a variety of animal phyla. Comparison of intron positions across phyla suggests a complex history, with a likely ancestral intronless gene undergoing frequent intron loss and gain, leading to extant intron/exon structures that are highly variable, even among species from the same phylum. Because introns are known to play no regulatory role in this gene and there is no alternative splicing, the structural differences may be interpreted more easily: intron positions, sizes, losses or gains may be more likely related to factors linked to splicing mechanisms and requirements, and to recognition of introns and exons, or to more extrinsic factors, such as life cycle and population size. We have shown that intron losses outnumbered gains in recent periods, but that “resets” of intron positions occurred at the origin of several phyla, including vertebrates. Rates of gain and loss appear to be positively correlated. No phase preference was found. We also found evidence for parallel gains and for intron sliding. Presence of introns at given positions was correlated to a strong protosplice consensus sequence AG/G, which was much weaker in the absence of intron. In contrast, recent intron insertions were not associated with a specific sequence. In animal Amy genes, population size and generation time seem to have played only minor roles in shaping gene structures. PMID:21611157

  18. Phylogenetic Distribution of Intron Positions in Alpha-Amylase Genes of Bilateria Suggests Numerous Gains and Losses

    OpenAIRE

    Da Lage, Jean-Luc; Maczkowiak, Frédérique; Cariou, Marie-Louise

    2011-01-01

    Most eukaryotes have at least some genes interrupted by introns. While it is well accepted that introns were already present at moderate density in the last eukaryote common ancestor, the conspicuous diversity of intron density among genomes suggests a complex evolutionary history, with marked differences between phyla. The question of the rates of intron gains and loss in the course of evolution and factors influencing them remains controversial. We have investigated a single gene family, al...

  19. Oxytocin administration enhances controlled social cognition in patients with schizophrenia.

    Science.gov (United States)

    Woolley, J D; Chuang, B; Lam, O; Lai, W; O'Donovan, A; Rankin, K P; Mathalon, D H; Vinogradov, S

    2014-09-01

    Individuals with schizophrenia have functionally significant deficits in automatic and controlled social cognition, but no currently available pharmacologic treatments reduce these deficits. The neuropeptide oxytocin has multiple prosocial effects when administered intranasally in humans and there is growing interest in its therapeutic potential in schizophrenia. We administered 40 IU of oxytocin and saline placebo intranasally to 29 male subjects with schizophrenia and 31 age-matched, healthy controls in a randomized, double-blind, placebo-controlled, cross-over study. Social cognition was assessed with The Awareness of Social Inference Test (TASIT) and the Reading the Mind in the Eyes Test (RMET). We examined the effects of oxytocin administration on automatic social cognition (the ability to rapidly interpret and understand emotional cues from the voice, face, and body); controlled social cognition (the ability to comprehend indirectly expressed emotions, thoughts, and intentions through complex deliberations over longer time periods); and a control task (the ability to comprehend truthful dialog and perform general task procedures) in individuals with and without schizophrenia using mixed factorial analysis of variance models. Patients with schizophrenia showed significant impairments in automatic and controlled social cognition compared to healthy controls, and administration of oxytocin significantly improved their controlled, but not automatic, social cognition, F(1, 58)=8.75; p=0.004. Conversely, oxytocin administration had limited effects on social cognition in healthy participants. Patients and controls performed equally well and there were no effects of oxytocin administration on the control task. Intact social cognitive abilities are associated with better functional outcomes in individuals with schizophrenia. Our data highlight the potentially complex effects of oxytocin on some but not all aspects of social cognition, and support the exploration of

  20. Conservation of intron and intein insertion sites: implications for life histories of parasitic genetic elements

    Directory of Open Access Journals (Sweden)

    Senejani Alireza G

    2009-12-01

    Full Text Available Abstract Background Inteins and introns are genetic elements that are removed from proteins and RNA after translation or transcription, respectively. Previous studies have suggested that these genetic elements are found in conserved parts of the host protein. To our knowledge this type of analysis has not been done for group II introns residing within a gene. Here we provide quantitative statistical support from an analyses of proteins that host inteins, group I introns, group II introns and spliceosomal introns across all three domains of life. Results To determine whether or not inteins, group I, group II, and spliceosomal introns are found preferentially in conserved regions of their respective host protein, conservation profiles were generated and intein and intron positions were mapped to the profiles. Fisher's combined probability test was used to determine the significance of the distribution of insertion sites across the conservation profile for each protein. For a subset of studied proteins, the conservation profile and insertion positions were mapped to protein structures to determine if the insertion sites correlate to regions of functional activity. All inteins and most group I introns were found to be preferentially located within conserved regions; in contrast, a bacterial intein-like protein, group II and spliceosomal introns did not show a preference for conserved sites. Conclusions These findings demonstrate that inteins and group I introns are found preferentially in conserved regions of their respective host proteins. Homing endonucleases are often located within inteins and group I introns and these may facilitate mobility to conserved regions. Insertion at these conserved positions decreases the chance of elimination, and slows deletion of the elements, since removal of the elements has to be precise as not to disrupt the function of the protein. Furthermore, functional constrains on the targeted site make it more difficult

  1. Diversity, mobility, and structural and functional evolution of group II introns carrying an unusual 3' extension

    Directory of Open Access Journals (Sweden)

    Tourasse Nicolas J

    2011-12-01

    Full Text Available Abstract Background Group II introns are widespread genetic elements endowed with a dual functionality. They are catalytic RNAs (ribozymes that are able of self-splicing and they are also mobile retroelements that can invade genomic DNA. The group II intron RNA secondary structure is typically made up of six domains. However, a number of unusual group II introns carrying a unique extension of 53-56 nucleotides at the 3' end have been identified previously in bacteria of the Bacillus cereus group. Methods In the present study, we conducted combined sequence comparisons and phylogenetic analyses of introns, host gene, plasmid and chromosome of host strains in order to gain insights into mobility, dispersal, and evolution of the unusual introns and their extension. We also performed in vitro mutational and kinetic experiments to investigate possible functional features related to the extension. Results We report the identification of novel copies of group II introns carrying a 3' extension including the first two copies in bacteria not belonging to the B. cereus group, Bacillus pseudofirmus OF4 and Bacillus sp. 2_A_57_CT2, an uncharacterized species phylogenetically close to B. firmus. Interestingly, the B. pseudofirmus intron has a longer extension of 70 bases. From sequence comparisons and phylogenetic analyses, several possible separate events of mobility involving the atypical introns could be identified, including both retrohoming and retrotransposition events. In addition, identical extensions were found in introns that otherwise exhibit little sequence conservation in the rest of their structures, with the exception of the conserved and catalytically critical domains V and VI, suggesting either separate acquisition of the extra segment by different group II introns or a strong selection pressure acting on the extension. Furthermore, we show by in vitro splicing experiments that the 3' extension affects the splicing properties differently in

  2. Replacement of Imu-Cmu intron by NeoR gene alters Imu germ-line expression but has no effect on V(D)J recombination.

    Science.gov (United States)

    Haddad, Dania; Dougier, Hei-Lanne; Laviolette, Nathalie; Puget, Nadine; Khamlichi, Ahmed Amine

    2010-02-01

    The NeoR gene has often been used to unravel the mechanisms underlying long-range interactions between promoters and enhancers during V(D)J assembly and class switch recombination (CSR) in the immunoglobulin heavy chain (IgH) locus. This approach led to the notion that CSR is regulated through competition of germ-line (GL) promoters for activities displayed by the 3' regulatory region (3'RR). This polarized long-range effect of the 3'RR is disturbed upon insertion of NeoR gene in the IgH constant (C(H)) region, where only GL transcription derived from upstream GL promoters is impaired. In the context of V(D)J recombination, replacement of Emu enhancer or Emu core enhancer (cEmu) by NeoR gene fully blocked V(D)J recombination and mu0 GL transcription which originates 5' of DQ52 and severely diminished Imu GL transcription derived from Emu/Imu promoter, suggesting a critical role for cEmu in the regulation of V(D)J recombination and of mu0 and Imu expression. Here we focus on the effect of NeoR gene on mu0 and Imu GL transcription in a mouse line in which the Imu-Cmu intron was replaced by a NeoR gene in the sense-orientation. B cell development was characterized by a marked but incomplete block at the pro-B cell stage. However, V(D)J recombination was unaffected in sorted pro-B and pre-B cells excluding an interference with the accessibility control function of Emu. mu0 GL transcription initiation was relatively normal but the maturation step seemed to be affected most likely through premature termination at NeoR polyadenylation sites. In contrast, Imu transcription initiation was impaired suggesting an interference of NeoR gene with the IgH enhancers that control Imu expression. Surprisingly, in stark contrast with the NeoR effect in the C(H) region, LPS-induced NeoR expression restored Imu transcript levels to normal. The data suggest that Emu enhancer may be the master control element that counteracts the down-regulatory "Neo effect" on Imu expression upon LPS

  3. Using Statistical Process Control to Enhance Student Progression

    Science.gov (United States)

    Hanna, Mark D.; Raichura, Nilesh; Bernardes, Ednilson

    2012-01-01

    Public interest in educational outcomes has markedly increased in the most recent decade; however, quality management and statistical process control have not deeply penetrated the management of academic institutions. This paper presents results of an attempt to use Statistical Process Control (SPC) to identify a key impediment to continuous…

  4. An Enhanced Control Scheme for Uninterruptible Power Supply

    DEFF Research Database (Denmark)

    Lu, Jinghang; Savaghebi, Mehdi; Wei, Baoze

    2017-01-01

    To address the active power feeding issue in the parallel Uninterruptible Power Supply (UPS) system, a DC-link Voltage Protection (DCVP) control strategy is proposed in this paper. The proposed control method only relies on local load information, which increases the system reliability...

  5. Microprocessor enhanced real time manual control of an industrial robot

    Energy Technology Data Exchange (ETDEWEB)

    Yount, J.A.; Phillips, R.H.

    1983-09-14

    Remote handling using commercial robotic devices can be a viable approach for manipulating hazardous materials. However, these operations can result in unforeseen situations that require interruption of a robot program, followed by manual adjustment to the path and subsequent resumption of program control. A microcomputer and precision joystick controller interfaced with the control unit of the robot provide an effective means of achieving this from a remote location. The paper will describe ongoing collaborative research between Westinghouse Hanford Company and the Robotics and Automation Laboratory of the University of Illinois at Chicago for achieving such control from a remote location. This paper discusses the approach being used to achieve real time control from a remote location and a microcomputer based system that has been constructed for a Cincinnati Milacron T3 hydraulic robot.

  6. The mitochondrial LSU rRNA group II intron of Ustilago maydis encodes an active homing endonuclease likely involved in intron mobility.

    Directory of Open Access Journals (Sweden)

    Anja Pfeifer

    Full Text Available BACKGROUND: The a2 mating type locus gene lga2 is critical for uniparental mitochondrial DNA inheritance during sexual development of Ustilago maydis. Specifically, the absence of lga2 results in biparental inheritance, along with efficient transfer of intronic regions in the large subunit rRNA gene between parental molecules. However, the underlying role of the predicted LAGLIDADG homing endonuclease gene I-UmaI located within the group II intron LRII1 has remained unresolved. METHODOLOGY/PRINCIPAL FINDINGS: We have investigated the enzymatic activity of I-UmaI in vitro based on expression of a tagged full-length and a naturally occurring mutant derivative, which harbors only the N-terminal LAGLIDADG domain. This confirmed Mg²⁺-dependent endonuclease activity and cleavage at the LRII1 insertion site to generate four base pair extensions with 3' overhangs. Specifically, I-UmaI recognizes an asymmetric DNA sequence with a minimum length of 14 base pairs (5'-GACGGGAAGACCCT-3' and tolerates subtle base pair substitutions within the homing site. Enzymatic analysis of the mutant variant indicated a correlation between the activity in vitro and intron homing. Bioinformatic analyses revealed that putatively functional or former functional I-UmaI homologs are confined to a few members within the Ustilaginales and Agaricales, including the phylogenetically distant species Lentinula edodes, and are linked to group II introns inserted into homologous positions in the LSU rDNA. CONCLUSIONS/SIGNIFICANCE: The present data provide strong evidence that intron homing efficiently operates under conditions of biparental inheritance in U. maydis. Conversely, uniparental inheritance may be critical to restrict the transmission of mobile introns. Bioinformatic analyses suggest that I-UmaI-associated introns have been acquired independently in distant taxa and are more widespread than anticipated from available genomic data.

  7. Variations of SSU rDNA group I introns in different isolates of Cordyceps militaris and the loss of an intron during cross-mating.

    Science.gov (United States)

    Lian, Tiantian; Yang, Tao; Sun, Junde; Guo, Suping; Yang, Huaijun; Dong, Caihong

    2014-08-01

    Cordyceps militaris, the type species of genus Cordyceps, is one of the most popular mushrooms and a nutraceutical in eastern Asia. It is considered a model organism for the study of Cordyceps species because it can complete its life cycle when cultured in vitro. In the present study, the occurrence and sequence variation of SSU rDNA group I introns, Cmi.S943 and Cmi.S1199, among different isolates of C. militaris were analyzed. Based on the secondary structure predictions, the Cmi.S943 intron has been placed in subgroup IC1, and the Cmi.S1199 intron has been placed in subgroup IE. No significant similarity between Cmi.S943 and Cmi.S1199 suggested different origins. Three genotypes, based on the frequency and distribution of introns, were described to discriminate the 57 surveyed C. militaris strains. It was found that the genotype was related to the stroma characteristics. The stromata of all of the genotype II strains, which possessed only Cmi.S943, could produce perithecium. In contrast, the stromata of all genotype III strains, which had both Cmi.S943 and Cmi.S1199, could not produce perithecium. Cmi.S1199 showed the lowest level of intra-specific variation among the tested strains. Group I introns can be lost during strain cross-mating. Therefore, we presumed that during cross-mating and recombination, intron loss could be driven by positive Darwinian selection due to the energetic cost of transcribing long introns.

  8. Disentangling the Impact of Control-Enhancing Mechanisms on Firm Performance

    DEFF Research Database (Denmark)

    Zattoni, Alessandro; Pedersen, Torben

    2011-01-01

    in five European countries (i.e. France, Germany, Italy, Spain, and the UK). Then we tested the consequences of control-enhancing mechanisms for firm performance using 2SLS regression models. Our results show that (i) mechanisms that lock-in control do have a direct and negative impact on firm performance......, and (ii) the negative impact on firm performance of mechanisms aimed at enhancing control by leveraging voting power is mediated by the divergence in voting and cash flow rights....

  9. The distribution, diversity, and importance of 16S rRNA gene introns in the order Thermoproteales.

    Science.gov (United States)

    Jay, Zackary J; Inskeep, William P

    2015-07-09

    Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which "universal" archaeal 16S rRNA gene primers are impacted by the presence of intron sequences. Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes. The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different "universal" 16S rRNA primers employed in environmental microbial community analysis.

  10. The brown algae Pl.LSU/2 group II intron-encoded protein has functional reverse transcriptase and maturase activities.

    Directory of Open Access Journals (Sweden)

    Madeleine Zerbato

    Full Text Available Group II introns are self-splicing mobile elements found in prokaryotes and eukaryotic organelles. These introns propagate by homing into precise genomic locations, following assembly of a ribonucleoprotein complex containing the intron-encoded protein (IEP and the spliced intron RNA. Engineered group II introns are now commonly used tools for targeted genomic modifications in prokaryotes but not in eukaryotes. We speculate that the catalytic activation of currently known group II introns is limited in eukaryotic cells. The brown algae Pylaiella littoralis Pl.LSU/2 group II intron is uniquely capable of in vitro ribozyme activity at physiological level of magnesium but this intron remains poorly characterized. We purified and characterized recombinant Pl.LSU/2 IEP. Unlike most IEPs, Pl.LSU/2 IEP displayed a reverse transcriptase activity without intronic RNA. The Pl.LSU/2 intron could be engineered to splice accurately in Saccharomyces cerevisiae and splicing efficiency was increased by the maturase activity of the IEP. However, spliced transcripts were not expressed. Furthermore, intron splicing was not detected in human cells. While further tool development is needed, these data provide the first functional characterization of the PI.LSU/2 IEP and the first evidence that the Pl.LSU/2 group II intron splicing occurs in vivo in eukaryotes in an IEP-dependent manner.

  11. Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris.

    Science.gov (United States)

    Zhang, Yongjie; Zhang, Shu; Zhang, Guozhen; Liu, Xingzhong; Wang, Chengshu; Xu, Jianping

    2015-04-01

    Intra-specific comparison of mitochondrial genomes can help elucidate the evolution of a species, however it has not been performed for hypocrealean fungi that form diverse symbiotic associations with other organisms. In this study, comparative analyses of three completely sequenced mitochondrial genomes of a hypocrealean fungus, Cordyceps militaris, the type species of Cordyceps genus, revealed that the introns were the main contributors to mitochondrial genome size variations among strains. Mitochondrial genes in C. militaris have been invaded by group I introns in at least eight positions. PCR assays of various C. militaris isolates showed abundant variations of intron presence/absence among strains at seven of the eight intronic loci. Although the ancestral intron pattern was inferred to contain all eight introns, loss and/or gain events occurred for seven of the eight introns. These introns invaded the C. militaris mitochondrial genome probably by horizontal transfer from other fungi, and intron insertions into intronless genes in C. militaris were accompanied by co-conversions of upstream exon sequences especially for those introns targeting protein-coding genes. We also detected phylogenetic congruence between the intron and exon trees at each individual locus, consistent with the ancestral mitochondria of C. militaris as having all eight introns. This study helps to explain the evolution of C. militaris mitochondrial genomes and will facilitate population genetic studies of this medicinally important fungus. Copyright © 2015 Elsevier Inc. All rights reserved.

  12. Enhanced Performance Controller Design for Stochastic Systems by Adding Extra State Estimation onto the Existing Closed Loop Control

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Yuyang; Zhang, Qichun; Wang, Hong

    2016-08-30

    To enhance the performance of the tracking property , this paper presents a novel control algorithm for a class of linear dynamic stochastic systems with unmeasurable states, where the performance enhancement loop is established based on Kalman filter. Without changing the existing closed loop with the PI controller, the compensative controller is designed to minimize the variances of the tracking errors using the estimated states and the propagation of state variances. Moreover, the stability of the closed-loop systems has been analyzed in the mean-square sense. A simulated example is included to show the effectiveness of the presented control algorithm, where encouraging results have been obtained.

  13. A Network Traffic Control Enhancement Approach over Bluetooth Networks

    DEFF Research Database (Denmark)

    Son, L.T.; Schiøler, Henrik; Madsen, Ole Brun

    2003-01-01

    This paper analyzes network traffic control issues in Bluetooth data networks as convex optimization problem. We formulate the problem of maximizing of total network flows and minimizing the costs of flows. An adaptive distributed network traffic control scheme is proposed as an approximated...... as capacity limitations and flow requirements in the network. Simulation shows that the performance of Bluetooth networks could be improved by applying the adaptive distributed network traffic control scheme...... solution of the stated optimization problem that satisfies quality of service requirements and topologically induced constraints in Bluetooth networks, such as link capacity and node resource limitations. The proposed scheme is decentralized and complies with frequent changes of topology as well...

  14. Traffic signal control enhancements under vehicle infrastructure integration systems.

    Science.gov (United States)

    2011-12-01

    Most current traffic signal systems are operated using a very archaic traffic-detection simple binary : logic (vehicle presence/non presence information). The logic was originally developed to provide input for old : electro-mechanical controllers th...

  15. Intronic sequences are required for AINTEGUMENTA-LIKE6 expression in Arabidopsis flowers.

    Science.gov (United States)

    Krizek, Beth A

    2015-10-12

    The AINTEGUMENTA-LIKE6/PLETHORA3 (AIL6/PLT3) gene of Arabidopsis thaliana is a key regulator of growth and patterning in both shoots and roots. AIL6 encodes an AINTEGUMENTA-LIKE/PLETHORA (AIL/PLT) transcription factor that is expressed in the root stem cell niche, the peripheral region of the shoot apical meristem and young lateral organ primordia. In flowers, AIL6 acts redundantly with AINTEGUMENTA (ANT) to regulate floral organ positioning, growth, identity and patterning. Experiments were undertaken to define the genomic regions required for AIL6 function and expression in flowers. Transgenic plants expressing a copy of the coding region of AIL6 in the context of 7.7 kb of 5' sequence and 919 bp of 3' sequence (AIL6:cAIL6-3') fail to fully complement AIL6 function when assayed in the ant-4 ail6-2 double mutant background. In contrast, a genomic copy of AIL6 with the same amount of 5' and 3' sequence (AIL6:gAIL6-3') can fully complement ant-4 ail6-2. In addition, a genomic copy of AIL6 with 590 bp of 5' sequence and 919 bp of 3' sequence (AIL6m:gAIL6-3') complements ant-4 ail6-2 and contains all regulatory elements needed to confer normal AIL6 expression in inflorescences. Efforts to map cis-regulatory elements reveal that the third intron of AIL6 contains enhancer elements that confer expression in young flowers but in a broader pattern than that of AIL6 mRNA in wild-type flowers. Some AIL6:gAIL6-3' and AIL6m:gAIL6-3' lines confer an over-rescue phenotype in the ant-4 ail6-2 background that is correlated with higher levels of AIL6 mRNA accumulation. The results presented here indicate that AIL6 intronic sequences serve as transcriptional enhancer elements. In addition, the results show that increased expression of AIL6 can partially compensate for loss of ANT function in flowers.

  16. Enhancing Schistosomiasis Control Strategy for Zimbabwe: Building on Past Experiences

    Directory of Open Access Journals (Sweden)

    Moses J. Chimbari

    2012-01-01

    Full Text Available Schistosoma haematobium and Schistosoma mansoni are prevalent in Zimbabwe to levels that make schistosomiasis a public health problem. Following three national surveys to map the disease prevalence, a national policy on control of schistosomiasis and soil transmitted helminths is being developed. This paper reviews the experiences that Zimbabwe has in the area of schistosomiasis control with a view to influence policy. A case study approach to highlight key experiences and outcomes was adopted. The benefits derived from intersectoral collaboration that led to the development of a model irrigation scheme that incorporates schistosomiasis control measures are highlighted. Similarly, the benefits of using plant molluscicides and fish and duck biological agents (Sargochromis codringtonii and Cairina moschata are highlighted. Emphasis was also placed on the importance of utilizing locally developed water and sanitation technologies and the critical human resource base in the area of schistosomiasis developed over years. After synthesis of the case studies presented, it was concluded that while there is a need to follow the WHO recommended guidelines for schistosomiasis control it is important to develop a control strategy that is informed by work already done in the country. The importance of having a policy and local guidelines for schistosomiasis control is emphasized.

  17. Alternative splicing of a group II intron in a surface layer protein gene in Clostridium tetani.

    Science.gov (United States)

    McNeil, Bonnie A; Simon, Dawn M; Zimmerly, Steven

    2014-02-01

    Group II introns are ribozymes and retroelements found in bacteria, and are thought to have been the ancestors of nuclear pre-mRNA introns. Whereas nuclear introns undergo prolific alternative splicing in some species, group II introns are not known to carry out equivalent reactions. Here we report a group II intron in the human pathogen Clostridium tetani, which undergoes four alternative splicing reactions in vivo. Together with unspliced transcript, five mRNAs are produced, each encoding a distinct surface layer protein isoform. Correct fusion of exon reading frames requires a shifted 5' splice site located 8 nt upstream of the canonical boundary motif. The shifted junction is accomplished by an altered IBS1-EBS1 pairing between the intron and 5' exon. Growth of C. tetani under a variety of conditions did not result in large changes in alternative splicing levels, raising the possibility that alternative splicing is constitutive. This work demonstrates a novel type of gene organization and regulation in bacteria, and provides an additional parallel between group II and nuclear pre-mRNA introns.

  18. Curcumin enhances human macrophage control of Mycobacterium tuberculosis infection.

    Science.gov (United States)

    Bai, Xiyuan; Oberley-Deegan, Rebecca E; Bai, An; Ovrutsky, Alida R; Kinney, William H; Weaver, Michael; Zhang, Gong; Honda, Jennifer R; Chan, Edward D

    2016-07-01

    With the worldwide emergence of highly drug-resistant tuberculosis (TB), novel agents that have direct antimycobacterial effects or that enhance host immunity are urgently needed. Curcumin is a polyphenol responsible for the bright yellow-orange colour of turmeric, a spice derived from the root of the perennial herb Curcuma longa. Curcumin is a potent inducer of apoptosis-an effector mechanism used by macrophages to kill intracellular Mycobacterium tuberculosis (MTB). An in vitro human macrophage infection model was used to determine the effects of curcumin on MTB survival. We found that curcumin enhanced the clearance of MTB in differentiated THP-1 human monocytes and in primary human alveolar macrophages. We also found that curcumin was an inducer of caspase-3-dependent apoptosis and autophagy. Curcumin mediated these anti-MTB cellular functions, in part, via inhibition of nuclear factor-kappa B (NFκB) activation. Curcumin protects against MTB infection in human macrophages. The host-protective role of curcumin against MTB in macrophages needs confirmation in an animal model; if validated, the immunomodulatory anti-TB effects of curcumin would be less prone to drug resistance development. © 2016 Asian Pacific Society of Respirology.

  19. Origin and evolution of chloroplast group I introns in lichen algae.

    Science.gov (United States)

    Del Hoyo, Alicia; Álvarez, Raquel; Gasulla, Francisco; Casano, Leonardo Mario; Del Campo, Eva María

    2018-02-01

    The history of group I introns is characterized by repeated horizontal transfers, even among phylogenetically distant species. The symbiogenetic thalli of lichens are good candidates for the horizontal transfer of genetic material among distantly related organisms, such as fungi and green algae. The main goal of this study was to determine whether there were different trends in intron distribution and properties among Chlorophyte algae based on their phylogenetic relationships and living conditions. Therefore, we investigated the occurrence, distribution and properties of group I introns within the chloroplast LSU rDNA in 87 Chlorophyte algae including lichen and free-living Trebouxiophyceae compared to free-living non-Trebouxiophyceae species. Overall, our findings showed that there was high diversity of group I introns and homing endonucleases (HEs) between Trebouxiophyceae and non-Trebouxiophyceae Chlorophyte algae, with divergence in their distribution patterns, frequencies and properties. However, the differences between lichen Trebouxiophyceae and free-living Trebouxiophyceae were smaller. An exception was the cL2449 intron, which was closely related to ω elements in yeasts. Such introns seem to occur more frequently in lichen Trebouxiophyceae compared to free-living Trebouxiophyceae. Our data suggest that lichenization and maintenance of lichen symbiosis for millions of years of evolution may have facilitated horizontal transfers of specific introns/HEs between symbionts. The data also suggest that sequencing of more chloroplast genes harboring group I introns in diverse algal groups may help us to understand the group I intron/HE transmission process within these organisms. © 2017 Phycological Society of America.

  20. In vivo expression of the nucleolar group I intron-encoded I-dirI homing endonuclease involves the removal of a spliceosomal intron

    DEFF Research Database (Denmark)

    Vader, A; Nielsen, Henrik; Johansen, S

    1999-01-01

    as truncation and polyadenylation downstream of the ORF 3' end. A spliceosomal intron, the first to be reported within a group I intron and the rDNA, is removed before the I-DirI mRNA associates with the polysomes. Taken together, our results imply that DiSSU1 uses a unique combination of intron......The Didymium iridis DiSSU1 intron is located in the nuclear SSU rDNA and has an unusual twin-ribozyme organization. One of the ribozymes (DiGIR2) catalyses intron excision and exon ligation. The other ribozyme (DiGIR1), which along with the endonuclease-encoding I-DirI open reading frame (ORF......) is inserted in DiGIR2, carries out hydrolysis at internal processing sites (IPS1 and IPS2) located at its 3' end. Examination of the in vivo expression of DiSSU1 shows that after excision, DiSSU1 is matured further into the I-DirI mRNA by internal DiGIR1-catalysed cleavage upstream of the ORF 5' end, as well...

  1. Size and compositionally controlled manganese ferrite nanoparticles with enhanced magnetization

    International Nuclear Information System (INIS)

    Vamvakidis, K.; Sakellari, D.; Angelakeris, M.; Dendrinou-Samara, C.

    2013-01-01

    A facile solvothermal approach was used to synthesize stable, superparamagnetic manganese ferrite nanoparticles with relatively small sizes ( 2 to Mn(acac) 3 , different sizes, 8 and 5 nm, of MnFe 2 O 4 nanoparticles were obtained respectively, while by tailoring the synthetic conditions iron-rich Mn 0.77 Fe 2.23 O 4 nanoparticles have been isolated with identical sizes and enhanced saturation magnetization. The magnetization values increased from 58.2 to 68.3 Am 2 /kg and from 53.3 to 60.2 Am 2 /kg for the nanoparticles of 8 and 5 nm, respectively. Blocking temperature (T B ), ranging from 80 to 180 K, and anisotropy constant (K eff ), ranging from 1.5 × 10 5 to 4.9 × 10 5 J/m 3 , were found higher for the iron-rich samples and associated with size and composition effects.

  2. Cognitive control in auditory working memory is enhanced in musicians

    DEFF Research Database (Denmark)

    Pallesen, Karen Johanne; Brattico, Elvira; Bailey, Christopher J.

    2010-01-01

    Musical competence may confer cognitive advantages that extend beyond processing of familiar musical sounds. Behavioural evidence indicates a general enhancement of both working memory and attention in musicians. It is possible that musicians, due to their training, are better able to maintain...... focus on task-relevant stimuli, a skill which is crucial to working memory. We measured the blood oxygenation-level dependent (BOLD) activation signal in musicians and non-musicians during working memory of musical sounds to determine the relation among performance, musical competence and generally...... hemisphere, and bilaterally in the posterior dorsal prefrontal cortex and anterior cingulate gyrus. The relationship between the task performance and the magnitude of the BOLD response was more positive in musicians than in non-musicians, particularly during the most difficult working memory task...

  3. Technology to enhance vegetable quality by the light environment control

    International Nuclear Information System (INIS)

    Higashio, H.

    2004-01-01

    Recent research information about the physiological function of the ultraviolet (UV) rays on plants, and in particular the technology to enhance vegetable quality with UV which we are studying at present are introduced. 1. UV rays have various physiological effects on plants, and the effect differs depending on wavelength. Flavonoid is thought to be one of the materials protecting against the UV rays. Some inductive mechanisms of flavonoid production in plant upon exposure to the UV rays are revealed, but optical receptors have not been found yet. 2. The UV rays influence the production of vitamins and flavonoid compounds such as anthocyanin and quercetin. UV rays irradiation technology is being developed as one of the means to increase levels of these compounds and so produce high quality vegetables

  4. Control Design of VSIs to Enhance Transient Performance in Microgrids

    DEFF Research Database (Denmark)

    Federico, de Bosio; Antonio DeSouza Ribeiro, Luiz; Savaghebi, Mehdi

    2016-01-01

    This paper discusses the control design for an islanded microgrid in order to ensure acceptable performance in terms of voltage quality and load sharing by focusing on transient conditions. To this aim, state feedback decoupling approach has been applied. Experimental tests have been performed...

  5. Financial Control Measures and the Enhancement of Administrative ...

    African Journals Online (AJOL)

    The major findings were that the principals have not adopted budget preparation, budget implementation and internal auditing for the control of school finances. It was found that there is significant relationship between the variables and principals' administrative effectiveness. The recommendations made based on the ...

  6. A new strategy to enhance polysialic acid production by controlling ...

    African Journals Online (AJOL)

    Polysialic acid (PSA) is a new pharmaceutical material used in control release of protein drugs and as scaffold material in biomedical applications. It is also a vital source of sialic acid and its derivatives. In this paper, we demonstrated that the substrate sorbitol has significant effect on bacterial growth and PSA formation in ...

  7. Intron Retention and TE Exonization Events in ZRANB2

    Directory of Open Access Journals (Sweden)

    Sang-Je Park

    2012-01-01

    Full Text Available The Zinc finger, RAN-binding domain-containing protein 2 (ZRANB2, contains arginine/serine-rich (RS domains that mediate its function in the regulation of alternative splicing. The ZRANB2 gene contains 2 LINE elements (L3b, Plat_L3 between the 9th and 10th exons. We identified the exonization event of a LINE element (Plat_L3. Using genomic PCR, RT-PCR amplification, and sequencing of primate DNA and RNA samples, we analyzed the evolutionary features of ZRANB2 transcripts. The results indicated that 2 of the LINE elements were integrated in human and all of the tested primate samples (hominoids: 3 species; Old World monkey: 8 species; New World monkey: 6 species; prosimian: 1 species. Human, rhesus monkey, crab-eating monkey, African-green monkey, and marmoset harbor the exon derived from LINE element (Plat_L3. RT-PCR amplification revealed the long transcripts and their differential expression patterns. Intriguingly, these long transcripts were abundantly expressed in Old World monkey lineages (rhesus, crab-eating, and African-green monkeys and were expressed via intron retention (IR. Thus, the ZRANB2 gene produces 3 transcript variants in which the Cterminus varies by transposable elements (TEs exonization and IR mechanisms. Therefore, ZRANB2 is valuable for investigating the evolutionary mechanisms of TE exonization and IR during primate evolution.

  8. Control Strategies for Islanded Microgrid using Enhanced Hierarchical Control Structure with Multiple Current-Loop Damping Schemes

    DEFF Research Database (Denmark)

    Han, Yang; Shen, Pan; Zhao, Xin

    2017-01-01

    In this paper, the modeling, controller design, and stability analysis of the islanded microgrid (MG) using enhanced hierarchical control structure with multiple current loop damping schemes is proposed. The islanded MG is consisted of the parallel-connected voltage source inverters using LCL...

  9. An intronic LINE-1 insertion in MERTK is strongly associated with retinopathy in Swedish Vallhund dogs.

    Directory of Open Access Journals (Sweden)

    Richard Everson

    Full Text Available The domestic dog segregates a significant number of inherited progressive retinal diseases, several of which mirror human retinal diseases and which are collectively termed progressive retinal atrophy (PRA. In 2014, a novel form of PRA was reported in the Swedish Vallhund breed, and the disease was mapped to canine chromosome 17. The causal mutation was not identified, but expression analyses of the retinas of affected Vallhunds demonstrated a 6-fold increased expression of the MERTK gene compared to unaffected dogs. Using 24 retinopathy cases and 97 controls with no clinical signs of retinopathy, we replicated the chromosome 17 association in Swedish Vallhunds from the UK and aimed to elucidate the causal variant underlying this association using whole genome sequencing (WGS of an affected dog. This revealed a 6-8 kb insertion in intron 1 of MERTK that was not present in WGS of 49 dogs of other breeds. Sequencing and BLASTN analysis of the inserted segment was consistent with the insertion comprising a full-length intact LINE-1 retroelement. Testing of the LINE-1 insertion for association with retinopathy in the UK set of 24 cases and 97 controls revealed a strong statistical association (P-value 6.0 x 10-11 that was subsequently replicated in the original Finnish study set (49 cases and 89 controls (P-value 4.3 x 10-19. In a pooled analysis of both studies (73 cases and 186 controls, the LINE-1 insertion was associated with a ~20-fold increased risk of retinopathy (odds ratio 23.41, 95% confidence intervals 10.99-49.86, P-value 1.3 x 10-27. Our study adds further support for regulatory disruption of MERTK in Swedish Vallhund retinopathy; however, further work is required to establish a functional overexpression model. Future work to characterise the mechanism by which this intronic mutation disrupts gene regulation will further improve the understanding of MERTK biology and its role in retinal function.

  10. PLS-based memory control scheme for enhanced process monitoring

    KAUST Repository

    Harrou, Fouzi

    2017-01-20

    Fault detection is important for safe operation of various modern engineering systems. Partial least square (PLS) has been widely used in monitoring highly correlated process variables. Conventional PLS-based methods, nevertheless, often fail to detect incipient faults. In this paper, we develop new PLS-based monitoring chart, combining PLS with multivariate memory control chart, the multivariate exponentially weighted moving average (MEWMA) monitoring chart. The MEWMA are sensitive to incipient faults in the process mean, which significantly improves the performance of PLS methods and widen their applicability in practice. Using simulated distillation column data, we demonstrate that the proposed PLS-based MEWMA control chart is more effective in detecting incipient fault in the mean of the multivariate process variables, and outperform the conventional PLS-based monitoring charts.

  11. Enhancing sensorimotor activity by controlling virtual objects with gaze.

    Directory of Open Access Journals (Sweden)

    Cristián Modroño

    Full Text Available This fMRI work studies brain activity of healthy volunteers who manipulated a virtual object in the context of a digital game by applying two different control methods: using their right hand or using their gaze. The results show extended activations in sensorimotor areas, not only when participants played in the traditional way (using their hand but also when they used their gaze to control the virtual object. Furthermore, with the exception of the primary motor cortex, regional motor activity was similar regardless of what the effector was: the arm or the eye. These results have a potential application in the field of the neurorehabilitation as a new approach to generate activation of the sensorimotor system to support the recovery of the motor functions.

  12. The Unspoken Consequence of Command, Control Communications Technology: Enhanced Micromanagement by Risk-Averse Commanders

    National Research Council Canada - National Science Library

    Carozza, John

    2004-01-01

    .... However, along with its benefits, this command, control and communications (C3) network includes the dangerous consequence of eroding the autonomy of tactical command through enhanced micromanagement by risk-averse operational commanders...

  13. Pest species diversity enhances control of spider mites and whiteflies by a generalist phytoseiid predator

    NARCIS (Netherlands)

    Messelink, G.J.; van Maanen, R.; van Holstein-Saj, R.; Sabelis, M.W.; Janssen, A.

    2010-01-01

    To test the hypothesis that pest species diversity enhances biological pest control with generalist predators, we studied the dynamics of three major pest species on greenhouse cucumber: Western flower thrips, Frankliniella occidentalis (Pergande), greenhouse whitefly, Trialeurodes vaporariorum

  14. Identification of a nuclear matrix attachment region like sequence in the last intron of PI3Kγ

    International Nuclear Information System (INIS)

    Dai Bingbing; Ying Lei; Cai Rong; Li Ying; Zhang Xingqian; Lu Jian; Qian Guanxiang

    2006-01-01

    MARs are not only the structure bases of chromatin higher order structure but also have much biological significance. In this study, the whole sequence of about 100 kb in length from BAC clone of GS1-223D4 (GI: 5931478), in which human PI3Kγ gene is localized, was analyzed by two online-based computer programs, MARFinder and SMARTest. A strong potential MAR was predicted in the last and largest intron of PI3Kγ. The predicted 2 kb MAR, we refer to PIMAR, was further analyzed through biochemical methods in vitro and in vivo. The results showed that the PIMAR could be associated with nuclear matrices from HeLa cells both in vitro and in vivo. Further reporter gene analysis showed that in the transient transfection the expression of reporter gene linked with reversed PIMAR was repressed slightly, while in stably integrated state, the luciferase reporter both linked with reversed and orientated PIMAR was enhanced greatly in NIH-3T3 and K-562. These results suggest that the PIMAR maybe has the capacity of shielding integrated heterogeneous gene from chromatin position effect. Through combination of computer program analysis with confirmation by biochemical methods, we identified, for First time, a 2 kb matrix attachment region like sequence in the last intron of human PI3Kγ

  15. Security-Enhanced Push Button Configuration for Home Smart Control.

    Science.gov (United States)

    Han, Junghee; Park, Taejoon

    2017-06-08

    With the emergence of smart and converged home services, the need for the secure and easy interplay of various devices has been increased. Push Button Configuration (PBC) is one of the technologies proposed for easy set-up of a secure session between IT and consumer devices. Although the Wi-Fi Direct specification explicitly states that all devices must support the PBC method, its applicability is very limited. This is because the security vulnerability of PBC can be maliciously exploited so that attackers can make illegitimate sessions with consumer devices. To address this problem, this paper proposes a novel Security-enhanced PBC (SePBC) scheme with which we can uncover suspicious or malicious devices. The proposed mechanism has several unique features. First, we develop a secure handshake distance measurement protocol by preventing an adversary sitting outside the region from maliciously manipulating its distance to be fake. Second, it is compatible with the original Wi-Fi PBC without introducing a brand-new methodology. Finally, SePBC uses lightweight operations without CPU-intensive cryptography computation and employs inexpensive H/W. Moreover, it needs to incur little overhead when there is no attack. This paper also designs and implements the proposed SePBC in the real world. Our experimental results and analysis show that the proposed SePBC scheme effectively defeats attacks on PBC while minimizing the modification of the original PBC equipment.

  16. Genetic Manipulation of Lactococcus lactis by Using Targeted Group II Introns: Generation of Stable Insertions without Selection

    Science.gov (United States)

    Frazier, Courtney L.; San Filippo, Joseph; Lambowitz, Alan M.; Mills, David A.

    2003-01-01

    Despite their commercial importance, there are relatively few facile methods for genomic manipulation of the lactic acid bacteria. Here, the lactococcal group II intron, Ll.ltrB, was targeted to insert efficiently into genes encoding malate decarboxylase (mleS) and tetracycline resistance (tetM) within the Lactococcus lactis genome. Integrants were readily identified and maintained in the absence of a selectable marker. Since splicing of the Ll.ltrB intron depends on the intron-encoded protein, targeted invasion with an intron lacking the intron open reading frame disrupted TetM and MleS function, and MleS activity could be partially restored by expressing the intron-encoded protein in trans. Restoration of splicing from intron variants lacking the intron-encoded protein illustrates how targeted group II introns could be used for conditional expression of any gene. Furthermore, the modified Ll.ltrB intron was used to separately deliver a phage resistance gene (abiD) and a tetracycline resistance marker (tetM) into mleS, without the need for selection to drive the integration or to maintain the integrant. Our findings demonstrate the utility of targeted group II introns as a potential food-grade mechanism for delivery of industrially important traits into the genomes of lactococci. PMID:12571038

  17. Recent mobility of plastid encoded group II introns and twintrons in five strains of the unicellular red alga Porphyridium

    Directory of Open Access Journals (Sweden)

    Marie-Mathilde Perrineau

    2015-06-01

    Full Text Available Group II introns are closely linked to eukaryote evolution because nuclear spliceosomal introns and the small RNAs associated with the spliceosome are thought to trace their ancient origins to these mobile elements. Therefore, elucidating how group II introns move, and how they lose mobility can potentially shed light on fundamental aspects of eukaryote biology. To this end, we studied five strains of the unicellular red alga Porphyridium purpureum that surprisingly contain 42 group II introns in their plastid genomes. We focused on a subset of these introns that encode mobility-conferring intron-encoded proteins (IEPs and found them to be distributed among the strains in a lineage-specific manner. The reverse transcriptase and maturase domains were present in all lineages but the DNA endonuclease domain was deleted in vertically inherited introns, demonstrating a key step in the loss of mobility. P. purpureum plastid intron RNAs had a classic group IIB secondary structure despite variability in the DIII and DVI domains. We report for the first time the presence of twintrons (introns-within-introns, derived from the same mobile element in Rhodophyta. The P. purpureum IEPs and their mobile introns provide a valuable model for the study of mobile retroelements in eukaryotes and offer promise for biotechnological applications.

  18. Enhanced Temperature Control Method Using ANFIS with FPGA

    Directory of Open Access Journals (Sweden)

    Chiung-Wei Huang

    2014-01-01

    Full Text Available Temperature control in etching process is important for semiconductor manufacturing technology. However, pressure variations in vacuum chamber results in a change in temperature, worsening the accuracy of the temperature of the wafer and the speed and quality of the etching process. This work develops an adaptive network-based fuzzy inference system (ANFIS using a field-programmable gate array (FPGA to improve the effectiveness. The proposed method adjusts every membership function to keep the temperature in the chamber stable. The improvement of the proposed algorithm is confirmed using a medium vacuum (MV inductively-coupled plasma- (ICP- type etcher.

  19. Single-dose protection against Plasmodium berghei by a simian adenovirus vector using a human cytomegalovirus promoter containing intron A.

    Science.gov (United States)

    Sridhar, S; Reyes-Sandoval, A; Draper, S J; Moore, A C; Gilbert, S C; Gao, G P; Wilson, J M; Hill, A V S

    2008-04-01

    Human adenovirus serotype 5 (AdH5) vector vaccines elicit strong immune responses to the encoded antigen and have been used in various disease models. We designed AdH5 vectors expressing antigen under the control of a human cytomegalovirus (HCMV) immediate-early promoter containing its intron A sequence. The transcriptional levels of antigen and immune responses to antigen for vectors with the HCMV promoter with the intron A sequence (LP) were greater than those for AdH5 vectors using the HCMV promoter sequence without intron A (SP). We compared an E1E3-deleted AdH5 adenoviral vector, which affords more space for insertion of foreign sequences, and showed it to be as immunogenic as an E1-deleted AdH5 vector. Neutralizing antibodies to AdH5 limit the efficacy of vaccines based on the AdH5 serotype, and simian adenoviral vectors offer an attractive option to overcome this problem. We constructed E1E3-deleted human and simian adenoviral vectors encoding the pre-erythrocytic-stage malarial antigen Plasmodium berghei circumsporozoite protein. We compared the immunogenicity and efficacy of AdC6, a recombinant simian adenovirus serotype 6 vector, in a murine malaria model to those of AdH5 and the poxviral vectors MVA and FP9. AdC6 induced sterile protection from a single dose in 90% of mice, in contrast to AdH5 (25%) and poxviral vectors MVA and FP9 (0%). Adenoviral vectors maintained potent CD8(+) T-cell responses for a longer period after immunization than did poxviral vectors and mainly induced an effector memory phenotype of cells. Significantly, AdC6 was able to maintain protection in the presence of preexisting immunity to AdH5.

  20. Comparative analysis of information contents relevant to recognition of introns in many species

    Directory of Open Access Journals (Sweden)

    Gotoh Osamu

    2011-01-01

    Full Text Available Abstract Background The basic process of RNA splicing is conserved among eukaryotic species. Three signals (5' and 3' splice sites and branch site are commonly used to directly conduct splicing, while other features are also related to the recognition of an intron. Although there is experimental evidence pointing to the significant species specificities in the features of intron recognition, a quantitative evaluation of the divergence of these features among a wide variety of eukaryotes has yet to be conducted. Results To better understand the splicing process from the viewpoints of evolution and information theory, we collected introns from 61 diverse species of eukaryotes and analyzed the properties of the nucleotide sequences relevant to splicing. We found that trees individually constructed from the five features (the three signals, intron length, and nucleotide composition within an intron roughly reflect the phylogenetic relationships among the species but sometimes extensively deviate from the species classification. The degree of topological deviation of each feature tree from the reference trees indicates the lowest discordance for the 5' splicing signal, followed by that for the 3' splicing signal, and a considerably greater discordance for the other three features. We also estimated the relative contributions of the five features to short intron recognition in each species. Again, moderate correlation was observed between the similarities in pattern of short intron recognition and the genealogical relationships among the species. When mammalian introns were categorized into three subtypes according to their terminal dinucleotide sequences, each subtype segregated into a nearly monophyletic group, regardless of the host species, with respect to the 5' and 3' splicing signals. It was also found that GC-AG introns are extraordinarily abundant in some species with high genomic G + C contents, and that the U12-type spliceosome might make a

  1. Novel intron markers to study the phylogeny of closely related mammalian species

    Directory of Open Access Journals (Sweden)

    Castresana Jose

    2010-11-01

    Full Text Available Abstract Background Multilocus phylogenies can be used to infer the species tree of a group of closely related species. In species trees, the nodes represent the actual separation between species, thus providing essential information about their evolutionary history. In addition, multilocus phylogenies can help in analyses of species delimitation, gene flow and genetic differentiation within species. However, few adequate markers are available for such studies. Results In order to develop nuclear markers that can be useful in multilocus studies of mammals, we analyzed the mammalian genomes of human, chimpanzee, macaque, dog and cow. Rodents were excluded due to their unusual genomic features. Introns were extracted from the mammalian genomes because of their greater genetic variability and ease of amplification from the flanking exons. To an initial set of more than 10,000 one-to-one orthologous introns we applied several filters to select introns that belong to single-copy genes, show neutral evolutionary rates and have an adequate length for their amplification. This analysis led to a final list of 224 intron markers randomly distributed along the genome. To experimentally test their validity, we amplified twelve of these introns in a panel of six mammalian species. The result was that seven of these introns gave rise to a PCR band of the expected size in all species. In addition, we sequenced these bands and analyzed the accumulation of substitutions in these introns in five pairs of closely related species. The results showed that the estimated genetic distances in the five species pairs was quite variable among introns and that this divergence cannot be directly predicted from the overall intron divergence in mammals. Conclusions We have designed a new set of 224 nuclear introns with optimal features for the phylogeny of closely related mammalian species. A large proportion of the introns tested experimentally showed a perfect amplification

  2. Applying Space Technology to Enhance Control of an Artificial Arm

    Science.gov (United States)

    Atkins, Diane; Donovan, William H.; Novy, Mara; Abramczyk, Robert

    1997-01-01

    At the present time, myoelectric prostheses perform only one function of the hand: open and close with the thumb, index and middle finger coming together to grasp various shaped objects. To better understand the limitations of the current single-function prostheses and the needs of the individuals who use them, The Institute for Rehabilitation and Research (TIRR), sponsored by the National Institutes of Health (August 1992 - November 1994), surveyed approximately 2500 individuals with upper limb loss. When asked to identify specific features of their current electric prosthesis that needed improvement, the survey respondents overwhelmingly identified the lack of wrist and finger movement as well as poor control capability. Simply building a mechanism with individual finger and wrist motion is not enough. Individuals with upper limb loss tend to reject prostheses that require continuous visual monitoring and concentration to control. Robotics researchers at NASA's Johnson Space Center (JSC) and Rice University have made substantial progress in myoelectric teleoperation. A myoelectric teleoperation system translates signals generated by an able-bodied robot operator's muscles during hand motions into commands that drive a robot's hand through identical motions. Farry's early work in myoelectric teleoperation used variations over time in the myoelectric spectrum as inputs to neural networks to discriminate grasp types and thumb motions. The resulting schemes yielded up to 93% correct classification on thumb motions. More recently, Fernandez achieved 100% correct non-realtime classification of thumb abduction, extension, and flexion on the same myoelectric data. Fernandez used genetic programming to develop functions that discriminate between thumb motions using myoelectric signal parameters. Genetic programming (GP) is an evolutionary programming method where the computer can modify the discriminating functions' form to improve its performance, not just adjust

  3. Asthma and COPD in cystic fibrosis intron-8 5T carriers. A population-based study

    DEFF Research Database (Denmark)

    Dahl, Morten; Tybjaerg-Hansen, Anne; Lange, Peter

    2005-01-01

    Carriers of cystic fibrosis intron-8 5T alleles with high exon-9 skipping could have increased annual lung function decline and increased risk for asthma or chronic obstructive pulmonary disease (COPD).......Carriers of cystic fibrosis intron-8 5T alleles with high exon-9 skipping could have increased annual lung function decline and increased risk for asthma or chronic obstructive pulmonary disease (COPD)....

  4. Unusual group II introns in bacteria of the Bacillus cereus group.

    Science.gov (United States)

    Tourasse, Nicolas J; Stabell, Fredrik B; Reiter, Lillian; Kolstø, Anne-Brit

    2005-08-01

    A combination of sequence and structure analysis and reverse transcriptase PCR experiments was used to characterize the group II introns in the complete genomes of two strains of the pathogen Bacillus cereus. While B. cereus ATCC 14579 harbors a single intron element in the chromosome, B. cereus ATCC 10987 contains three introns in the chromosome and four in its 208-kb pBc10987 plasmid. The most striking finding is the presence in B. cereus ATCC 10987 of an intron [B.c.I2(a)] located on the reverse strand of a gene encoding a putative cell surface protein which appears to be correlated to strains of clinical origin. Because of the opposite orientation of B.c.I2(a), the gene is disrupted. Even more striking is that B.c.I2(a) splices out of an RNA transcript corresponding to the opposite DNA strand. All other intragenic introns studied here are inserted in the same orientation as their host genes and splice out of the mRNA in vivo, setting the flanking exons in frame. Noticeably, B.c.I3 in B. cereus ATCC 10987 represents the first example of a group II intron entirely included within a conserved replication gene, namely, the alpha subunit of DNA polymerase III. Another striking finding is that the observed 3' splice site of B.c.I4 occurs 56 bp after the predicted end of the intron. This apparently unusual splicing mechanism may be related to structural irregularities in the 3' terminus. Finally, we also show that the intergenic introns of B. cereus ATCC 10987 are transcribed with their upstream genes and do splice in vivo.

  5. Clinical significance of intronic variants in BRAF inhibitor resistant melanomas with altered BRAF transcript splicing

    OpenAIRE

    Pupo, Gulietta M.; Boyd, Suzanah C.; Fung, Carina; Carlino, Matteo S.; Menzies, Alexander M.; Pedersen, Bernadette; Johansson, Peter; Hayward, Nicholas K.; Kefford, Richard F.; Scolyer, Richard A.; Long, Georgina V.; Rizos, Helen

    2017-01-01

    Alternate BRAF splicing is the most common mechanism of acquired resistance to BRAF inhibitor treatment in melanoma. Recently, alternate BRAF exon 4?8 splicing was shown to involve an intronic mutation, located 51 nucleotides upstream of BRAF exon 9 within a predicted splicing branch point. This intronic mutation was identified in a single cell line but has not been examined in vivo. Herein we demonstrate that in three melanomas biopsied from patients with acquired resistance to BRAF inhibito...

  6. Control of nano-structure for enhancing the superconductors' performance

    International Nuclear Information System (INIS)

    Dou, S.X.

    2003-01-01

    Full text: In this talk I will show that the solution to a number of stumbling blocks in bringing high temperature superconductors (HTS) and MgB 2 to commercial application depends critically on the decisive role of materials engineering, in particular, the development of nanomaterials and nanofabrication. Large-scale superconducting electric devices for the power industry will require low-loss high J c wires capable of operating at temperatures where cryogenic losses are tolerable. This restricts the materials choice to the HTS and MgB 2 . Further development and growth of the field depends on the solution of fundamental materials and fabrication problems directed towards increases in flux pinning and critical current density (J c ). In order to secure the future of superconductor technology it will be essential to increase the J c by introducing effective pinning sites at the nanoscales level to enhance the superconductors' performance. This talk will provide evidences that the great breakthrough made since the discovery of HTS is largely related to the advancement of nano-technology. I will present details on the nano-SiC doping into MgB 2 wires, resulting in orders of magnitude in critical current density. Compared to the un-doped sample, J c for the 10wt% SiC-doped sample increased by a factor of 32 at 5K and 8T, 42 at 20K and 5T, and 14 at 30K and 2T. At 20K and 2T, the J c for the doped sample was 2.4x10 5 A/cm 2 , which is comparable to J c values for the best Ag/Bi-2223 tapes. At 20K and 4T, J c was twice as high as for the best MgB 2 thin films and an order of magnitude higher than for the best Fe/MgB 2 tapes The magnetic J c is consistent with the transport J c which remains at 20,000A/cm 2 even at 10T and 5K for the doped sample, an order of magnitude higher than the undoped one Because of such high performance, it is anticipated that the future MgB 2 conductors will be made using a formula of MgB x Si y C z instead of pure MgB 2

  7. An approach to enhanced control room crew performance

    International Nuclear Information System (INIS)

    Frye, S.R.

    1988-01-01

    The function of a nuclear power plant control room team is similar to that of an airline cockpit crew or a critical task military team such as a flight crew, tank crew, combat squad or platoon. These teams encounter many of the same problems or challenges in their environments when dealing with abnormal or emergency situations. The competency of these teams in bringing about successful conclusions in situations depends on their ability to coordinate their actions. This is often referred to as teamwork and includes the interactions between team members which must occur during highly critical situations. The purpose of this paper is to present team skills training and the advances made in this crucial area by utilizing both classroom and high fidelity simulator training

  8. tRNA-like recognition of group I introns by a tyrosyl-tRNA synthetase.

    Science.gov (United States)

    Myers, Christopher A; Kuhla, Birte; Cusack, Stephen; Lambowitz, Alan M

    2002-03-05

    The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (CYT-18 protein) functions in splicing group I introns by promoting the formation of the catalytically active RNA structure. Previous work suggested that CYT-18 recognizes a conserved tRNA-like structure of the group I intron catalytic core. Here, directed hydroxyl-radical cleavage assays show that the nucleotide-binding fold and C-terminal domains of CYT-18 interact with the expected group I intron cognates of the aminoacyl-acceptor stem and D-anticodon arms, respectively. Further, three-dimensional graphic modeling, supported by biochemical data, shows that conserved regions of group I introns can be superimposed over interacting regions of the tRNA in a Thermus thermophilus TyrRS/tRNA(Tyr) cocrystal structure. Our results support the hypothesis that CYT-18 and other aminoacyl-tRNA synthetases interact with group I introns by recognizing conserved tRNA-like structural features of the intron RNAs.

  9. Characterization of the molecular basis of group II intron RNA recognition by CRS1-CRM domains.

    Science.gov (United States)

    Keren, Ido; Klipcan, Liron; Bezawork-Geleta, Ayenachew; Kolton, Max; Shaya, Felix; Ostersetzer-Biran, Oren

    2008-08-22

    CRM (chloroplast RNA splicing and ribosome maturation) is a recently recognized RNA-binding domain of ancient origin that has been retained in eukaryotic genomes only within the plant lineage. Whereas in bacteria CRM domains exist as single domain proteins involved in ribosome maturation, in plants they are found in a family of proteins that contain between one and four repeats. Several members of this family with multiple CRM domains have been shown to be required for the splicing of specific plastidic group II introns. Detailed biochemical analysis of one of these factors in maize, CRS1, demonstrated its high affinity and specific binding to the single group II intron whose splicing it facilitates, the plastid-encoded atpF intron RNA. Through its association with two intronic regions, CRS1 guides the folding of atpF intron RNA into its predicted "catalytically active" form. To understand how multiple CRM domains cooperate to achieve high affinity sequence-specific binding to RNA, we analyzed the RNA binding affinity and specificity associated with each individual CRM domain in CRS1; whereas CRM3 bound tightly to the RNA, CRM1 associated specifically with a unique region found within atpF intron domain I. CRM2, which demonstrated only low binding affinity, also seems to form specific interactions with regions localized to domains I, III, and IV. We further show that CRM domains share structural similarities and RNA binding characteristics with the well known RNA recognition motif domain.

  10. Evidence for intron length conservation in a set of mammalian genes associated with embryonic development

    LENUS (Irish Health Repository)

    2011-10-05

    Abstract Background We carried out an analysis of intron length conservation across a diverse group of nineteen mammalian species. Motivated by recent research suggesting a role for time delays associated with intron transcription in gene expression oscillations required for early embryonic patterning, we searched for examples of genes that showed the most extreme conservation of total intron content in mammals. Results Gene sets annotated as being involved in pattern specification in the early embryo or containing the homeobox DNA-binding domain, were significantly enriched among genes with highly conserved intron content. We used ancestral sequences reconstructed with probabilistic models that account for insertion and deletion mutations to distinguish insertion and deletion events on lineages leading to human and mouse from their last common ancestor. Using a randomization procedure, we show that genes containing the homeobox domain show less change in intron content than expected, given the number of insertion and deletion events within their introns. Conclusions Our results suggest selection for gene expression precision or the existence of additional development-associated genes for which transcriptional delay is functionally significant.

  11. Structural Metals in the Group I Intron: A Ribozyme with a Multiple Metal Ion Core

    Energy Technology Data Exchange (ETDEWEB)

    Stahley,M.; Adams, P.; Wang, J.; Strobel, S.

    2007-01-01

    Metal ions play key roles in the folding and function for many structured RNAs, including group I introns. We determined the X-ray crystal structure of the Azoarcus bacterial group I intron in complex with its 5' and 3' exons. In addition to 222 nucleotides of RNA, the model includes 18 Mg2+ and K+ ions. Five of the metals bind within 12 Angstroms of the scissile phosphate and coordinate the majority of the oxygen atoms biochemically implicated in conserved metal-RNA interactions. The metals are buried deep within the structure and form a multiple metal ion core that is critical to group I intron structure and function. Eight metal ions bind in other conserved regions of the intron structure, and the remaining five interact with peripheral structural elements. Each of the 18 metals mediates tertiary interactions, facilitates local bends in the sugar-phosphate backbone or binds in the major groove of helices. The group I intron has a rich history of biochemical efforts aimed to identify RNA-metal ion interactions. The structural data are correlated to the biochemical results to further understand the role of metal ions in group I intron structure and function.

  12. Group II introns break new boundaries: presence in a bilaterian's genome.

    Directory of Open Access Journals (Sweden)

    Yvonne Vallès

    Full Text Available Group II introns are ribozymes, removing themselves from their primary transcripts, as well as mobile genetic elements, transposing via an RNA intermediate, and are thought to be the ancestors of spliceosomal introns. Although common in bacteria and most eukaryotic organelles, they have never been reported in any bilaterian animal genome, organellar or nuclear. Here we report the first group II intron found in the mitochondrial genome of a bilaterian worm. This location is especially surprising, since animal mitochondrial genomes are generally distinct from those of plants, fungi, and protists by being small and compact, and so are viewed as being highly streamlined, perhaps as a result of strong selective pressures for fast replication while establishing germ plasm during early development. This intron is found in the mtDNA of an annelid worm, (an undescribed species of Nephtys, where the complete sequence revealed a 1819 bp group II intron inside the cox1 gene. We infer that this intron is the result of a recent horizontal gene transfer event from a viral or bacterial vector into the mitochondrial genome of Nephtys sp. Our findings hold implications for understanding mechanisms, constraints, and selective pressures that account for patterns of animal mitochondrial genome evolution.

  13. Protecting exons from deleterious R-loops: a potential advantage of having introns

    Directory of Open Access Journals (Sweden)

    Niu Deng-Ke

    2007-04-01

    Full Text Available Abstract Background Accumulating evidence indicates that the nascent RNA can invade and pair with one strand of DNA, forming an R-loop structure that threatens the stability of the genome. In addition, the cost and benefit of introns are still in debate. Results At least three factors are likely required for the R-loop formation: 1 sequence complementarity between the nascent RNA and the target DNA, 2 spatial juxtaposition between the nascent RNA and the template DNA, and 3 accessibility of the template DNA and the nascent RNA. The removal of introns from pre-mRNA reduces the complementarity between RNA and the template DNA and avoids the spatial juxtaposition between the nascent RNA and the template DNA. In addition, the secondary structures of group I and group II introns may act as spatial obstacles for the formation of R-loops between nearby exons and the genomic DNA. Conclusion Organisms may benefit from introns by avoiding deleterious R-loops. The potential contribution of this benefit in driving intron evolution is discussed. I propose that additional RNA polymerases may inhibit R-loop formation between preceding nascent RNA and the template DNA. This idea leads to a testable prediction: intermittently transcribed genes and genes with frequently prolonged transcription should have higher intron density. Reviewers This article was reviewed by Dr. Eugene V. Koonin, Dr. Alexei Fedorov (nominated by Dr. Laura F Landweber, and Dr. Scott W. Roy (nominated by Dr. Arcady Mushegian.

  14. Surfactant Based Enhanced Oil Recovery and Foam Mobility Control

    Energy Technology Data Exchange (ETDEWEB)

    George J. Hirasaki; Clarence A. Miller

    2006-09-09

    Surfactant flooding has the potential to significantly increase recovery over that of conventional waterflooding. The availability of a large number of surfactant structures makes it possible to conduct a systematic study of the relation between surfactant structure and its efficacy for oil recovery. A mixture of two surfactants was found to be particularly effective for application in carbonate formations at low temperature. The mixture is single phase for higher salinity or calcium concentrations than that for either surfactant used alone. This makes it possible to inject the surfactant slug with polymer close to optimal conditions and yet be single phase. A formulation has been designed for a particular field application. It uses partially hydrolyzed polyacrylamide for mobility control. The addition of an alkali such as sodium carbonate makes possible in situ generation of naphthenic soap and significant reduction of synthetic surfactant adsorption. The design of the process to maximize the region of ultra-low IFT takes advantage of the observation that the ratio of soap to synthetic surfactant is a parameter in the conditions for optimal salinity. Even for a fixed ratio of soap to surfactant, the range of salinity for low IFT was wider than that reported for surfactant systems in the literature. Low temperature, forced displacement experiments in dolomite and silica sandpacks demonstrate that greater than 95% recovery of the waterflood remaining oil is possible with 0.2% surfactant concentration, 0.5 PV surfactant slug, with no alcohol. Compositional simulation of the displacement process demonstrates the role of soap/surfactant ratio on passage of the profile through the ultralow IFT region, the importance of a wide salinity range of low IFT, and the importance of the viscosity of the surfactant slug. Mobility control is essential for surfactant EOR. Foam is evaluated to improve the sweep efficiency of surfactant injected into fractured reservoirs as well as a

  15. ENHANCEMENTS IN UAV FLIGHT CONTROL AND SENSOR ORIENTATION

    Directory of Open Access Journals (Sweden)

    M. Bäumker

    2013-08-01

    Full Text Available The acquisition of photogrammetric image data by means of Unmanned Aerial Vehicles (UAV has developed in recent years to an interesting new measurement method especially for small to medium sizes of objects. In addition the latest developments in the field of navigation systems (GNSS, of inertial sensors and other sensors in combination with powerful and easy to program microcontrollers have made a major contribution to this. In particular, the development of MEMS sensors has triggered the boom of the UAV and has given decisively influence and it is still going on. The integration of sensors on a single board not only enables a cost-effective manufacturing and mass production, but also the use in accordance with small, lightweight UAV. The latest developments on a 50 mm × 50 mm-sized circuit board combine the sensors and the microcontroller for the flight control and flight navigation. Both the board and the microcontroller are easy to program and maintain several interfaces for connecting additional sensors, such as GNSS, ultrasonic sensors and telemetry. This article presents the UAV system of the Bochum University of Applied Sciences, the used sensors and the obtained results for accurate georeferencing.

  16. Enhanced Communication Network Solution for Positive Train Control Implementation

    Science.gov (United States)

    Fatehi, M. T.; Simon, J.; Chang, W.; Chow, E. T.; Burleigh, S. C.

    2011-01-01

    The commuter and freight railroad industry is required to implement Positive Train Control (PTC) by 2015 (2012 for Metrolink), a challenging network communications problem. This paper will discuss present technologies developed by the National Aeronautics and Space Administration (NASA) to overcome comparable communication challenges encountered in deep space mission operations. PTC will be based on a new cellular wireless packet Internet Protocol (IP) network. However, ensuring reliability in such a network is difficult due to the "dead zones" and transient disruptions we commonly experience when we lose calls in commercial cellular networks. These disruptions make it difficult to meet PTC s stringent reliability (99.999%) and safety requirements, deployment deadlines, and budget. This paper proposes innovative solutions based on space-proven technologies that would help meet these challenges: (1) Delay Tolerant Networking (DTN) technology, designed for use in resource-constrained, embedded systems and currently in use on the International Space Station, enables reliable communication over networks in which timely data acknowledgments might not be possible due to transient link outages. (2) Policy-Based Management (PBM) provides dynamic management capabilities, allowing vital data to be exchanged selectively (with priority) by utilizing alternative communication resources. The resulting network may help railroads implement PTC faster, cheaper, and more reliably.

  17. Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1

    Directory of Open Access Journals (Sweden)

    Viigimaa Margus

    2007-07-01

    Full Text Available Abstract Background Human linkage and animal QTL studies have indicated the contribution of genes on Chr17 into blood pressure regulation. One candidate gene is PNMT, coding for phenylethanolamine-N-methyltransferase, catalyzing the synthesis of epinephrine from norepinephrine. Methods Fine-scale variation of PNMT was screened by resequencing hypertensive (n = 50 and normotensive (n = 50 individuals from two European populations (Estonians and Czechs. The resulting polymorphism data were analyzed by statistical genetics methods using Genepop 3.4, PHASE 2.1 and DnaSP 4.0 software programs. In silico prediction of transcription factor binding sites for intron 1 was performed with MatInspector 2.2 software. Results PNMT was characterized by minimum variation and excess of rare SNPs in both normo- and hypertensive individuals. None of the SNPs showed significant differences in allelic frequencies among population samples, as well as between screened hypertensives and normotensives. In the joint case-control analysis of the Estonian and the Czech samples, hypertension patients had a significant excess of heterozygotes for two promoter region polymorphisms (SNP-184; SNP-390. The identified variation pattern of PNMT reflects the effect of purifying selection consistent with an important role of PNMT-synthesized epinephrine in the regulation of cardiovascular and metabolic functions, and as a CNS neurotransmitter. A striking feature is the lack of intronic variation. In silico analysis of PNMT intron 1 confirmed the presence of a human-specific putative Glucocorticoid Responsive Element (GRE, inserted by Alu-mediated transfer. Further analysis of intron 1 supported the possible existence of a full Glucocorticoid Responsive Unit (GRU predicted to consist of multiple gene regulatory elements known to cooperate with GRE in driving transcription. The role of these elements in regulating PNMT expression patterns and thus determining the dynamics of the

  18. Multi-level Control Framework for Enhanced Flexibility of Active Distribution Network

    DEFF Research Database (Denmark)

    Nainar, Karthikeyan; Pokhrel, Basanta Raj; Pillai, Jayakrishnan Radhakrishna

    2017-01-01

    In this paper, the control objectives of future active distribution networks with high penetration of renewables and flexible loads are analyzed and reviewed. From a state of the art review, the important control objectives seen from the perspective of a distribution system operator are identified...... the selected control objectives and provides enhanced flexibility. The control architecture is supported by generation/load forecasting and distribution state estimation techniques to improve the controllability of the network. The multi-level control architecture consists of three levels of hierarchical...... control and an improved interface to the transmission system operator. The functions and the appropriate control methods to be used in each control level are described based on the state of the art review. A combined control action of these control layers is aimed for efficient co...

  19. Strategy For Yield Control And Enhancement In VLSI Wafer Manufacturing

    Science.gov (United States)

    Neilson, B.; Rickey, D.; Bane, R. P.

    1988-01-01

    In most fully utilized integrated circuit (IC) production facilities, profit is very closely linked with yield. In even the most controlled manufacturing environments, defects due to foreign material are a still major contributor to yield loss. Ideally, an IC manufacturer will have ample engineering resources to address any problem that arises. In the real world, staffing limitations require that some tasks must be left undone and potential benefits left unrealized. Therefore, it is important to prioritize problems in a manner that will give the maximum benefit to the manufacturer. When offered a smorgasbord of problems to solve, most people (engineers included) will start with what is most interesting or the most comfortable to work on. By providing a system that accurately predicts the impact of a wide variety of defect types, a rational method of prioritizing engineering effort can be made. To that effect, a program was developed to determine and rank the major yield detractors in a mixed analog/digital FET manufacturing line. The two classical methods of determining yield detractors are chip failure analysis and defect monitoring on drop in test die. Both of these methods have short comings: 1) Chip failure analysis is painstaking and very time consuming. As a result, the sample size is very small. 2) Drop in test die are usually designed for device parametric analysis rather than defect analysis. To provide enough wafer real estate to do meaningful defect analysis would render the wafer worthless for production. To avoid these problems, a defect monitor was designed that provided enough area to detect defects at the same rate or better than the NMOS product die whose yield was to be optimized. The defect monitor was comprehensive and electrically testable using such equipment as the Prometrix LM25 and other digital testers. This enabled the quick accumulation of data which could be handled statistically and mapped individually. By scaling the defect densities

  20. An Enhanced Instantaneous Circulating Current Control for Reactive power and Harmonic Load Sharing in Islanded Microgrids

    DEFF Research Database (Denmark)

    Lorzadeh, Iman; Askarian Abyaneh, Hossein; Savaghebi, Mehdi

    2017-01-01

    To address inaccurate load demand sharing problems among parallel inverter-interfaced voltage-controlled distributed generation (DG) units in islanded microgrids with different DG power ratings and mismatched feeder impedances, an enhanced voltage control scheme based on actively compensation of ...

  1. An enhanced hierarchical control strategy for the Internet of Things-based home scale microgrid

    DEFF Research Database (Denmark)

    Guan, Yajuan; Quintero, Juan Carlos Vasquez; Guerrero, Josep M.

    2017-01-01

    As the intelligent control and detection technology improving, more and more smart devices/sensors can be used to increase the living standard. In order to integrate the Internet of Things (IoT) with microgrid (MG), an enhanced hierarchical control strategy for IoT-based home scale MG is proposed...

  2. Lidar-Enhanced Wind Turbine Control: Past, Present, and Future: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Scholbrock, Andrew; Fleming, Paul; Wright, Alan; Wang, Na; Schlipf, David; Johnson, Kathryn

    2016-07-01

    This paper will look at the development of lidar-enhanced controls and how they have been used for turbine load reduction with pitch actuation, as well as increased energy production with improved yaw control. Ongoing work will also be discussed to show that combining pitch and torque control using feedforward nonlinear model predictive control can lead to both reduced loads and increased energy production. Future work is also proposed on extending individual wind turbine controls to the wind plant level and determining how lidars can be used for control methods to further lower the cost of wind energy by minimizing wake impacts in a wind farm.

  3. Distributed Secondary Control for DC Microgrid Applications with Enhanced Current Sharing Accuracy

    DEFF Research Database (Denmark)

    Lu, Xiaonan; Guerrero, Josep M.; Sun, Kai

    2013-01-01

    are used locally as the distributed secondary controllers in each converter to enhance the current sharing accuracy and restore the dc bus voltage simultaneously. All the controllers are realized locally and the LBC system is only used for changing the data of dc voltage and current. Thus, a decentralized......, a distributed secondary control method is proposed. Droop control is employed as the primary control method for load current sharing. Meanwhile, the dc output voltage and current in each module is transferred to the others by the low bandwidth communication (LBC) network. Average voltage and current controllers...

  4. Enhanced situation awareness and decision making for an intelligent reconfigurable reactor power controller

    International Nuclear Information System (INIS)

    Kenney, S.J.; Edwards, R.M.

    1996-01-01

    A Learning Automata based intelligent reconfigurable controller has been adapted for use as a reactor power controller to achieve improved reactor temperature performance. The intelligent reconfigurable controller is capable of enforcing either a classical or an optimal reactor power controller based on control performance feedback. Four control performance evaluation measures: dynamically estimated average quadratic temperature error, power, rod reactivity and rod reactivity rate were developed to provide feedback to the control decision component of the intelligent reconfigurable controller. Fuzzy Logic and Neural Network controllers have been studied for inclusion in the bank of controllers that form the intermediate level of an enhanced intelligent reconfigurable reactor power controller (IRRPC). The increased number of alternatives available to the supervisory level of the IRRPC requires enhanced situation awareness. Additional performance measures have been designed and a method for synthesizing them into a single indication of the overall performance of the currently enforced reactor power controller has been conceptualized. Modification of the reward/penalty scheme implemented in the existing IRRPC to increase the quality of the supervisory level decision process has been studied. The logogen model of human memory (Morton, 1969) and individual controller design information could be used to allocate reward to the most appropriate controller. Methods for allocating supervisory level attention were also studied with the goal of maximizing learning rate

  5. Exon sequence requirements for excision in vivo of the bacterial group II intron RmInt1

    Directory of Open Access Journals (Sweden)

    Toro Nicolás

    2011-05-01

    Full Text Available Abstract Background Group II intron splicing proceeds through two sequential transesterification reactions in which the 5' and 3'-exons are joined together and the lariat intron is released. The intron-encoded protein (IEP assists the splicing of the intron in vivo and remains bound to the excised intron lariat RNA in a ribonucleoprotein particle (RNP that promotes intron mobility. Exon recognition occurs through base-pairing interactions between two guide sequences on the ribozyme domain dI known as EBS1 and EBS2 and two stretches of sequence known as IBS1 and IBS2 on the 5' exon, whereas the 3' exon is recognized through interaction with the sequence immediately upstream from EBS1 [(δ-δ' interaction (subgroup IIA] or with a nucleotide [(EBS3-IBS3 interaction (subgroup IIB and IIC] located in the coordination-loop of dI. The δ nucleotide is involved in base pairing with another intron residue (δ' in subgroup IIB introns and this interaction facilitates base pairing between the 5' exon and the intron. Results In this study, we investigated nucleotide requirements in the distal 5'- and 3' exon regions, EBS-IBS interactions and δ-δ' pairing for excision of the group IIB intron RmInt1 in vivo. We found that the EBS1-IBS1 interaction was required and sufficient for RmInt1 excision. In addition, we provide evidence for the occurrence of canonical δ-δ' pairing and its importance for the intron excision in vivo. Conclusions The excision in vivo of the RmInt1 intron is a favored process, with very few constraints for sequence recognition in both the 5' and 3'-exons. Our results contribute to understand how group II introns spread in nature, and might facilitate the use of RmInt1 in gene targeting.

  6. The Agaricus bisporus cox1 gene: the longest mitochondrial gene and the largest reservoir of mitochondrial group i introns.

    Directory of Open Access Journals (Sweden)

    Cyril Férandon

    Full Text Available In eukaryotes, introns are located in nuclear and organelle genes from several kingdoms. Large introns (up to 5 kbp are frequent in mitochondrial genomes of plant and fungi but scarce in Metazoa, even if these organisms are grouped with fungi among the Opisthokonts. Mitochondrial introns are classified in two groups (I and II according to their RNA secondary structure involved in the intron self-splicing mechanism. Most of these mitochondrial group I introns carry a "Homing Endonuclease Gene" (heg encoding a DNA endonuclease acting in transfer and site-specific integration ("homing" and allowing intron spreading and gain after lateral transfer even between species from different kingdoms. Opposed to this gain mechanism, is another which implies that introns, which would have been abundant in the ancestral genes, would mainly evolve by loss. The importance of both mechanisms (loss and gain is matter of debate. Here we report the sequence of the cox1 gene of the button mushroom Agaricus bisporus, the most widely cultivated mushroom in the world. This gene is both the longest mitochondrial gene (29,902 nt and the largest group I intron reservoir reported to date with 18 group I and 1 group II. An exhaustive analysis of the group I introns available in cox1 genes shows that they are mobile genetic elements whose numerous events of loss and gain by lateral transfer combine to explain their wide and patchy distribution extending over several kingdoms. An overview of intron distribution, together with the high frequency of eroded heg, suggests that they are evolving towards loss. In this landscape of eroded and lost intron sequences, the A. bisporus cox1 gene exhibits a peculiar dynamics of intron keeping and catching, leading to the largest collection of mitochondrial group I introns reported to date in a Eukaryote.

  7. Self-splicing of a group IIC intron: 5? exon recognition and alternative 5? splicing events implicate the stem?loop motif of a transcriptional terminator

    OpenAIRE

    Toor, Navtej; Robart, Aaron R.; Christianson, Joshua; Zimmerly, Steven

    2006-01-01

    Bacterial IIC introns are a newly recognized subclass of group II introns whose ribozyme properties have not been characterized in detail. IIC introns are typically located downstream of transcriptional terminator motifs (inverted repeat followed by T's) or other inverted repeats in bacterial genomes. Here we have characterized the self-splicing activity of a IIC intron, B.h.I1, from Bacillus halodurans. B.h.I1 self-splices in vitro through hydrolysis to produce linear intron, but interesting...

  8. Coordinated corrective control for transient stability enhancement in future Great Britain transmission system

    OpenAIRE

    Martinez Sanz, I; Chaudhuri, B; Strbac, G

    2016-01-01

    This paper demonstrates a corrective control strategy through fast actuators (TCSC FACTS and HVDC links, both LCC and VSC) in order to enhance the transient stability in the future Great Britain (GB) transmission network. A model predictive control (MPC) scheme that relies on system wide-area measurements is employed for coordinated control action through these power electronic devices with the aim of preserving the system stability without having to constrain pre-fault transfer levels. Case ...

  9. Enhanced photoelectrochemical water splitting performance using morphology-controlled BiVO4 with W doping

    Directory of Open Access Journals (Sweden)

    Xin Zhao

    2017-12-01

    Full Text Available Nanostructures exhibit numerous merits to improve the efficiency in solar-to-energy conversion. These include shortened carrier collection pathways, an increased volume ratio between depletion layer and bulk, enhanced light capture due to multiple light scattering in nanostructures, and a high surface area for photochemical conversion reactions. In this study, we describe the synthesis of morphology-controlled W-doped BiVO4 by simply tuning the solvent ratio in precursor solutions. Planar and porous W-doped BiVO4 thin films were prepared and compared. The porous film, which exhibits increased surface area and enhanced light absorption, has displayed enhanced charge separation and interfacial charge injection. Our quantitative analysis showed an enhancement of about 50% of the photoelectrochemical performance for the porous structure compared to the planar structure. This enhancement is attributed to improved light absorption (13% increase, charge separation (14% increase, and interfacial charge injection (20% increase.

  10. An exploration of exercise-induced cognitive enhancement and transfer effects to dietary self-control.

    Science.gov (United States)

    Lowe, Cassandra J; Kolev, Dimitar; Hall, Peter A

    2016-12-01

    The primary objective of this study was to examine the effects of aerobic exercise on executive function, specifically inhibitory control, and the transfer to self-control in the dietary domain. It was hypothesized that exercise would enhance inhibitory control, and that this enhancement would facilitate self-control in a laboratory taste test paradigm. Using a crossover design, 51 participants completed counterbalanced sessions of both moderate exercise (experimental condition) and minimal effort walking (control condition) using a treadmill; the intersession interval was 7days. Prior to each exercise bout participants completed a Stroop task. Following each bout participants completed a second Stoop task, as well as a bogus taste test involving three appetitive calorie dense snack foods and two control foods; the amount of each food type consumed during the taste test was covertly measured. Results revealed that moderate exercise significantly improved performance on the Stroop task, and also reduced food consumption during the taste test for appetitive calorie dense snack foods; there was no exercise effect on control food consumption. Exercise-induced gains in Stroop performance mediated the effects of moderate exercise on appetitive snack food consumption. Together these findings provide evidence that a bout of a moderate aerobic exercise can enhance inhibitory control, and support for cross-domain transfer effects to dietary self-control. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Multiple recent horizontal transfers of the cox1 intron in Solanaceae and extended co-conversion of flanking exons.

    Science.gov (United States)

    Sanchez-Puerta, Maria V; Abbona, Cinthia C; Zhuo, Shi; Tepe, Eric J; Bohs, Lynn; Olmstead, Richard G; Palmer, Jeffrey D

    2011-09-27

    The most frequent case of horizontal transfer in plants involves a group I intron in the mitochondrial gene cox1, which has been acquired via some 80 separate plant-to-plant transfer events among 833 diverse angiosperms examined. This homing intron encodes an endonuclease thought to promote the intron's promiscuous behavior. A promising experimental approach to study endonuclease activity and intron transmission involves somatic cell hybridization, which in plants leads to mitochondrial fusion and genome recombination. However, the cox1 intron has not yet been found in the ideal group for plant somatic genetics - the Solanaceae. We therefore undertook an extensive survey of this family to find members with the intron and to learn more about the evolutionary history of this exceptionally mobile genetic element. Although 409 of the 426 species of Solanaceae examined lack the cox1 intron, it is uniformly present in three phylogenetically disjunct clades. Despite strong overall incongruence of cox1 intron phylogeny with angiosperm phylogeny, two of these clades possess nearly identical intron sequences and are monophyletic in intron phylogeny. These two clades, and possibly the third also, contain a co-conversion tract (CCT) downstream of the intron that is extended relative to all previously recognized CCTs in angiosperm cox1. Re-examination of all published cox1 genes uncovered additional cases of extended co-conversion and identified a rare case of putative intron loss, accompanied by full retention of the CCT. We infer that the cox1 intron was separately and recently acquired by at least three different lineages of Solanaceae. The striking identity of the intron and CCT from two of these lineages suggests that one of these three intron captures may have occurred by a within-family transfer event. This is consistent with previous evidence that horizontal transfer in plants is biased towards phylogenetically local events. The discovery of extended co

  12. A STAT6 Intronic Single-Nucleotide Polymorphism is Associated with Clinical Malaria in Ghanaian Children

    Directory of Open Access Journals (Sweden)

    Daniel Amoako-Sakyi

    2016-01-01

    Full Text Available Malaria pathogenesis may be influenced by IgE responses and cytokine cross-regulation. Several mutations in the IL-4/STAT6 signaling pathway can alter cytokine cross-regulation and IgE responses during a Plasmodium falciparum malarial infection. This study investigated the relationship between a STAT6 intronic single-nucleotide polymorphism (rs3024974, total IgE, cytokines, and malaria severity in 238 Ghanaian children aged between 0.5 and 13 years. Total IgE and cytokine levels were measured by ELISA, while genotyping was done by polymerase chain reaction-restriction fragment length polymorphism (RFLP. Compared with healthy controls, heterozygosity protected against clinical malaria: uncomplicated malaria (odds ratios [OR] = 0.13, P < 0.001, severe malarial anemia (OR = 0.18, P < 0.001, and cerebral malaria (OR = 0.39, P = 0.022. Levels of total IgE significantly differed among malaria phenotypes (P = 0.044 and rs3024974 genotypes (P = 0.037. Neither cytokine levels nor IL-6/IL-10 ratios were associated with malaria phenotypes or rs3024974 genotypes. This study suggests a role for rs3024974 in malaria pathogenesis and offers further insights into an IL-4/STAT6 pathway mutation in malaria pathogenesis.

  13. DNA methylation in an intron of the IBM1 histone demethylase gene stabilizes chromatin modification patterns.

    Science.gov (United States)

    Rigal, Mélanie; Kevei, Zoltán; Pélissier, Thierry; Mathieu, Olivier

    2012-06-29

    The stability of epigenetic patterns is critical for genome integrity and gene expression. This highly coordinated process involves interrelated positive and negative regulators that impact distinct epigenetic marks, including DNA methylation and dimethylation at histone H3 lysine 9 (H3K9me2). In Arabidopsis, mutations in the DNA methyltransferase MET1, which maintains CG methylation, result in aberrant patterns of other epigenetic marks, including ectopic non-CG methylation and the relocation of H3K9me2 from heterochromatin into gene-rich chromosome regions. Here, we show that the expression of the H3K9 demethylase IBM1 (increase in BONSAI methylation 1) requires DNA methylation. Surprisingly, the regulatory methylated region is contained in an unusually large intron that is conserved in IBM1 orthologues. The re-establishment of IBM1 expression in met1 mutants restored the wild-type H3K9me2 nuclear patterns, non-CG DNA methylation and transcriptional patterns at selected loci, which included DNA demethylase genes. These results provide a mechanistic explanation for long-standing puzzling observations in met1 mutants and reveal yet another layer of control in the interplay between DNA methylation and histone modification, which stabilizes DNA methylation patterns at genes.

  14. Nanoscale control of Ag nanostructures for plasmonic fluorescence enhancement of near-infrared dyes

    KAUST Repository

    Xie, Fang

    2013-05-23

    Potential utilization of proteins for early detection and diagnosis of various diseases has drawn considerable interest in the development of protein-based detection techniques. Metal induced fluorescence enhancement offers the possibility of increasing the sensitivity of protein detection in clinical applications. We report the use of tunable plasmonic silver nanostructures for the fluorescence enhancement of a near-infrared (NIR) dye (Alexa Fluor 790). Extensive fluorescence enhancement of ∼2 orders of magnitude is obtained by the nanoscale control of the Ag nanostructure dimensions and interparticle distance. These Ag nanostructures also enhanced fluorescence from a dye with very high quantum yield (7.8 fold for Alexa Fluor 488, quantum efficiency (Qy) = 0.92). A combination of greatly enhanced excitation and an increased radiative decay rate, leading to an associated enhancement of the quantum efficiency leads to the large enhancement. These results show the potential of Ag nanostructures as metal induced fluorescence enhancement (MIFE) substrates for dyes in the NIR "biological window" as well as the visible region. Ag nanostructured arrays fabricated by colloidal lithography thus show great potential for NIR dye-based biosensing applications. [Figure not available: see fulltext.] © 2013 Tsinghua University Press and Springer-Verlag Berlin Heidelberg.

  15. Impaired Feedforward Control and Enhanced Feedback Control of Speech in Patients with Cerebellar Degeneration.

    Science.gov (United States)

    Parrell, Benjamin; Agnew, Zarinah; Nagarajan, Srikantan; Houde, John; Ivry, Richard B

    2017-09-20

    The cerebellum has been hypothesized to form a crucial part of the speech motor control network. Evidence for this comes from patients with cerebellar damage, who exhibit a variety of speech deficits, as well as imaging studies showing cerebellar activation during speech production in healthy individuals. To date, the precise role of the cerebellum in speech motor control remains unclear, as it has been implicated in both anticipatory (feedforward) and reactive (feedback) control. Here, we assess both anticipatory and reactive aspects of speech motor control, comparing the performance of patients with cerebellar degeneration and matched controls. Experiment 1 tested feedforward control by examining speech adaptation across trials in response to a consistent perturbation of auditory feedback. Experiment 2 tested feedback control, examining online corrections in response to inconsistent perturbations of auditory feedback. Both male and female patients and controls were tested. The patients were impaired in adapting their feedforward control system relative to controls, exhibiting an attenuated anticipatory response to the perturbation. In contrast, the patients produced even larger compensatory responses than controls, suggesting an increased reliance on sensory feedback to guide speech articulation in this population. Together, these results suggest that the cerebellum is crucial for maintaining accurate feedforward control of speech, but relatively uninvolved in feedback control. SIGNIFICANCE STATEMENT Speech motor control is a complex activity that is thought to rely on both predictive, feedforward control as well as reactive, feedback control. While the cerebellum has been shown to be part of the speech motor control network, its functional contribution to feedback and feedforward control remains controversial. Here, we use real-time auditory perturbations of speech to show that patients with cerebellar degeneration are impaired in adapting feedforward control of

  16. Enhanced hybrid electromyogram/Eye Gaze Tracking cursor control system for hands-free computer interaction.

    Science.gov (United States)

    Chin, Craig A; Barreto, Armando

    2006-01-01

    This paper outlines the development and initial testing of a new hybrid computer cursor control system based on Eye Gaze Tracking (EGT) and electromyogram (EMG) processing for hands-free control of the computer cursor. The ultimate goal of the system is to provide an efficient computer interaction mechanism for individuals with severe motor disabilities (or specialized operators whose hands are committed to other tasks, such as surgeons, pilots, etc.) The paper emphasizes the enhancements that have been made on different areas of the architecture, with respect to a previous prototype developed by our group, and demonstrates the performance improvement verified for some of the enhancements.

  17. Two self-splicing group I introns in the ribonucleotide reductase large subunit gene of Staphylococcus aureus phage Twort

    OpenAIRE

    Landthaler, Markus; Begley, Ulrike; Lau, Nelson C.; Shub, David A.

    2002-01-01

    We have recently described three group I introns inserted into a single gene, orf142, of the staphylococcal bacteriophage Twort and suggested the presence of at least two additional self-splicing introns in this phage genome. Here we report that two previously uncharacterized introns, 429 and 1087 nt in length, interrupt the Twort gene coding for the large subunit of ribonucleotide reductase (nrdE). Reverse transcription-polymerase chain reaction (RT-PCR) of RNA isolated from Staphylococcus a...

  18. Short-term sequence evolution and vertical inheritance of the Naegleria twin-ribozyme group I intron

    Directory of Open Access Journals (Sweden)

    De Jonckheere Johan F

    2006-05-01

    Full Text Available Abstract Background Ribosomal DNA of several species of the free-living Naegleria amoeba harbors an optional group I intron within the nuclear small subunit ribosomal RNA gene. The intron (Nae.S516 has a complex organization of two ribozyme domains (NaGIR1 and NaGIR2 and a homing endonuclease gene (NaHEG. NaGIR2 is responsible for intron excision, exon ligation, and full-length intron RNA circularization, reactions typical for nuclear group I intron ribozymes. NaGIR1, however, is essential for NaHEG expression by generating the 5' end of the homing endonuclease messenger RNA. Interestingly, this unusual class of ribozyme adds a lariat-cap at the mRNA. Results To elucidate the evolutionary history of the Nae.S516 twin-ribozyme introns we have analyzed 13 natural variants present in distinct Naegleria isolates. Structural variabilities were noted within both the ribozyme domains and provide strong comparative support to the intron secondary structure. One of the introns, present in N. martinezi NG872, contains hallmarks of a degenerated NaHEG. Phylogenetic analyses performed on separate data sets representing NaGIR1, NaGIR2, NaHEG, and ITS1-5.8S-ITS2 ribosomal DNA are consistent with an overall vertical inheritance pattern of the intron within the Naegleria genus. Conclusion The Nae.S516 twin-ribozyme intron was gained early in the Naegleria evolution with subsequent vertical inheritance. The intron was lost in the majority of isolates (70%, leaving a widespread but scattered distribution pattern. Why the apparent asexual Naegleria amoebae harbors active intron homing endonucleases, dependent on sexual reproduction for its function, remains a puzzle.

  19. Evolution of small putative group I introns in the SSU rRNA gene locus of Phialophora species

    Directory of Open Access Journals (Sweden)

    Harris Lorena B

    2011-07-01

    Full Text Available Abstract Background Group I introns (specifically subgroup IC1 are common in the nuclear ribosomal RNA genes of fungi. While most range in length from more than 200 to nearly 1800 nucleotides (nt in length, several small putative (or degenerate group I introns have been described that are between 56 and 81 nt. Although small, previously we demonstrated that the PaSSU intron in the rRNA small subunit gene of Phialophora americana isolate Wang 1046 is capable of in vitro splicing using a standard group I intron pathway, thus qualifying it as a functional ribozyme. Findings Here, we describe eight short putative group I introns, ranging in length from 63 to 75 nt, in the rRNA small subunit genes of Phialophora isolates, a fungal genus that ranges from saprobic to pathogenic on plants and animals. All contain putative pairing regions P1, P7, and P10, as well as a pairing region formed between the middle of the intron and part of the 3' exon. The other pairing regions common in the core of standard group I introns are absent. However, parts of the 3' exon may aid in the stabilization of these small introns. Although the eight putative group I introns were from at least three species of Phialophora, phylogenetic analysis indicated that the eight are monophyletic. They are also monophyletic with the small introns of two lichen-forming fungi, Porpidia crustulata and Arthonia lapidicola. Conclusions The small putative group I introns in Phialophora have common features that may represent group I introns at their minima. They appear to have a single origin as indicated by their monophyly in phylogenetic analyses.

  20. Whole exon 5 and intron 5 replaced by RHCE in DVa(Hus).

    Science.gov (United States)

    Shao, Chaopeng; Xiong, Wen; Wang, Wei

    2004-01-01

    The DVa(Hus) was previously investigated through cDNA analysis, which revealed an RHD-CE(5)-D hybrid allele. However, the 5' and 3' breakpoints remain unknown. In this article, gene recombinations between the RHD and RHCE alleles were investigated by a combination approach of a sequence-specific primer PCR (PCR-SSP) and an RHD full-length coding region sequencing method on two Chinese subjects with weak D phenotypes. The hybrid Rhesus box of each individual was also investigated through an established PCR-based method. As a result, two partial D phenotypes, DVa(Hus) and DVI type III, were identified, each carrying one hybrid RHD-CE-D allele. The two samples were also serotyped with Rh phontypes of DccEe and DCcee, respectively. Other sequencing analyses of the DVaHus sample showed that the sequence of intron 4 is identical with RHD, whereas the whole sequence of exon 5 and intron 5 is identical with RHCE except for seven polymorphisms in the intron 5. We may concluded that in the case of this Chinese DVa(Hus), the whole exon 5 and complete intron 5 of a total segment of 1801 nucleotides were replaced by RHCE suggesting that the breakpoints of the replaced region are the 5' end of the exon 5 and the 3' end of the intron 5.

  1. Introns regulate gene expression in Cryptococcus neoformans in a Pab2p dependent pathway.

    Directory of Open Access Journals (Sweden)

    Carolin Goebels

    Full Text Available Most Cryptococccus neoformans genes are interrupted by introns, and alternative splicing occurs very often. In this study, we examined the influence of introns on C. neoformans gene expression. For most tested genes, elimination of introns greatly reduces mRNA accumulation. Strikingly, the number and the position of introns modulate the gene expression level in a cumulative manner. A screen for mutant strains able to express functionally an intronless allele revealed that the nuclear poly(A binding protein Pab2 modulates intron-dependent regulation of gene expression in C. neoformans. PAB2 deletion partially restored accumulation of intronless mRNA. In addition, our results demonstrated that the essential nucleases Rrp44p and Xrn2p are implicated in the degradation of mRNA transcribed from an intronless allele in C. neoformans. Double mutant constructions and over-expression experiments suggested that Pab2p and Xrn2p could act in the same pathway whereas Rrp44p appears to act independently. Finally, deletion of the RRP6 or the CID14 gene, encoding the nuclear exosome nuclease and the TRAMP complex associated poly(A polymerase, respectively, has no effect on intronless allele expression.

  2. Introns Regulate Gene Expression in Cryptococcus neoformans in a Pab2p Dependent Pathway

    Science.gov (United States)

    Goebels, Carolin; Thonn, Aline; Gonzalez-Hilarion, Sara; Rolland, Olga; Moyrand, Frederique; Beilharz, Traude H.; Janbon, Guilhem

    2013-01-01

    Most Cryptococccus neoformans genes are interrupted by introns, and alternative splicing occurs very often. In this study, we examined the influence of introns on C. neoformans gene expression. For most tested genes, elimination of introns greatly reduces mRNA accumulation. Strikingly, the number and the position of introns modulate the gene expression level in a cumulative manner. A screen for mutant strains able to express functionally an intronless allele revealed that the nuclear poly(A) binding protein Pab2 modulates intron-dependent regulation of gene expression in C. neoformans. PAB2 deletion partially restored accumulation of intronless mRNA. In addition, our results demonstrated that the essential nucleases Rrp44p and Xrn2p are implicated in the degradation of mRNA transcribed from an intronless allele in C. neoformans. Double mutant constructions and over-expression experiments suggested that Pab2p and Xrn2p could act in the same pathway whereas Rrp44p appears to act independently. Finally, deletion of the RRP6 or the CID14 gene, encoding the nuclear exosome nuclease and the TRAMP complex associated poly(A) polymerase, respectively, has no effect on intronless allele expression. PMID:23966870

  3. PCR primers for an aldolase-B intron in acanthopterygian fishes

    Directory of Open Access Journals (Sweden)

    Jones William J

    2001-11-01

    Full Text Available Abstract Background Nuclear DNA sequences provide genetic information that complements studies using mitochondrial DNA. Some 'universal' primer sets have been developed that target introns within protein-coding loci, but many simultaneously amplify introns from paralogous loci. Refining existing primer sets to target a single locus could circumvent this problem. Results Aldolase intron 'G' was amplified from four fish species using previously described primer sets that target several loci indiscriminately. Phylogenetic analyses were used to group these fragments and other full-length aldolase proteins from teleost fishes into orthologous clades and a primer set was designed to target specifically an intron within the aldolase-B locus in acanthopterygian fishes. DNA amplifications were tried in a variety of acanthopterygian fishes and amplification products, identifiable as aldolase-B intron 'G', were observed in all atherinomorph and percomorph taxa examined. Sequence variation within this locus was found within and among several species examined. Conclusions Using 'universal' primer sets coupled with phylogenetic analyses it was possible to develop a genetic assay to target a specific locus in a variety of fish taxa. Sequence variation was observed within and among species suggesting that this targeted assay might facilitate interspecific and intraspecific comparisons.

  4. Long-term evolution of the S788 fungal nuclear small subunit rRNA group I introns

    OpenAIRE

    HAUGEN, PEIK; RUNGE, HENRY JOSEPH; BHATTACHARYA, DEBASHISH

    2004-01-01

    More than 1000 group I introns have been identified in fungal rDNA. Little is known, however, of the splicing and secondary structure evolution of these ribozymes. Here, we use a combination of comparative and biochemical methods to address the evolution and splicing of a vertically inherited group I intron found at position 788 in the fungal small subunit (S) rRNA. The ancestral state of the S788 intron contains a highly conserved core and an extended P5 domain typical of IC1 introns. In con...

  5. AtnMat2, a nuclear-encoded maturase required for splicing of group-II introns in Arabidopsis mitochondria

    OpenAIRE

    Keren, Ido; Bezawork-Geleta, Ayenachew; Kolton, Max; Maayan, Inbar; Belausov, Eduard; Levy, Maggie; Mett, Anahit; Gidoni, David; Shaya, Felix; Ostersetzer-Biran, Oren

    2009-01-01

    Mitochondria (mt) in plants house about 20 group-II introns, which lie within protein-coding genes required in both organellar genome expression and respiration activities. While in nonplant systems the splicing of group-II introns is mediated by proteins encoded within the introns themselves (known as “maturases”), only a single maturase ORF (matR) has retained in the mitochondrial genomes in plants; however, its putative role(s) in the splicing of organellar introns is yet to be established...

  6. Modern control of static var compensator for power system stability enhancement

    Directory of Open Access Journals (Sweden)

    Stelian-Emilian Oltean

    2012-06-01

    Full Text Available The effects of shunt compensation on power system transmission stability and modern approach of the reactive power control scheme have been investigated in this paper. Reactive power compensation is realized in shunt connection with two components: thyristor controlled reactor (TCR and thyristor switched capacitor (TSC. A special attention has been given in the following paragraphs to a modern control approach for power system stability enhancement which uses fuzzy logic. In the final part of the paper the modern control block scheme of static VAR compensator for reactive power in transmission systems is presented.

  7. Measures to enhance the reliability of digital reactor instrumentation and control system

    International Nuclear Information System (INIS)

    Li Duo; Zhang Liangju

    2005-01-01

    The instrumentation and control (I and C) system of an in-constriction research reactor is fully based on digital technology, which greatly improves system performance in many aspects such as MMI, data processing accurately, centralized control and monitoring ability, and maintainability. The reliability should be an essential issue for the successfulness of a digital I and C. This paper describes measures taken in the design of the reactor I and C to enhance the overall reliability, including distributed data processing; and control functions, redundancy, autonomous control, and diversified MMI, which would greatly contribute to the system reliability. (authors)

  8. Multi-species comparative analysis of the equine ACE gene identifies a highly conserved potential transcription factor binding site in intron 16.

    Directory of Open Access Journals (Sweden)

    Natasha A Hamilton

    Full Text Available Angiotensin converting enzyme (ACE is essential for control of blood pressure. The human ACE gene contains an intronic Alu indel (I/D polymorphism that has been associated with variation in serum enzyme levels, although the functional mechanism has not been identified. The polymorphism has also been associated with cardiovascular disease, type II diabetes, renal disease and elite athleticism. We have characterized the ACE gene in horses of breeds selected for differing physical abilities. The equine gene has a similar structure to that of all known mammalian ACE genes. Nine common single nucleotide polymorphisms (SNPs discovered in pooled DNA were found to be inherited in nine haplotypes. Three of these SNPs were located in intron 16, homologous to that containing the Alu polymorphism in the human. A highly conserved 18 bp sequence, also within that intron, was identified as being a potential binding site for the transcription factors Oct-1, HFH-1 and HNF-3β, and lies within a larger area of higher than normal homology. This putative regulatory element may contribute to regulation of the documented inter-individual variation in human circulating enzyme levels, for which a functional mechanism is yet to be defined. Two equine SNPs occurred within the conserved area in intron 16, although neither of them disrupted the putative binding site. We propose a possible regulatory mechanism of the ACE gene in mammalian species which was previously unknown. This advance will allow further analysis leading to a better understanding of the mechanisms underpinning the associations seen between the human Alu polymorphism and enzyme levels, cardiovascular disease states and elite athleticism.

  9. A Comprehensive LVRT Control Strategy for DFIG Wind Turbines With Enhanced Reactive Power Support

    DEFF Research Database (Denmark)

    Xie, Dongliang; Xu, Zhao; Yang, Lihui

    2013-01-01

    The paper presents a new control strategy to enhance the ability of reactive power support of a doubly fed induction generator (DFIG) based wind turbine during serious voltage dips. The proposed strategy is an advanced low voltage ride through (LVRT) control scheme, with which a part of the captu......The paper presents a new control strategy to enhance the ability of reactive power support of a doubly fed induction generator (DFIG) based wind turbine during serious voltage dips. The proposed strategy is an advanced low voltage ride through (LVRT) control scheme, with which a part......'s excessive inertia energy into the grid. Based on these designs, the DFIG's reactive power capacity on the stator and the grid side converter is handled carefully to satisfy the new grid code requirements strictly. Simulation studies are presented and discussed....

  10. tRNALeu intron (UAA) of Ficus carica L.: genetic diversity and evolutionary patterns.

    Science.gov (United States)

    Baraket, G; Abdelkrim, A B; Salhi-Hannachi, A

    2015-04-22

    Cytoplasmic chloroplast DNA was explored to establish genetic relationships among Ficus carica cultivars and elucidate the molecular evolution of the species. The results suggest the occurrence of haplotype and nucleotide diversity. Conserved group I intron sequence motifs were detected and showed a common secondary structure, despite the presence of some mutations on their sequences. The neighbor-joining dendrogram showed a continuous diversity that characterizes local resources. The maximum parsimony tree, with an RI index of 0.507, indicated minimal homoplasy within the data set. Furthermore, our results demonstrate that the trnL intron is the seat of numerous substitutions. Herein, new insight on the mechanism involved in the evolution of the trnL intron in the fig is presented. From the study, it appears that there is an explicit rejection of the null hypothesis in F. carica. A scenario of positive selection and recent expansion of F. carica genotypes across Tunisia seems to be retained.

  11. An Islanding Microgrid Power Sharing Approach Using Enhanced Virtual Impedance Control Scheme

    DEFF Research Database (Denmark)

    He, Jinwei; Li, Yun Wei; Guerrero, Josep M.

    2013-01-01

    In order to address the load sharing problem in islanding microgrids, this paper proposes an enhanced distributed generation (DG) unit virtual impedance control approach. The proposed method can realize accurate regulation of DG unit equivalent impedance at both fundamental and selected harmonic...... and PCC harmonic voltage compensation are achieved without using any fundamental and harmonic components extractions. Experimental results from a scaled single-phase microgrid prototype are provided to validate the feasibility of the proposed virtual impedance control approach....

  12. PENGEMBANGAN PROGRAM APLIKASI ENHANCED MACHINE CONTROL DENGAN PYTHON UNTUK METODE INTERPOLASI NEWTON

    OpenAIRE

    Alexander Agung Santoso Gunawan; Jimmy Linggarjati

    2012-01-01

    Nowadays, one of industrial main problems is the flexibility of machines to be customized since they are designed based on certain standard. This research develops software for CNC (Computer Numerically Controlled) machine in order to execute the Newton Interpolation using Python. The platform used in the CNCmachine is EMC (Enhanced Machine Control) and GUI (Graphical User Interface) AXIS on the operating system Linux Ubuntu. The Newton interpolation is used to create a curve based on several...

  13. Control, synchronization, and enhanced reliability of aperiodic oscillations in the Mercury Beating Heart system

    Science.gov (United States)

    Kumar, Pawan; Parmananda, P.

    2018-04-01

    Experiments involving the Mercury Beating Heart (MBH) oscillator, exhibiting irregular (aperiodic) dynamics, are performed. In the first set of experiments, control over irregular dynamics of the MBH oscillator was obtained via a superimposed periodic voltage signal. These irregular (aperiodic) dynamics were recovered once the control was switched off. Subsequently, two MBH oscillators were coupled to attain synchronization of their aperiodic oscillations. Finally, two uncoupled MBH oscillators were subjected, repeatedly, to a common stochastic forcing, resulting in an enhancement of their mutual phase correlation.

  14. Acute Caffeine Consumption Enhances the Executive Control of Visual Attention in Habitual Consumers

    Science.gov (United States)

    Brunye, Tad T.; Mahoney, Caroline R.; Lieberman, Harris R.; Giles, Grace E.; Taylor, Holly A.

    2010-01-01

    Recent work suggests that a dose of 200-400mg caffeine can enhance both vigilance and the executive control of visual attention in individuals with low caffeine consumption profiles. The present study seeks to determine whether individuals with relatively high caffeine consumption profiles would show similar advantages. To this end, we examined…

  15. Enhanced s-triazine Degradation and Sugar Cane Weed Control Options

    Science.gov (United States)

    Soil borne bacteria on all continents except Antarctica have developed the ability to rapidly degrade the herbicide atrazine. Reduced residual weed control with atrazine in soils exhibiting enhanced degradation was confirmed under Mississippi Delta corn production and is expected to be occurring in...

  16. Enhanced LVRT Control Strategy for DFIG-Based WECS in Weak Grid

    DEFF Research Database (Denmark)

    Abulanwar, Elsayed; Chen, Zhe; Iov, Florin

    2013-01-01

    An enhanced coordinated low voltage ride-through, LVRT, control strategy for a Doubly-fed Induction generator (DFIG)-based wind energy conversion system, WECS, connected to a weak grid is presented in this paper. The compliance with the grid code commitments is also considered. A proposed decoupled...

  17. NATIONAL STORMWATER CALCULATOR: LOW IMPACT DEVELOPMENT STORMWATER CONTROL COST ESTIMATION PROGRAMMING & FUTURE ENHANCEMENTS

    Science.gov (United States)

    National Stormwater Calculator: Low Impact Development Stormwater Control Cost Estimation Programming & Future EnhancementsJason Berner1; Michael Tryby1; Scott Struck2, Dan Pankani2, Marion Deerhake3, Michelle Simon11. USEPA2. GeoSyntec, Inc.3. RTI, Inc.The National Stormwater Ca...

  18. Pre-germinated conidia of Coniothyrium minitans enhances the foliar biological control of Sclerotinia sclerotiorum.

    Science.gov (United States)

    Shi, Junling; Li, Yin; Qian, Huali; Du, Guocheng; Chen, Jian

    2004-11-01

    The relatively slow germination rate of Coniothyrium minitans limits its control efficiency against Sclerotinia sclerotiorum. Pre-germinated conidia of C. minitans enhanced its efficiency significantly: in foliar experiments with oilseed rape, hyphal extension of S. sclerotiorum was inhibited by 68%, while formation of sclerotia was completely inhibited when pre-germinated conidia were applied.

  19. Conflict-driven adaptive control is enhanced by integral negative emotion on a short time scale.

    Science.gov (United States)

    Yang, Qian; Pourtois, Gilles

    2018-02-05

    Negative emotion influences cognitive control, and more specifically conflict adaptation. However, discrepant results have often been reported in the literature. In this study, we broke down negative emotion into integral and incidental components using a modern motivation-based framework, and assessed whether the former could change conflict adaptation. In the first experiment, we manipulated the duration of the inter-trial-interval (ITI) to assess the actual time-scale of this effect. Integral negative emotion was induced by using loss-related feedback contingent on task performance, and measured at the subjective and physiological levels. Results showed that conflict-driven adaptive control was enhanced when integral negative emotion was elicited, compared to a control condition without changes in defensive motivation. Importantly, this effect was only found when a short, as opposed to long ITI was used, suggesting that it had a short time scale. In the second experiment, we controlled for effects of feature repetition and contingency learning, and replicated an enhanced conflict adaptation effect when integral negative emotion was elicited and a short ITI was used. We interpret these new results against a standard cognitive control framework assuming that integral negative emotion amplifies specific control signals transiently, and in turn enhances conflict adaptation.

  20. Novel RNA structural features of an alternatively splicing group II intron from Clostridium tetani.

    Science.gov (United States)

    McNeil, Bonnie A; Zimmerly, Steven

    2014-06-01

    Group II introns are ribozymes in bacterial and organellar genomes that function as self-splicing introns and as retroelements. Previously, we reported that the group II intron C.te.I1 of Clostridium tetani alternatively splices in vivo to produce five distinct coding mRNAs. Accurate fusion of upstream and downstream reading frames requires a shifted 5' splice site located 8 nt upstream of the usual 5' GUGYG motif. This site is specified by the ribozyme through an altered intron/exon-binding site 1 (IBS1-EBS1) pairing. Here we use mutagenesis and self-splicing assays to investigate in more detail the significance of the structural features of the C.te.I1 ribozyme. The shifted 5' splice site is shown to be affected by structures in addition to IBS1-EBS1, and unlike other group II introns, C.te.I1 appears to require a spacer between IBS1 and the GUGYG motif. In addition, the mechanism of 3' exon recognition is modified from the ancestral IIB mechanism to a IIA-like mechanism that appears to be longer than the typical single base-pair interaction and may extend up to 4 bp. The novel ribozyme properties that have evolved for C.te.I1 illustrate the plasticity of group II introns in adapting new structural and catalytic properties that can be utilized to affect gene expression. © 2014 McNeil and Zimmerly; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  1. Macronuclear genome structure of the ciliate Nyctotherus ovalis: Single-gene chromosomes and tiny introns

    Directory of Open Access Journals (Sweden)

    Landweber Laura F

    2008-12-01

    Full Text Available Abstract Background Nyctotherus ovalis is a single-celled eukaryote that has hydrogen-producing mitochondria and lives in the hindgut of cockroaches. Like all members of the ciliate taxon, it has two types of nuclei, a micronucleus and a macronucleus. N. ovalis generates its macronuclear chromosomes by forming polytene chromosomes that subsequently develop into macronuclear chromosomes by DNA elimination and rearrangement. Results We examined the structure of these gene-sized macronuclear chromosomes in N. ovalis. We determined the telomeres, subtelomeric regions, UTRs, coding regions and introns by sequencing a large set of macronuclear DNA sequences (4,242 and cDNAs (5,484 and comparing them with each other. The telomeres consist of repeats CCC(AAAACCCCn, similar to those in spirotrichous ciliates such as Euplotes, Sterkiella (Oxytricha and Stylonychia. Per sequenced chromosome we found evidence for either a single protein-coding gene, a single tRNA, or the complete ribosomal RNAs cluster. Hence the chromosomes appear to encode single transcripts. In the short subtelomeric regions we identified a few overrepresented motifs that could be involved in gene regulation, but there is no consensus polyadenylation site. The introns are short (21–29 nucleotides, and a significant fraction (1/3 of the tiny introns is conserved in the distantly related ciliate Paramecium tetraurelia. As has been observed in P. tetraurelia, the N. ovalis introns tend to contain in-frame stop codons or have a length that is not dividable by three. This pattern causes premature termination of mRNA translation in the event of intron retention, and potentially degradation of unspliced mRNAs by the nonsense-mediated mRNA decay pathway. Conclusion The combination of short leaders, tiny introns and single genes leads to very minimal macronuclear chromosomes. The smallest we identified contained only 150 nucleotides.

  2. Plant siRNAs from introns mediate DNA methylation of host genes.

    Science.gov (United States)

    Chen, Dijun; Meng, Yijun; Yuan, Chunhui; Bai, Lin; Huang, Donglin; Lv, Shaolei; Wu, Ping; Chen, Ling-Ling; Chen, Ming

    2011-06-01

    Small RNAs (sRNAs), largely known as microRNAs (miRNAs) and short interfering RNAs (siRNAs), emerged as the critical components of genetic and epigenetic regulation in eukaryotic genomes. In animals, a sizable portion of miRNAs reside within the introns of protein-coding genes, designated as mirtron genes. Recently, high-throughput sequencing (HTS) revealed a huge amount of sRNAs that derived from introns in plants, such as the monocot rice (Oryza sativa). However, the biogenesis and the biological functions of this kind of sRNAs remain elusive. Here, we performed a genome-scale survey of intron-derived sRNAs in rice based on HTS data. Several introns were found to have great potential to form internal hairpin structures, and the short hairpins could generate miRNAs while the larger ones could produce siRNAs. Furthermore, 22 introns, termed "sirtrons," were identified from the rice protein-coding genes. The single-stranded sirtrons produced a diverse set of siRNAs from long hairpin structures. These sirtron-derived siRNAs are dominantly 21 nt, 22 nt, and 24 nt in length, whose production relied on DCL4, DCL2, and DCL3, respectively. We also observed a strong tendency for the sirtron-derived siRNAs to be coexpressed with their host genes. Finally, the 24-nt siRNAs incorporated with Argonaute 4 (AGO4) could direct DNA methylation on their host genes. In this regard, homeostatic self-regulation between intron-derived siRNAs and their host genes was proposed.

  3. Computer Controlled Portable Greenhouse Climate Control System for Enhanced Energy Efficiency

    Science.gov (United States)

    Datsenko, Anthony; Myer, Steve; Petties, Albert; Hustek, Ryan; Thompson, Mark

    2010-04-01

    This paper discusses a student project at Kettering University focusing on the design and construction of an energy efficient greenhouse climate control system. In order to maintain acceptable temperatures and stabilize temperature fluctuations in a portable plastic greenhouse economically, a computer controlled climate control system was developed to capture and store thermal energy incident on the structure during daylight periods and release the stored thermal energy during dark periods. The thermal storage mass for the greenhouse system consisted of a water filled base unit. The heat exchanger consisted of a system of PVC tubing. The control system used a programmable LabView computer interface to meet functional specifications that minimized temperature fluctuations and recorded data during operation. The greenhouse was a portable sized unit with a 5' x 5' footprint. Control input sensors were temperature, water level, and humidity sensors and output control devices were fan actuating relays and water fill solenoid valves. A Graphical User Interface was developed to monitor the system, set control parameters, and to provide programmable data recording times and intervals.

  4. Enhancer transcription reveals subtype-specific gene expression programs controlling breast cancer pathogenesis.

    Science.gov (United States)

    Franco, Hector L; Nagari, Anusha; Malladi, Venkat S; Li, Wenqian; Xi, Yuanxin; Richardson, Dana; Allton, Kendra L; Tanaka, Kaori; Li, Jing; Murakami, Shino; Keyomarsi, Khandan; Bedford, Mark T; Shi, Xiaobing; Li, Wei; Barton, Michelle C; Dent, Sharon Y R; Kraus, W Lee

    2018-02-01

    Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene expression. To determine the relationship between enhancer activity and biological outcomes in breast cancers, we profiled the transcriptomes (using GRO-seq and RNA-seq) and epigenomes (using ChIP-seq) of 11 different human breast cancer cell lines representing five major molecular subtypes of breast cancer, as well as two immortalized ("normal") human breast cell lines. In addition, we developed a robust and unbiased computational pipeline that simultaneously identifies putative subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcription, TF mRNA expression levels, TF motif P -values, and enrichment of H3K4me1 and H3K27ac. When applied across the 13 different cell lines noted above, the Total Functional Score of Enhancer Elements (TFSEE) identified key breast cancer subtype-specific TFs that act at transcribed enhancers to dictate gene expression patterns determining growth outcomes, including Forkhead TFs, FOSL1, and PLAG1. FOSL1, a Fos family TF, (1) is highly enriched at the enhancers of triple negative breast cancer (TNBC) cells, (2) acts as a key regulator of the proliferation and viability of TNBC cells, but not Luminal A cells, and (3) is associated with a poor prognosis in TNBC breast cancer patients. Taken together, our results validate our enhancer identification pipeline and reveal that enhancers transcribed in breast cancer cells direct critical gene regulatory networks that promote pathogenesis. © 2018 Franco et al.; Published by Cold Spring Harbor Laboratory Press.

  5. Enhancing the stabilization of aircraft pitch motion control via intelligent and classical method

    Science.gov (United States)

    Lukman, H.; Munawwarah, S.; Azizan, A.; Yakub, F.; Zaki, S. A.; Rasid, Z. A.

    2017-12-01

    The pitching movement of an aircraft is very important to ensure passengers are intrinsically safe and the aircraft achieve its maximum stability. The equations governing the motion of an aircraft are a complex set of six nonlinear coupled differential equations. Under certain assumptions, it can be decoupled and linearized into longitudinal and lateral equations. Pitch control is a longitudinal problem and thus, only the longitudinal dynamics equations are involved in this system. It is a third order nonlinear system, which is linearized about the operating point. The system is also inherently unstable due to the presence of a free integrator. Because of this, a feedback controller is added in order to solve this problem and enhance the system performance. This study uses two approaches in designing controller: a conventional controller and an intelligent controller. The pitch control scheme consists of proportional, integral and derivatives (PID) for conventional controller and fuzzy logic control (FLC) for intelligent controller. Throughout the paper, the performance of the presented controllers are investigated and compared based on the common criteria of step response. Simulation results have been obtained and analysed by using Matlab and Simulink software. The study shows that FLC controller has higher ability to control and stabilize the aircraft's pitch angle as compared to PID controller.

  6. Evidence for transitional stages in the evolution of euglenid group II introns and twintrons in the Monomorphina aenigmatica plastid genome.

    Directory of Open Access Journals (Sweden)

    Jean-François Pombert

    Full Text Available Photosynthetic euglenids acquired their plastid by secondary endosymbiosis of a prasinophyte-like green alga. But unlike its prasinophyte counterparts, the plastid genome of the euglenid Euglena gracilis is riddled with introns that interrupt almost every protein-encoding gene. The atypical group II introns and twintrons (introns-within-introns found in the E. gracilis plastid have been hypothesized to have been acquired late in the evolution of euglenids, implying that massive numbers of introns may be lacking in other taxa. This late emergence was recently corroborated by the plastid genome sequences of the two basal euglenids, Eutreptiella gymnastica and Eutreptia viridis, which were found to contain fewer introns.To gain further insights into the proliferation of introns in euglenid plastids, we have characterized the complete plastid genome sequence of Monomorphina aenigmatica, a freshwater species occupying an intermediate phylogenetic position between early and late branching euglenids. The M. aenigmatica UTEX 1284 plastid genome (74,746 bp, 70.6% A+T, 87 genes contains 53 intron insertion sites, of which 41 were found to be shared with other euglenids including 12 of the 15 twintron insertion sites reported in E. gracilis.The pattern of insertion sites suggests an ongoing but uneven process of intron gain in the lineage, with perhaps a minimum of two bursts of rapid intron proliferation. We also identified several sites that represent intermediates in the process of twintron evolution, where the external intron is in place, but not the internal one, offering a glimpse into how these convoluted molecular contraptions originate.

  7. Model-Based Control of Industrial Batch Crystallizers : Experiments on Enhanced Controllability by Seeding Actuation

    NARCIS (Netherlands)

    Kalbasenka, A.N.

    2009-01-01

    Crystallization is one of the oldest separation and purification techniques. Batch crystallizers are widely used in production of fine chemicals, food ingredients, specialty chemicals, and active pharmaceutical ingredients. Control of the crystalline material properties is a challenging task due to

  8. Enhancing the Frequency Adaptability of Periodic Current Controllers for Grid-Connected Power Converters

    DEFF Research Database (Denmark)

    Yang, Yongheng; Zhou, Keliang; Blaabjerg, Frede

    2015-01-01

    It is mandatory for grid-connected power converters to synchronize the feed-in currents with the grid. Moreover, the power converters should produce feed-in currents with low total harmonic distortions according to the demands, by employing advanced current controllers, e.g., Proportional Resonant...... controllers are investigated by analyzing the frequency adaptability of these current controllers. Subsequently, strategies to enhance the frequency variation immunity for the current controllers are proposed for the power converters to produce high quality feed-in currents even in the presence of frequency...... (PR) and Repetitive Controllers (RC). The synchronization is actually to detect the instantaneous grid information (e.g., frequency and phase of the grid voltage) for the current control, which is commonly performed by a Phase-Locked-Loop (PLL) system. As a consequence, harmonics and deviations...

  9. Enhancing the NCSU PULSTAR reactor control room with human factors considerations

    International Nuclear Information System (INIS)

    Glover, B.L.; Pupons, D.E.; Perez, P.B.

    1993-01-01

    The North Carolina PULSTAR research reactor was constructed to support teaching, training, and research. The training provided is not limited to academic students but encompasses plant operators, managers, engineers, designers, and supporting organizations in the nuclear industry. Our facility is under-going design changes to maximize teaching effectiveness and continued safe operation by providing current technology in the control room. The opportunity for the enhancements is a result of the generosity of neighboring utilities and the US Department of Energy instrumentation upgrade funds. Our objective, to provide a control room environment that conforms to selected industry practices, required human factors input. A human factors course, offered jointly between the industrial engineering and the psychology departments, included the PULSTAR control room enhancement as a case study

  10. Establishment of Systematic Design Control/Configuration Management Processes to Enhance Engineering Capability

    International Nuclear Information System (INIS)

    Inagaki, T.; Hamada, T.; Ihara, T.

    2016-01-01

    Full text: After the accident of Fukushima Daiichi Nuclear Power Plant in 2011, Tokyo Electric Power Company (TEPCO) launched various measures to enhance plant safety and safety culture of its employees. One of the important aspects of these measures is to enhance engineering capability and TEPCO is conducting actions to establish systematic design control and configuration management processes as an important foundation of such engineering capability. This paper describes how TEPCO is establishing systematic configuration management processes from three aspects, i.e., design requirement and bases management, facility configuration control, and configuration change management. It also provides brief information of the IT systems that are being introduced and will support the systematic design control and configuration management processes. (author

  11. Optimization design of optical waveguide control by nanoslit-enhanced THz field

    DEFF Research Database (Denmark)

    Novitsky, Andrey; Malureanu, Radu; Zalkovskij, Maksim

    2013-01-01

    We discuss design issues of devices which were proposed recently [Opt. Lett. 37 (2012) 3903] for terahertz (THz) control of the propagation of an optical waveguide mode. The mode propagates through a nonlinear dielectric material placed in a metallic nanoslit illuminated by THz radiation. The THz...... field in the slit is strongly localized and thus significantly enhanced, facilitating nonlinear interactions with the dielectric waveguide material. This enhancement can lead to notable changes in the refractive index of the waveguide. The closer the waveguide is to the slit walls, the higher...

  12. The combination of colesevelam with sitagliptin enhances glycemic control in diabetic ZDF rat model

    DEFF Research Database (Denmark)

    Shang, Quan; Liu, Matthew K; Saumoy, Monica

    2012-01-01

    . In the present study, we tested whether adding sitagliptin (Januvia) (SIT), which prolongs bioactive GLP-1 half life, to COL would further enhance glycemic control. Male Zucker diabetic fatty (ZDF) rats were assigned to four groups: diabetic model without treatment (the model), the model treated with 2% COL or 0...... to levels similar to the model. Histological examination of the pancreatic ß-cell islets showed that islet sizes were larger, proliferation enhanced, and cell apoptosis reduced in the COL+SIT but not the SIT alone group compared with the model. We hypothesize that the combination of COL with SIT extends...

  13. Application and Evaluation of Control Modes for Risk-Based Engine Performance Enhancements

    Science.gov (United States)

    Liu, Yuan; Litt, Jonathan S.; Sowers, T. Shane; Owen, A. Karl; Guo, Ten-Huei

    2015-01-01

    The engine control system for civil transport aircraft imposes operational limits on the propulsion system to ensure compliance with safety standards. However, during certain emergency situations, aircraft survivability may benefit from engine performance beyond its normal limits despite the increased risk of failure. Accordingly, control modes were developed to improve the maximum thrust output and responsiveness of a generic high-bypass turbofan engine. The algorithms were designed such that the enhanced performance would always constitute an elevation in failure risk to a consistent predefined likelihood. This paper presents an application of these risk-based control modes to a combined engine/aircraft model. Through computer and piloted simulation tests, the aim is to present a notional implementation of these modes, evaluate their effects on a generic airframe, and demonstrate their usefulness during emergency flight situations. Results show that minimal control effort is required to compensate for the changes in flight dynamics due to control mode activation. The benefits gained from enhanced engine performance for various runway incursion scenarios are investigated. Finally, the control modes are shown to protect against potential instabilities during propulsion-only flight where all aircraft control surfaces are inoperable.

  14. SVC control enhancement applying self-learning fuzzy algorithm for islanded microgrid

    Directory of Open Access Journals (Sweden)

    Hossam Gabbar

    2016-03-01

    Full Text Available Maintaining voltage stability, within acceptable levels, for islanded Microgrids (MGs is a challenge due to limited exchange power between generation and loads. This paper proposes an algorithm to enhance the dynamic performance of islanded MGs in presence of load disturbance using Static VAR Compensator (SVC with Fuzzy Model Reference Learning Controller (FMRLC. The proposed algorithm compensates MG nonlinearity via fuzzy membership functions and inference mechanism imbedded in both controller and inverse model. Hence, MG keeps the desired performance as required at any operating condition. Furthermore, the self-learning capability of the proposed control algorithm compensates for grid parameter’s variation even with inadequate information about load dynamics. A reference model was designed to reject bus voltage disturbance with achievable performance by the proposed fuzzy controller. Three simulations scenarios have been presented to investigate effectiveness of proposed control algorithm in improving steady-state and transient performance of islanded MGs. The first scenario conducted without SVC, second conducted with SVC using PID controller and third conducted using FMRLC algorithm. A comparison for results shows ability of proposed control algorithm to enhance disturbance rejection due to learning process.

  15. A CRM domain protein functions dually in group I and group II intron splicing in land plant chloroplasts.

    Science.gov (United States)

    Asakura, Yukari; Barkan, Alice

    2007-12-01

    The CRM domain is a recently recognized RNA binding domain found in three group II intron splicing factors in chloroplasts, in a bacterial protein that associates with ribosome precursors, and in a family of uncharacterized proteins in plants. To elucidate the functional repertoire of proteins with CRM domains, we studied CFM2 (for CRM Family Member 2), which harbors four CRM domains. RNA coimmunoprecipitation assays showed that CFM2 in maize (Zea mays) chloroplasts is associated with the group I intron in pre-trnL-UAA and group II introns in the ndhA and ycf3 pre-mRNAs. T-DNA insertions in the Arabidopsis thaliana ortholog condition a defective-seed phenotype (strong allele) or chlorophyll-deficient seedlings with impaired splicing of the trnL group I intron and the ndhA, ycf3-int1, and clpP-int2 group II introns (weak alleles). CFM2 and two previously described CRM proteins are bound simultaneously to the ndhA and ycf3-int1 introns and act in a nonredundant fashion to promote their splicing. With these findings, CRM domain proteins are implicated in the activities of three classes of catalytic RNA: group I introns, group II introns, and 23S rRNA.

  16. DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure.

    Science.gov (United States)

    Gelfman, Sahar; Cohen, Noa; Yearim, Ahuvi; Ast, Gil

    2013-05-01

    DNA methylation is known to regulate transcription and was recently found to be involved in exon recognition via cotranscriptional splicing. We recently observed that exon-intron architectures can be grouped into two classes: one with higher GC content in exons compared to the flanking introns, and the other with similar GC content in exons and introns. The first group has higher nucleosome occupancy on exons than introns, whereas the second group exhibits weak nucleosome marking of exons, suggesting another type of epigenetic marker distinguishes exons from introns when GC content is similar. We find different and specific patterns of DNA methylation in each of the GC architectures; yet in both groups, DNA methylation clearly marks the exons. Exons of the leveled GC architecture exhibit a significantly stronger DNA methylation signal in relation to their flanking introns compared to exons of the differential GC architecture. This is accentuated by a reduction of the DNA methylation level in the intronic sequences in proximity to the splice sites and shows that different epigenetic modifications mark the location of exons already at the DNA level. Also, lower levels of methylated CpGs on alternative exons can successfully distinguish alternative exons from constitutive ones. Three positions at the splice sites show high CpG abundance and accompany elevated nucleosome occupancy in a leveled GC architecture. Overall, these results suggest that DNA methylation affects exon recognition and is influenced by the GC architecture of the exon and flanking introns.

  17. Comprehensive phylogenetic analysis of bacterial group II intron-encoded ORFs lacking the DNA endonuclease domain reveals new varieties.

    Directory of Open Access Journals (Sweden)

    Nicolás Toro

    Full Text Available Group II introns are self-splicing RNAs that act as mobile retroelements in the organelles of plants, fungi and protists. They are also widely distributed in bacteria, and are generally assumed to be the ancestors of nuclear spliceosomal introns. Most bacterial group II introns have a multifunctional intron-encoded protein (IEP ORF within the ribozyme domain IV (DIV. This ORF encodes an N-terminal reverse transcriptase (RT domain, followed by a putative RNA-binding domain with RNA splicing or maturase activity and, in some cases, a C-terminal DNA-binding (D region followed by a DNA endonuclease (En domain. In this study, we focused on bacterial group II intron ORF phylogenetic classes containing only reverse transcriptase/maturase open reading frames, with no recognizable D/En region (classes A, C, D, E, F and unclassified introns. On the basis of phylogenetic analyses of the maturase domain and its C-terminal extension, which appears to be a signature characteristic of ORF phylogenetic class, with support from the phylogeny inferred from the RT domain, we have revised the proposed new class F, defining new intron ORF varieties. Our results increase knowledge of the lineage of group II introns encoding proteins lacking the En-domain.

  18. Control technique for enhancing the stable operation of distributed generation units within a microgrid

    International Nuclear Information System (INIS)

    Mehrasa, Majid; Pouresmaeil, Edris; Mehrjerdi, Hasan; Jørgensen, Bo Nørregaard; Catalão, João P.S.

    2015-01-01

    Highlights: • A control technique for enhancing the stable operation of distributed generation units is proposed. • Passivity-based control technique is considered to analyze the dynamic and steady-state behaviors. • The compensation of instantaneous variations in the reference current components is considered. • Simulation results confirm the performance of the control scheme within the microgrid. - Abstract: This paper describes a control technique for enhancing the stable operation of distributed generation (DG) units based on renewable energy sources, during islanding and grid-connected modes. The Passivity-based control technique is considered to analyze the dynamic and steady-state behaviors of DG units during integration and power sharing with loads and/or power grid, which is an appropriate tool to analyze and define a stable operating condition for DG units in microgrid technology. The compensation of instantaneous variations in the reference current components of DG units in ac-side, and dc-link voltage variations in dc-side of interfaced converters, are considered properly in the control loop of DG units, which is the main contribution and novelty of this control technique over other control strategies. By using the proposed control technique, DG units can provide the continuous injection of active power from DG sources to the local loads and/or utility grid. Moreover, by setting appropriate reference current components in the control loop of DG units, reactive power and harmonic current components of loads can be supplied during the islanding and grid-connected modes with a fast dynamic response. Simulation results confirm the performance of the control scheme within the microgrid during dynamic and steady-state operating conditions

  19. Targeting of highly conserved Dengue virus sequences with anti-Dengue virus trans-splicing group I introns

    Directory of Open Access Journals (Sweden)

    Fraser Tresa S

    2010-11-01

    Full Text Available Abstract Background Dengue viruses (DENV are one of the most important viral diseases in the world with approximately 100 million infections and 200,000 deaths each year. The current lack of an approved tetravalent vaccine and ineffective insecticide control measures warrant a search for alternatives to effectively combat DENV. The trans-splicing variant of the Tetrahymena thermophila group I intron catalytic RNA, or ribozyme, is a powerful tool for post-transcriptional RNA modification. The nature of the ribozyme and the predictability with which it can be directed makes it a powerful tool for modifying RNA in nearly any cell type without the need for genome-altering gene therapy techniques or dependence on native cofactors. Results Several anti-DENV Group I trans-splicing introns (αDENV-GrpIs were designed and tested for their ability to target DENV-2 NGC genomes in situ. We have successfully targeted two different uracil bases on the positive sense genomic strand within the highly conserved 5'-3' cyclization sequence (CS region common to all serotypes of DENV with our αDENV-GrpIs. Our ribozymes have demonstrated ability to specifically trans-splice a new RNA sequence downstream of the targeted site in vitro and in transfected insect cells as analyzed by firefly luciferase and RT-PCR assays. The effectiveness of these αDENV-GrpIs to target infecting DENV genomes is also validated in transfected or transformed Aedes mosquito cell lines upon infection with unattenuated DENV-2 NGC. Conclusions Analysis shows that our αDENV-GrpIs have the ability to effectively trans-splice the DENV genome in situ. Notably, these results show that the αDENV-GrpI 9v1, designed to be active against all forms of Dengue virus, effectively targeted the DENV-2 NGC genome in a sequence specific manner. These novel αDENV-GrpI introns provide a striking alternative to other RNA based approaches for the transgenic suppression of DENV in transformed mosquito cells and

  20. Interplay between exonic splicing enhancers, mRNA processing, and mRNA surveillance in the dystrophic Mdx mouse.

    Directory of Open Access Journals (Sweden)

    Massimo Buvoli

    2007-05-01

    Full Text Available Pre-mRNA splicing, the removal of introns from RNA, takes place within the spliceosome, a macromolecular complex composed of five small nuclear RNAs and a large number of associated proteins. Spliceosome assembly is modulated by the 5' and 3' splice site consensus sequences situated at the ends of each intron, as well as by exonic and intronic splicing enhancers/silencers recognized by SR and hnRNP proteins. Nonsense mutations introducing a premature termination codon (PTC often result in the activation of cellular quality control systems that reduce mRNA levels or alter the mRNA splicing pattern. The mdx mouse, a commonly used genetic model for Duchenne muscular dystrophy (DMD, lacks dystrophin by virtue of a premature termination codon (PTC in exon 23 that also severely reduces the level of dystrophin mRNA. However, the effect of the mutation on dystrophin RNA processing has not yet been described.Using combinations of different biochemical and cellular assays, we found that the mdx mutation partially disrupts a multisite exonic splicing enhancer (ESE that is recognized by a 40 kDa SR protein. In spite of the presence of an inefficient intron 22 3' splice site containing the rare GAG triplet, the mdx mutation does not activate nonsense-associated altered splicing (NAS, but induces exclusively nonsense-mediated mRNA decay (NMD. Functional binding sites for SR proteins were also identified in exon 22 and 24, and in vitro experiments show that SR proteins can mediate direct association between exon 22, 23, and 24.Our findings highlight the complex crosstalk between trans-acting factors, cis-elements and the RNA surveillance machinery occurring during dystrophin mRNA processing. Moreover, they suggest that dystrophin exon-exon interactions could play an important role in preventing mdx exon 23 skipping, as well as in facilitating the pairing of committed splice sites.

  1. IPCS: An integrated process control system for enhanced in-situ bioremediation

    International Nuclear Information System (INIS)

    Huang, Y.F.; Wang, G.Q.; Huang, G.H.; Xiao, H.N.; Chakma, A.

    2008-01-01

    To date, there has been little or no research related to process control of subsurface remediation systems. In this study, a framework to develop an integrated process control system for improving remediation efficiencies and reducing operating costs was proposed based on physical and numerical models, stepwise cluster analysis, non-linear optimization and artificial neural networks. Process control for enhanced in-situ bioremediation was accomplished through incorporating the developed forecasters and optimizers with methods of genetic algorithm and neural networks modeling. Application of the proposed approach to a bioremediation process in a pilot-scale system indicated that it was effective in dynamic optimization and real-time process control of the sophisticated bioremediation systems. - A framework of process control system was developed to improve in-situ bioremediation efficiencies and reducing operating costs

  2. Design and Experimental Evolution of trans-Splicing Group I Intron Ribozymes

    Directory of Open Access Journals (Sweden)

    Ulrich F. Müller

    2017-01-01

    Full Text Available Group I intron ribozymes occur naturally as cis-splicing ribozymes, in the form of introns that do not require the spliceosome for their removal. Instead, they catalyze two consecutive trans-phosphorylation reactions to remove themselves from a primary transcript, and join the two flanking exons. Designed, trans-splicing variants of these ribozymes replace the 3′-portion of a substrate with the ribozyme’s 3′-exon, replace the 5′-portion with the ribozyme’s 5′-exon, or insert/remove an internal sequence of the substrate. Two of these designs have been evolved experimentally in cells, leading to variants of group I intron ribozymes that splice more efficiently, recruit a cellular protein to modify the substrate’s gene expression, or elucidate evolutionary pathways of ribozymes in cells. Some of the artificial, trans-splicing ribozymes are promising as tools in therapy, and as model systems for RNA evolution in cells. This review provides an overview of the different types of trans-splicing group I intron ribozymes that have been generated, and the experimental evolution systems that have been used to improve them.

  3. Selection-driven extinction dynamics for group II introns in Enterobacteriales.

    Directory of Open Access Journals (Sweden)

    Sébastien Leclercq

    Full Text Available Transposable elements (TEs are one of the major driving forces of genome evolution, raising the question of the long-term dynamics underlying their evolutionary success. Some TEs were proposed to evolve under a pattern of periodic extinctions-recolonizations, in which elements recurrently invade and quickly proliferate within their host genomes, then start to disappear until total extinction. Depending on the model, TE extinction is assumed to be driven by purifying selection against colonized host genomes (Sel-DE model or by saturation of host genomes (Sat-DE model. Bacterial group II introns are suspected to follow an extinction-recolonization model of evolution, but whether they follow Sel-DE or Sat-DE dynamics is not known. Our analysis of almost 200 group II intron copies from 90 sequenced Enterobacteriales genomes confirms their extinction-recolonization dynamics: patchy element distributions among genera and even among strains within genera, acquisition of new group II introns through plasmids or other mobile genetic elements, and evidence for recent proliferations in some genomes. Distributions of recent and past proliferations and of their respective homing sites further provide strong support for the Sel-DE model, suggesting that group II introns are deleterious to their hosts. Overall, our observations emphasize the critical impact of host properties on TE dynamics.

  4. A method for construction, cloning and expression of intron-less gene from unannotated genomic DNA.

    Science.gov (United States)

    Agrawal, Vineet; Gupta, Bharti; Banerjee, Uttam Chand; Roy, Nilanjan

    2008-11-01

    The present century has witnessed an unprecedented rise in genome sequences owing to various genome-sequencing programs. However, the same has not been replicated with cDNA or expressed sequence tags (ESTs). Hence, prediction of protein coding sequence of genes from this enormous collection of genomic sequences presents a significant challenge. While robust high throughput methods of cloning and expression could be used to meet protein requirements, lack of intron information creates a bottleneck. Computational programs designed for recognizing intron-exon boundaries for a particular organism or group of organisms have their own limitations. Keeping this in view, we describe here a method for construction of intron-less gene from genomic DNA in the absence of cDNA/EST information and organism-specific gene prediction program. The method outlined is a sequential application of bioinformatics to predict correct intron-exon boundaries and splicing by overlap extension PCR for spliced gene synthesis. The gene construct so obtained can then be cloned for protein expression. The method is simple and can be used for any eukaryotic gene expression.

  5. Allelic polymorphism in introns 1 and 2 of the HLA-DQA1 gene.

    Science.gov (United States)

    Voorter, C E M; de Groot, N G; Meertens, C M H; Bontrop, R E; van den Berg-Loonen, E M

    2005-01-01

    Human leukocyte antigen (HLA) class II antigens are highly polymorphic membrane glycoproteins, encoded by the A and B genes of DR, DQ, and DP. The polymorphism is mainly located in exon 2, with the exception of DQA1. Of the 27 DQA1 alleles presently known, 18 cannot be identified on the basis of exon 2 alone, but need additional information from the other exons. DQA1 has been reported to be the most ancient class II gene. For evolutionary comparison and to assess the degree of polymorphism outside the exons, the sequences of introns 1 and 2 were determined from 30 different cell lines, encompassing 15 different DQA1 alleles. The sequences revealed major nucleotide differences between the different lineages, whereas within each lineage few differences were present. Phylogenetic analysis of intron and exon sequences confirmed this lineage specificity. Altogether, the present data indicate that the HLA-DQA1 lineages represent ancient entities. The observed variation of the introns in alleles with identical exon sequences implicates conservative selection of the exons within a given lineage. Intron sequences may provide the means to set up an accurate typing system.

  6. Archaeal rRNA operons, intron splicing and homing endonucleases, RNA polymerase operons and phylogeny

    DEFF Research Database (Denmark)

    Garrett, Roger Antony; Aagaard, Claus Sindbjerg; Andersen, Morten

    1994-01-01

    Over the past decade our laboratory has had a strong interest in defining the phylogenetic status of the archaea. This has involved determining and analysing the sequences of operons of both rRNAs and RNA polymerases and it led to the discovery of the first archaeal rRNA intron. What follows...

  7. When a mid-intronic variation of DMD gene creates an ESE site.

    Science.gov (United States)

    Trabelsi, Madiha; Beugnet, Caroline; Deburgrave, Nathalie; Commere, Virgine; Orhant, Lucie; Leturcq, France; Chelly, Jamel

    2014-12-01

    Duchenne and Becker muscular dystrophy are X-linked allelic disorders caused by mutations in the DMD gene. The majority (65%) of these mutations are intragenic deletions/duplications that often lead to frameshift errors. Among the remaining ones, we find the mid-intronic mutations that usually create cryptic exons by activating potential splice sites. In this report, we identified, in a Becker muscular dystrophy patient, a mid-intronic variation that creates two ESE sites in intron 26 of DMD gene resulting in the insertion of a new cryptic exon in mRNA. Despite the out of frame character of this mutation, we observed the production of a reduced amount of full-size dystrophin which could be explained by the alternation between normal and altered splicing of dystrophin mRNA in this patient. To our knowledge, this is the first case report describing this novel pathogenic mechanism of mid-intronic variations of DMD gene. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. BIALLELIC POLYMORPHISM IN THE INTRON REGION OF B-TUBULIN GENE OF CRYPTOSPORIDIUM PARASITES

    Science.gov (United States)

    Nucleotide sequencing of polymerase chain reaction-amplified intron region of the Cryptosporidium parvum B-tubulin gene in 26 human and 15 animal isolates revealed distinct genetic polymorphism between the human and bovine genotypes. The separation of 2 genotypes of C. parvum is...

  9. Genomewide analysis of intronic microRNAs in rice and Arabidopsis

    Indian Academy of Sciences (India)

    mented with 3% sucrose and stratified at 4. ◦. C for two days in the dark prior to germination. .... RT-PCR results and the deep sequencing analysis together strongly suggest that most of the identified intronic miRNAs ...... Published on the Web: 13 December 2012. 324. Journal of Genetics, Vol. 91, No. 3, December 2012.

  10. Performance enhancement of pneumatic vibration isolation tables in low frequency range by time delay control

    Science.gov (United States)

    Shin, Yun-Ho; Kim, Kwang-Joon

    2009-04-01

    As environmental vibration requirements on precision equipment become more stringent, the use of pneumatic isolators has become more popular and their performance is subsequently required to be further improved. Dynamic performance of passive pneumatic isolators is related to various design parameters in a complicated manner and that in low-frequency range is limited by resonance frequency or volume of pneumatic chambers in practice. In this study, an active control technique, called as time delay control, is applied to a pneumatic isolator to enhance the isolation performance in the low frequency range where the passive techniques have difficulties. This time delay control technique is taken especially because it is known to be useful for the low frequency control. The procedure of applying the time delay control technique to the pneumatic isolator is presented, together with how to resolve distortion problems in actuator dynamics in implementing the active control technique into a pneumatic system. Effectiveness of the technique in enhancement of transmissibility performance is shown based on simulation as well as experiments. Comparisons with passive pneumatic isolators are also presented.

  11. Molecular evolution and phylogenetic utility of the petD group II intron: a case study in basal angiosperms.

    Science.gov (United States)

    Löhne, Cornelia; Borsch, Thomas

    2005-02-01

    Sequences of spacers and group I introns in plant chloroplast genomes have recently been shown to be very effective in phylogenetic reconstruction at higher taxonomic levels and not only for inferring relationships among species. Group II introns, being more frequent in those genomes than group I introns, may be further promising markers. Because group II introns are structurally constrained, we assumed that sequences of a group II intron should be alignable across seed plants. We designed universal amplification primers for the petD intron and sequenced this intron in a representative selection of 47 angiosperms and three gymnosperms. Our sampling of taxa is the most representative of major seed plant lineages to date for group II introns. Through differential analysis of structural partitions, we studied patterns of molecular evolution and their contribution to phylogenetic signal. Nonpairing stretches (loops, bulges, and interhelical nucleotides) were considerably more variable in both substitutions and indels than in helical elements. Differences among the domains are basically a function of their structural composition. After the exclusion of four mutational hotspots accounting for less than 18% of sequence length, which are located in loops of domains I and IV, all sequences could be aligned unambiguously across seed plants. Microstructural changes predominantly occurred in loop regions and are mostly simple sequence repeats. An indel matrix comprising 241 characters revealed microstructural changes to be of lower homoplasy than are substitutions. In showing Amborella first branching and providing support for a magnoliid clade through a synapomorphic indel, the petD data set proved effective in testing between alternative hypotheses on the basal nodes of the angiosperm tree. Within angiosperms, group II introns offer phylogenetic signal that is intermediate in information content between that of spacers and group I introns on the one hand and coding sequences

  12. Controlling Plasmon-Enhanced Fluorescence via Intersystem Crossing in Photoswitchable Molecules.

    Science.gov (United States)

    Wang, Mingsong; Hartmann, Gregory; Wu, Zilong; Scarabelli, Leonardo; Rajeeva, Bharath Bangalore; Jarrett, Jeremy W; Perillo, Evan P; Dunn, Andrew K; Liz-Marzán, Luis M; Hwang, Gyeong S; Zheng, Yuebing

    2017-10-01

    By harnessing photoswitchable intersystem crossing (ISC) in spiropyran (SP) molecules, active control of plasmon-enhanced fluorescence in the hybrid systems of SP molecules and plasmonic nanostructures is achieved. Specifically, SP-derived merocyanine (MC) molecules formed by photochemical ring-opening reaction display efficient ISC due to their zwitterionic character. In contrast, ISC in quinoidal MC molecules formed by thermal ring-opening reaction is negligible. The high ISC rate can improve fluorescence quantum yield of the plasmon-modified spontaneous emission, only when the plasmonic electromagnetic field enhancement is sufficiently high. Along this line, extensive photomodulation of fluorescence is demonstrated by switching the ISC in MC molecules at Au nanoparticle aggregates, where strongly enhanced plasmonic hot spots exist. The ISC-mediated plasmon-enhanced fluorescence represents a new approach toward controlling the spontaneous emission of fluorophores near plasmonic nanostructures, which expands the applications of active molecular plasmonics in information processing, biosensing, and bioimaging. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Proliferation of group II introns in the chloroplast genome of the green alga Oedocladium carolinianum (Chlorophyceae

    Directory of Open Access Journals (Sweden)

    Jean-Simon Brouard

    2016-10-01

    Full Text Available Background The chloroplast genome sustained extensive changes in architecture during the evolution of the Chlorophyceae, a morphologically and ecologically diverse class of green algae belonging to the Chlorophyta; however, the forces driving these changes are poorly understood. The five orders recognized in the Chlorophyceae form two major clades: the CS clade consisting of the Chlamydomonadales and Sphaeropleales, and the OCC clade consisting of the Oedogoniales, Chaetophorales, and Chaetopeltidales. In the OCC clade, considerable variations in chloroplast DNA (cpDNA structure, size, gene order, and intron content have been observed. The large inverted repeat (IR, an ancestral feature characteristic of most green plants, is present in Oedogonium cardiacum (Oedogoniales but is lacking in the examined members of the Chaetophorales and Chaetopeltidales. Remarkably, the Oedogonium 35.5-kb IR houses genes that were putatively acquired through horizontal DNA transfer. To better understand the dynamics of chloroplast genome evolution in the Oedogoniales, we analyzed the cpDNA of a second representative of this order, Oedocladium carolinianum. Methods The Oedocladium cpDNA was sequenced and annotated. The evolutionary distances separating Oedocladium and Oedogonium cpDNAs and two other pairs of chlorophycean cpDNAs were estimated using a 61-gene data set. Phylogenetic analysis of an alignment of group IIA introns from members of the OCC clade was performed. Secondary structures and insertion sites of oedogonialean group IIA introns were analyzed. Results The 204,438-bp Oedocladium genome is 7.9 kb larger than the Oedogonium genome, but its repertoire of conserved genes is remarkably similar and gene order differs by only one reversal. Although the 23.7-kb IR is missing the putative foreign genes found in Oedogonium, it contains sequences coding for a putative phage or bacterial DNA primase and a hypothetical protein. Intergenic sequences are 1.5-fold

  14. Angular control of optical cavities in a radiation-pressure-dominated regime: the Enhanced LIGO case.

    Science.gov (United States)

    Dooley, Katherine L; Barsotti, Lisa; Adhikari, Rana X; Evans, Matthew; Fricke, Tobin T; Fritschel, Peter; Frolov, Valera; Kawabe, Keita; Smith-Lefebvre, Nicolás

    2013-12-01

    We describe the angular sensing and control (ASC) of 4 km detectors of the Laser Interferometer Gravitational-Wave Observatory (LIGO). Enhanced LIGO, the culmination of the first generation LIGO detectors, operated between 2009 and 2010 with about 40 kW of laser power in the arm cavities. In this regime, radiation-pressure effects are significant and induce instabilities in the angular opto-mechanical transfer functions. Here we present and motivate the ASC design in this extreme case and present the results of its implementation in Enhanced LIGO. Highlights of the ASC performance are successful control of opto-mechanical torsional modes, relative mirror motions of ≤ 1×10(-7) rad rms, and limited impact on in-band strain sensitivity.

  15. MR Damper Controlled Vibration Absorber for Enhanced Mitigation of Harmonic Vibrations

    Directory of Open Access Journals (Sweden)

    Felix Weber

    2016-12-01

    Full Text Available This paper describes a semi-active vibration absorber (SVA concept based on a real-time controlled magnetorheological damper (MR-SVA for the enhanced mitigation of structural vibrations due to harmonic disturbing forces. The force of the MR damper is controlled in real-time to generate the frequency and damping controls according to the behaviour of the undamped vibration absorber for the actual frequency of vibration. As stiffness and damping emulations in semi-active actuators are coupled quantities the control is formulated to prioritize the frequency control by the controlled stiffness. The control algorithm is augmented by a stiffness correction method ensuring precise frequency control when the desired control force is constrained by the semi-active restriction and residual force of the MR damper. The force tracking task is solved by a model-based feed forward with feedback correction. The MR-SVA is numerically and experimentally validated for the primary structure with nominal eigenfrequency and when de-tuning of −10%, −5%, +5% and +10% is present. Both validations demonstrate that the MR-SVA improves the vibration reduction in the primary structure by up to 55% compared to the passive tuned mass damper (TMD. Furthermore, it is shown that the MR-SVA with only 80% of tuned mass leads to approximately the same enhanced performance while the associated increased relative motion amplitude of the tuned mass is more than compensated be the reduced dimensions of the mass. Therefore, the MR-SVA is an appropriate solution for the mitigation of tall buildings where the pendulum mass can be up to several thousands of metric tonnes and space for the pendulum damper is limited.

  16. Control of ordered mesoporous titanium dioxide nanostructures formed using plasma enhanced glancing angle deposition

    Energy Technology Data Exchange (ETDEWEB)

    Gibson, Des [Institute of Thin Films, Sensors & Imaging, Scottish Universities Physics Alliance, University of West of Scotland, Paisley, PA1 2BE (United Kingdom); Child, David, E-mail: david.child@uws.ac.uk [Institute of Thin Films, Sensors & Imaging, Scottish Universities Physics Alliance, University of West of Scotland, Paisley, PA1 2BE (United Kingdom); Song, Shigeng; Zhao, Chao [Institute of Thin Films, Sensors & Imaging, Scottish Universities Physics Alliance, University of West of Scotland, Paisley, PA1 2BE (United Kingdom); Alajiani, Yahya [Institute of Thin Films, Sensors & Imaging, Scottish Universities Physics Alliance, University of West of Scotland, Paisley, PA1 2BE (United Kingdom); Department of Physics, Faculty of Science, Jazan University, Jazan (Saudi Arabia); Waddell, Ewan [Thin Film Solutions Ltd, West of Scotland Science Park, Glasgow, G20 0TH (United Kingdom)

    2015-10-01

    Three dimensional nanostructures of mesoporous (pore diameter between 2-50 nm) nanocrystalline titania (TiO{sub 2}) were produced using glancing angle deposition combined with plasma ion assisted deposition, providing plasma enhanced glancing angle deposition eliminating the need for post-annealing to achieve film crystallinity. Electron beam evaporation was chosen to deposit nanostructures at various azimuthal angles, achieving designed variation in three dimensional nanostructure. A thermionic broad beam hollow cathode plasma source was used to enhance electron beam deposition, with ability to vary in real time ion fluxes and energies providing a means to modify and control TiO{sub 2} nanostructure real time with controlled density and porosity along and lateral to film growth direction. Plasma ion assisted deposition was carried out at room temperature using a hollow cathode plasma source, ensuring low heat loading to the substrate during deposition. Plasma enhanced glancing angle TiO{sub 2} structures were deposited onto borosilicate microscope slides and used to characterise the effects of glancing angle and plasma ion energy distribution function on the optical and nanostructural properties. Variation in TiO{sub 2} refractive index from 1.40 to 2.45 (@ 550 nm) using PEGLAD is demonstrated. Results and analysis of the influence of plasma enhanced glancing angle deposition on evaporant path and resultant glancing angle deviation from standard GLAD are described. Control of mesoporous morphology is described, providing a means of optimising light trapping features and film porosity, relevant to applications such as fabrication of dye sensitised solar cells. - Highlights: • Plasma assistance during glancing angle deposition enables control of morphology. • Ion energy variation during glancing angle deposition varies columnar angle • Column thickness of glancing angle deposition dependant on ion current density • Ion current density variation during

  17. Dynamic Stability Enhancement of a Multi Machine Electric Power System Using Unified Power Flow Controller

    OpenAIRE

    Ahmad Memaripour; Sayed Mojtaba Shirvani Boroujeni; Reza Hemmati

    2011-01-01

    This study presents the application of Unified Power Flow Controller (UPFC) to improvement dynamic stability of a multi-machine electric power system installed with UPFC. Since UPFC is considered to mitigate Low Frequency Oscillations (LFO) and stability enhancement, therefore a supplementary stabilizer based on UPFC (like power system stabilizer) is designed to reach the defined purpose. Intelligence optimization methods such as Particle Swarm Optimization (PSO) and Genetic Algorithms (GA) a...

  18. Intelligent Control of UPFC for Enhancing Transient Stability on Multi-Machine Power Systems

    Directory of Open Access Journals (Sweden)

    Hassan Barati

    2010-01-01

    Full Text Available One of the benefit of FACTS devices is increase of stability in power systems with control active and reactive power at during the fault in power system. Although, the power system stabilizers (PSSs have been one of the most common controls used to damp out oscillations, this device may not produce enough damping especially to inter-area mode and therefore, there is an increasing interest in using FACTS devices to aid in damping of these oscillations. In This paper, UPFC is used for damping oscillations and to enhance the transient stability performance of power systems. The controller parameters are designed using an efficient version of the Takagi-Sugeno fuzzy control scheme. The function based Takagi-Sugeno-Kang (TSK fuzzy controller uses. For optimization parameters of fuzzy PI controller, the GA, PSO and HGAPSO algorithms are used. The computer simulation results, the effect of UPFC with conventional PI controller, fuzzy PI controller and intelligent controllers (GA, PSO and HGAPSO for damping the local-mode and inter-area mode of under large and small disturbances in the four-machine two-area power system evaluated and compared.

  19. Structural control of metamaterial oscillator strength and electric field enhancement at terahertz frequencies

    DEFF Research Database (Denmark)

    Keiser, G. R.; Seren, H. R.; Strikwerda, Andrew C.

    2014-01-01

    The design of artificial nonlinear materials requires control over internal resonant charge densities and local electric field distributions. We present a MM design with a structurally controllable oscillator strength and local electric field enhancement at terahertz frequencies. The MM consists...... of a split ring resonator (SRR) array stacked above an array of closed conducting rings. An in-plane, lateral shift of a half unit cell between the SRR and closed ring arrays results in an increase of the MM oscillator strength by a factor of 4 and a 40% change in the amplitude of the resonant electric field...

  20. Enhanced LVRT Control Strategy for DFIG-Based WECS in Weak Grid

    DEFF Research Database (Denmark)

    Abulanwar, Elsayed; Chen, Zhe; Iov, Florin

    2013-01-01

    An enhanced coordinated low voltage ride-through, LVRT, control strategy for a Doubly-fed Induction generator (DFIG)-based wind energy conversion system, WECS, connected to a weak grid is presented in this paper. The compliance with the grid code commitments is also considered. A proposed decoupled...... protection scheme. Furthermore, additional compensation terms are incorporated with the traditional GSC and rotor side converter, RSC, controllers to effectively suppress rotor as well as stator currents and meanwhile regulate the rotor speed. A diverse set of voltage excursions are conducted to evaluate...

  1. A videotaped intervention to enhance child control and reduce anxiety of the pain of dental injections.

    Science.gov (United States)

    Weinstein, P; Raadal, M; Naidu, S; Yoshida, T; Kvale, G; Milgrom, P

    2003-12-01

    While the psychological literature shows that perceptions of uncontrollability contribute to anxiety and other pathologies, interventions that enhance perceived control have been shown to reduce anxiety. This study attempted to assess a brief videotape to enhance child perceived control in a dental setting. 101 children aged 7-9 years completed warm-up procedures and viewed either: a) the experimental intervention, a 2 minutes video of a dentist explaining what an injection will feel like and proposing hand raising as a signal mechanism; or b) the control condition, a 2 minutes video of Disneyland. Fear of dental injections was assessed on a 10 cm visual analogue scale before and after the intervention. In the experimental group there was a significant fear reduction from pre- to post-intervention, while this was not the case in the control group. Children with higher pre-existing levels of fear benefited more from the intervention than children with lower levels of fear. The results of this pilot study suggest that intervention packages that impact child control have promise in lowering anxiety.

  2. Enhancing brain-machine interface (BMI) control of a hand exoskeleton using electrooculography (EOG).

    Science.gov (United States)

    Witkowski, Matthias; Cortese, Mario; Cempini, Marco; Mellinger, Jürgen; Vitiello, Nicola; Soekadar, Surjo R

    2014-12-16

    Brain-machine interfaces (BMIs) allow direct translation of electric, magnetic or metabolic brain signals into control commands of external devices such as robots, prostheses or exoskeletons. However, non-stationarity of brain signals and susceptibility to biological or environmental artifacts impede reliable control and safety of BMIs, particularly in daily life environments. Here we introduce and tested a novel hybrid brain-neural computer interaction (BNCI) system fusing electroencephalography (EEG) and electrooculography (EOG) to enhance reliability and safety of continuous hand exoskeleton-driven grasping motions. 12 healthy volunteers (8 male, mean age 28.1 ± 3.63y) used EEG (condition #1) and hybrid EEG/EOG (condition #2) signals to control a hand exoskeleton. Motor imagery-related brain activity was translated into exoskeleton-driven hand closing motions. Unintended motions could be interrupted by eye movement-related EOG signals. In order to evaluate BNCI control and safety, participants were instructed to follow a visual cue indicating either to move or not to move the hand exoskeleton in a random order. Movements exceeding 25% of a full grasping motion when the device was not supposed to be moved were defined as safety violation. While participants reached comparable control under both conditions, safety was frequently violated under condition #1 (EEG), but not under condition #2 (EEG/EOG). EEG/EOG biosignal fusion can substantially enhance safety of assistive BNCI systems improving their applicability in daily life environments.

  3. Active control of electromagnetic radiation through an enhanced thermo-optic effect.

    Science.gov (United States)

    Sheng, Chong; Liu, Hui; Zhu, Shining; Genov, Dentcho A

    2015-03-09

    The control of electromagnetic radiation in transformation optical metamaterials brings the development of vast variety of optical devices. Of a particular importance is the possibility to control the propagation of light with light. In this work, we use a structured planar cavity to enhance the thermo-optic effect in a transformation optical waveguide. In the process, a control laser produces apparent inhomogeneous refractive index change inside the waveguides. The trajectory of a second probe laser beam is then continuously tuned in the experiment. The experimental results agree well with the developed theory. The reported method can provide a new approach toward development of transformation optical devices where active all-optical control of the impinging light can be achieved.

  4. Controller Parameter Optimization for Nonlinear Systems Using Enhanced Bacteria Foraging Algorithm

    Directory of Open Access Journals (Sweden)

    V. Rajinikanth

    2012-01-01

    Full Text Available An enhanced bacteria foraging optimization (EBFO algorithm-based Proportional + integral + derivative (PID controller tuning is proposed for a class of nonlinear process models. The EBFO algorithm is a modified form of standard BFO algorithm. A multiobjective performance index is considered to guide the EBFO algorithm for discovering the best possible value of controller parameters. The efficiency of the proposed scheme has been validated through a comparative study with classical BFO, adaptive BFO, PSO, and GA based controller tuning methods proposed in the literature. The proposed algorithm is tested in real time on a nonlinear spherical tank system. The real-time results show that, EBFO tuned PID controller gives a smooth response for setpoint tracking performance.

  5. tDCS over the left prefrontal cortex enhances cognitive control for positive affective stimuli.

    Directory of Open Access Journals (Sweden)

    Marie-Anne Vanderhasselt

    Full Text Available Transcranial Direct Current Stimulation (tDCS is a neuromodulation technique with promising results for enhancing cognitive information processes. So far, however, research has mainly focused on the effects of tDCS on cognitive control operations for non-emotional material. Therefore, our aim was to investigate the effects on cognitive control considering negative versus positive material. For this sham-controlled, within-subjects study, we selected a homogeneous sample of twenty-five healthy participants. By using behavioral measures and event related potentials (ERP as indexes, we aimed to investigate whether a single session of anodal tDCS of the left dorsolateral prefrontal cortex (DLPFC would have specific effects in enhancing cognitive control for positive and negative valenced stimuli. After tDCS over the left DLPFC (and not sham control stimulation, we observed more negative N450 amplitudes along with faster reaction times when inhibiting a habitual response to happy compared to sad facial expressions. Gender did not influence the effects of tDCS on cognitive control for emotional information. In line with the Valence Theory of side-lateralized activity, this stimulation protocol might have led to a left dominant (relative to right prefrontal cortical activity, resulting in augmented cognitive control specifically for positive relative to negative stimuli. To verify that tDCS induces effects that are in line with all aspects of the well known Valence Theory, future research should investigate the effects of tDCS over the left vs. right DLPFC on cognitive control for emotional information.

  6. Genetic analysis of optic nerve head coloboma in the Nova Scotia Duck Tolling Retriever identifies discordance with the NHEJ1 intronic deletion (collie eye anomaly mutation).

    Science.gov (United States)

    Brown, Emily A; Thomasy, Sara M; Murphy, Christopher J; Bannasch, Danika L

    2018-03-01

    Collie eye anomaly (CEA) encompasses a spectrum of different ophthalmic phenotypes from clinically inconsequential choroidal hypoplasia to blindness from coloboma of the optic nerve head (ONH). A previous study found a 7.8-kb deletion in intron 4 of the NHEJ1 gene to be associated with CEA. A genetic test based on this association is recommended for many breeds, including the Nova Scotia Duck Tolling Retriever (NSDTR). Collection of ONH coloboma-affected NSDTR showed lack of concordance of the NHEJ1 intronic deletion with ONH coloboma. Using genomewide single nucleotide polymorphism (SNP) genotyping in 7 ONH coloboma-affected NSDTR cases and 47 unaffected NSDTR controls with no ophthalmic signs, one SNP, located on chromosome 7, demonstrated genomewide significance. However, high genomic inflation may have confounded the results. Therefore, the genomewide association study was repeated using EMMAX to control for population structure in the cohort of 7 cases and 47 controls. However, no regions of the genome were significantly associated with ONH coloboma. These results failed to document significant association with the CEA locus. Due to the complex genetic etiology of ONH coloboma, the NHEJ1 intronic deletion test results should be carefully considered when making breeding decisions. If the goal is to select for visually competent dogs, our data suggest that eye examinations of puppies would be more effective as a guide in selection of breeding pairs than relying solely on currently available genetic tests. © 2017 The Authors. Veterinary Ophthalmology published by Wiley Periodicals, Inc. on behalf of American College of Veterinary Ophthalmologists.

  7. Power system security enhancement through direct non-disruptive load control

    Science.gov (United States)

    Ramanathan, Badri Narayanan

    The transition to a competitive market structure raises significant concerns regarding reliability of the power grid. A need to build tools for security assessment that produce operating limit boundaries for both static and dynamic contingencies is recognized. Besides, an increase in overall uncertainty in operating conditions makes corrective actions at times ineffective leaving the system vulnerable to instability. The tools that are in place for stability enhancement are mostly corrective and suffer from lack of robustness to operating condition changes. They often pose serious coordination challenges. With deregulation, there have also been ownership and responsibility issues associated with stability controls. However, the changing utility business model and the developments in enabling technologies such as two-way communication, metering, and control open up several new possibilities for power system security enhancement. This research proposes preventive modulation of selected loads through direct control for power system security enhancement. Two main contributions of this research are the following: development of an analysis framework and two conceptually different analysis approaches for load modulation to enhance oscillatory stability, and the development and study of algorithms for real-time modulation of thermostatic loads. The underlying analysis framework is based on the Structured Singular Value (SSV or mu) theory. Based on the above framework, two fundamentally different approaches towards analysis of the amount of load modulation for desired stability performance have been developed. Both the approaches have been tested on two different test systems: CIGRE Nordic test system and an equivalent of the Western Electric Coordinating Council test system. This research also develops algorithms for real-time modulation of thermostatic loads that use the results of the analysis. In line with some recent load management programs executed by utilities, two

  8. A novel control strategy for enhancing the LVRT and voltage support capabilities of DFIG

    Science.gov (United States)

    Shen, Yangwu; Zhang, Bin; Liang, Liqing; Cui, Ting

    2018-02-01

    A novel integrated control strategy is proposed in this paper to enhance the low voltage ride through capacity for the double-fed induction generator by equipping an energy storage system. The energy storage system is installed into the DC-link capacitor of the DFIG and used to control the DC-link voltage during normal or transient operations. The energy storage device will absorb or compensate the power difference between the captured wind power and the power injected to the grid during the normal and transient period, and the grid side converter can be free from maintaining the voltage stability of the DC-link capacitor. Thus, the grid-side converter is changed to reactive power support while the rotor-side converter is used to control the maximum power production during normal operation. The grid-side converter and rotor-side converter will act as reactive power sources to further enhance the voltage support capability of double-fed induction generator during the transient period. Numerical Simulation are performed to validate the effectiveness of the proposed control designs.

  9. Robust control design of PSS for dynamic stability enhancement of power system

    Directory of Open Access Journals (Sweden)

    Abdelghani Choucha

    2017-06-01

    Full Text Available A Sliding Mode Controller (SMC is adopted in this work with a Proportional Integral Derivative (PID to achieve robust control signal and employ it instead of Power System Stabilizer (PSS. The major technique is basically focusing on the control accuracy. The main proposal is that the effective property of PID and high characteristics of SMC are combined to eliminate the chattering effect of SMC in order to generate best control signal to the excitation system. Speed deviation is chosen as sliding variables. The robust design of SMC-PID has been employed to enhance the power system stability and further to damp out strongly the system oscillations that caused by the disturbances. In order to validate the robustness of the mentioned scheme, the proposed proposition is evaluated on Single Machine Infinite Bus (SMIB power system under different perturbations with pre-specified operating condition. For comparison, the tested power system is carried separately through different designed controllers. The simulation results have demonstrated the high performance of mentioned controller that attained best results compared to various controllers.

  10. Energy Conservation in an Office Building Using an Enhanced Blind System Control

    Directory of Open Access Journals (Sweden)

    Edorta Carrascal-Lekunberri

    2017-02-01

    Full Text Available The two spaces office module is usually considered as a representative case-study to analyse the energetic improvement in office buildings. In this kind of buildings, the use of a model predictive control (MPC scheme for the climate system control provides energy savings over 15% in comparison to classic control policies. This paper focuses on the influence of solar radiation on the climate control of the office module under Belgian weather conditions. Considering MPC as main climate control, it proposes a novel distributed enhanced control for the blind system (BS that takes into account part of the predictive information of the MPC. In addition to the savings that are usually achieved by MPC, it adds a potential 15% improvement in global energy use with respect to the usually proposed BS hysteresis control. Moreover, from the simulation results it can be concluded that the thermal comfort is also improved. The proposed BS scheme increases the energy use ratio between the thermally activated building system (TABS and air-handling unit (AHU; therefore increasing the use of TABS and allowing economic savings, due to the use of more cost-effective thermal equipment.

  11. Available transfer capability evaluation and enhancement using various FACTS controllers: Special focus on system security

    Directory of Open Access Journals (Sweden)

    M. Venkateswara Rao

    2016-03-01

    Full Text Available Nowadays, because of the deregulation of the power industry the continuous increase of the load increases the necessity of calculation of available transfer capability (ATC of a system to analyze the system security. With this calculation, the scheduling of generator can be decided to decrease the system severity. Further, constructing new transmission lines, new substations are very cost effective to meet the increasing load and to increase the transfer capability. Hence, an alternative way to increase the transfer capability is use of flexible ac transmission system (FACTS controllers. In this paper, SSSC, STACOM and UPFC are considered to show the effect of these controllers in enhancing system ATC. For this, a novel current based modeling and optimal location strategy of these controllers are presented. The proposed methodology is tested on standard IEEE-30 bus and IEEE-57 bus test systems with supporting numerical and graphical results.

  12. Voltage-controlled colour-tunable microcavity OLEDs with enhanced colour purity

    International Nuclear Information System (INIS)

    Choy, Wallace C H; Niu, J H; Li, W L; Chui, P C

    2008-01-01

    The emission spectrum of single-unit voltage-controlled colour-tunable organic light emitting devices (OLEDs) has been theoretically and experimentally studied. Our results show that by introducing the microcavity structure, the colour purity of not only the destination colour but also the colour-tunable route can be enhanced, while colour purity is still an issue in typical single-unit voltage-controlled colour-tunable OLEDs. With the consideration of the periodical cycling of resonant wavelength and absorption loss of the metal electrodes, the appropriate change in the thickness of the microcavity structure has been utilized to achieve voltage-controlled red-to-green and red-to-blue colour-tunable OLEDs without adding dyes or other organic materials to the OLEDs

  13. Robustness Enhancement of MRAC Using Modification Techniques for Speed Control of Three Phase Induction Motor

    Directory of Open Access Journals (Sweden)

    Amjad J. Humaidi

    2017-12-01

    Full Text Available This paper addresses the lack of robustness in three phase Induction Motors (I.M speed control in presence of uncertainty and external unknown disturbance of Model Reference Adaptive Control (MRAC, and present an enhancement of robustness by employing the adaptive law modifications for robustness. Considered modifications were Dead zone modification, Sigma modification, e-modification and projection operator algorithm modification. Speed control of three phase induction motor in this paper was depend on decoupling benefits of rotor flux Indirect Field Orientation (IFO. Simulation results shows improved robustness characteristics and performance. In order to make the case study under consideration more realistic, the work considered the limitation imposed on supplied voltage in real application, where this was the other challenge which has been avoided by many researchers.

  14. Chaos Enhanced Differential Evolution in the Task of Evolutionary Control of Discrete Chaotic LOZI Map

    Directory of Open Access Journals (Sweden)

    Roman Senkerik

    2016-01-01

    Full Text Available In this paper, evolutionary technique Differential Evolution (DE is used for the evolutionary tuning of controller parameters for the stabilization of selected discrete chaotic system, which is the two-dimensional Lozi map. The novelty of the approach is that the selected controlled discrete dissipative chaotic system is used within Chaos enhanced heuristic concept as the chaotic pseudo-random number generator to drive the mutation and crossover process in the DE. The idea was to utilize the hidden chaotic dynamics in pseudo-random sequences given by chaotic map to help Differential evolution algorithm in searching for the best controller settings for the same chaotic system. The optimizations were performed for three different required final behavior of the chaotic system, and two types of developed cost function. To confirm the robustness of presented approach, comparisons with canonical DE strategy and PSO algorithm have been performed.

  15. Power system security enhancement with unified power flow controller under multi-event contingency conditions

    Directory of Open Access Journals (Sweden)

    S. Ravindra

    2017-03-01

    Full Text Available Power system security analysis plays key role in enhancing the system security and to avoid the system collapse condition. In this paper, a novel severity function is formulated using transmission line loadings and bus voltage magnitude deviations. The proposed severity function and generation fuel cost objectives are analyzed under transmission line(s and/or generator(s contingency conditions. The system security under contingency conditions is analyzed using optimal power flow problem. An improved teaching learning based optimization (ITLBO algorithm has been presented. To enhance the system security under contingency conditions in the presence of unified power flow controller (UPFC, it is necessary to identify an optimal location to install this device. Voltage source based power injection model of UPFC, incorporation procedure and optimal location identification strategy based on line overload sensitivity indexes are proposed. The entire proposed methodology is tested on standard IEEE-30 bus test system with supporting numerical and graphical results.

  16. A randomized controlled trial study of a technology-enhanced approach to early literacy

    Directory of Open Access Journals (Sweden)

    Roisin P. Corcoran

    2014-01-01

    Full Text Available This paper describes a plan to formatively evaluate, via a cluster randomized control trial (RCT design, a U.S. Department of Education Investing in Innovation (i3 study of Around the Corner, a technology-enhanced approach to early literacy that combines the Success for All Foundation’s Curiosity Corner preschool and kindergarten programs with technology enhancements from the award-winning PBS show Between the Lions and other multimedia content. After development and piloting in collaboration with partner schools, a formative evaluation of Around the Corner will be carried out, with qualitative measures and a quantitative evaluation with random assignment of 12 schools and students within schools to conditions. The expected outcome is a fully-developed program ready to be more broadly evaluated and disseminated nationally.

  17. Nanoparticle-Enabled Transdermal Drug Delivery Systems for Enhanced Dose Control and Tissue Targeting

    Directory of Open Access Journals (Sweden)

    Brian C. Palmer

    2016-12-01

    Full Text Available Transdermal drug delivery systems have been around for decades, and current technologies (e.g., patches, ointments, and creams enhance the skin permeation of low molecular weight, lipophilic drugs that are efficacious at low doses. The objective of current transdermal drug delivery research is to discover ways to enhance skin penetration of larger, hydrophilic drugs and macromolecules for disease treatment and vaccination. Nanocarriers made of lipids, metals, or polymers have been successfully used to increase penetration of drugs or vaccines, control drug release, and target drugs to specific areas of skin in vivo. While more research is needed to identify the safety of nanocarriers, this technology has the potential to expand the use of transdermal routes of administration to a wide array of therapeutics. Here, we review the current state of nanoparticle skin delivery systems with special emphasis on targeting skin diseases.

  18. Ab initio quantum-enhanced optical phase estimation using real-time feedback control

    DEFF Research Database (Denmark)

    Berni, Adriano; Gehring, Tobias; Nielsen, Bo Melholt

    2015-01-01

    as demonstrated in a variety of different optical systems(3-8). Most of these accounts, however, deal with the measurement of a very small shift of an already known phase, which is in stark contrast to ab initio phase estimation where the initial phase is unknown(9-12). Here, we report on the realization......Optical phase estimation is a vital measurement strategy that is used to perform accurate measurements of various physical quantities including length, velocity and displacements(1,2). The precision of such measurements can be greatly enhanced by the use of entangled or squeezed states of light...... of a quantum-enhanced and fully deterministic ab initio phase estimation protocol based on real-time feedback control. Using robust squeezed states of light combined with a real-time Bayesian adaptive estimation algorithm, we demonstrate deterministic phase estimation with a precision beyond the quantum shot...

  19. The T -786C, G894T, and Intron 4 VNTR (4a/b) Polymorphisms of the Endothelial Nitric Oxide Synthase Gene in Prostate Cancer Cases.

    Science.gov (United States)

    Diler, S B; Öden, A

    2016-02-01

    In previously conducted some studies it has been revealed that nitric oxide (NO) and nitric oxide synthase (NOS) system play a significant role in carcinogenesis. Nitric oxide (NO) is regulated by endothelial nitric oxide synthase (eNOS) enzyme which is one of the isoenzymes of NO synthase (NOS). In this study we have tried to come to a conclusion about whether eNOS gene T -786C, G894T and Intron 4 VNTR (4a/b) polymorphisms might be considered as a risk factor causing prostate cancer (PCa) or not. A total of 200 subjects were included in this research. 84 patients with PCa (mean age 70.0 ± 6.4) and 116 healthy controls (mean age 69.9 ± 7.5) were recruited in this case-control study. Genomic DNA was extracted using the QIAamp DNA Blood Mini Kit (QIAGEN GmbH, Maryland, USA), according to the manufacturer's guidelines. The T-786C, G894T and Intron 4 VNTR (4a/b) polymorphisms were amplified using polymerase chain reation (PCR), detected by restriction fragment length polymorphism (RFLP). For T -786C polymorphism CC genotype [odds ratio (OR): 0.34, 95% confidence interval (CI): 0.15-0.78, P = 0.009)] and allele frequency (OR: 0.631, CI: 0.421-0.946, P = 0.026) is significant for control. In patients with PCa eNOS G894T polymorphism, both GT (OR: 0.069, CI: 0.027-0.174; P = 0.0001) and TT (OR: 0.040, CI: 0.013-0.123; P = = 0.0001) genotype distribution, and also T allele frequency (OR: 0.237, CI: 0.155-0.362, P = 0.0001) were considered significant statistically. While genotype distribution for the other polymorphism eNOS, intron 4 VNTR (4a/b), is insignificant statistically, "a" allele frequency was found out to be significant (OR: 2.223, CI: 1.311-3.769, P = 0.003). In this study we indicated that genotype and allele frequencies of eNOS T -786C and G894T polymorphisms are statistically significant in patients with PCa. eNOS T -786C and G894T polymorphisms may be associated with PCa susceptibility in the Turkish population. In contrast, intron 4 VNTR (4a

  20. Output-Feedback Control of a Chaotic MEMS Resonator for Oscillation Amplitude Enhancement

    Directory of Open Access Journals (Sweden)

    Alexander Jimenez-Triana

    2014-01-01

    Full Text Available The present work addresses the problem of chaos control in an electrostatic MEMS resonator by using an output-feedback control scheme. One of the unstable orbits immersed in the chaotic attractor is stabilized in order to produce a sustained oscillation of the movable plate composing the microstructure. The orbit is carefully chosen so as to produce a high amplitude oscillation. This approach allows the enhancement of oscillation amplitude of the resonator at a reduced control effort, since the unstable orbit already exists in the system and it is not necessary to spend energy to create it. Realistic operational conditions of the MEMS are considered including parametric uncertainties in the model and constraints due to the difficulty in measuring the speed of the plates of the microstructure. A control law is constructed recursively by using the technique of backstepping. Finally, numerical simulations are carried out to confirm the validity of the developed control scheme and to demonstrate the effect of controlling orbits immersed in the chaotic attractor.

  1. Insulin enhances the gain of arterial baroreflex control of muscle sympathetic nerve activity in humans.

    Science.gov (United States)

    Young, Colin N; Deo, Shekhar H; Chaudhary, Kunal; Thyfault, John P; Fadel, Paul J

    2010-09-15

    Recent animal studies indicate that insulin increases arterial baroreflex control of lumbar sympathetic nerve activity; however, the extent to which these findings can be extrapolated to humans is unknown. To begin to address this, muscle sympathetic nerve activity (MSNA) and arterial blood pressure were measured in 19 healthy subjects (27 ± 1 years) before, and for 120 min following, two common methodologies used to evoke sustained increases in plasma insulin: a mixed meal and a hyperinsulinaemic euglycaemic clamp. Weighted linear regression analysis between MSNA and diastolic blood pressure was used to determine the gain (i.e. sensitivity) of arterial baroreflex control of MSNA. Plasma insulin was significantly elevated within 30 min following meal intake (34 ± 6 uIU ml(1); P gain for burst incidence and total MSNA was increased and remained elevated for the duration of the protocol (e.g. burst incidence gain: 3.29 ± 0.54 baseline vs. 5.64 ± 0.67 bursts (100 heart beats)(1) mmHg(1) at 120 min; P gain was similarly enhanced (e.g. burst incidence gain: 2.44 ± 0.29 baseline vs. 4.74 ± 0.71 bursts (100 heart beats)(1) mmHg(1) at 120 min; P gain remained unchanged. These findings demonstrate, for the first time in healthy humans, that increases in plasma insulin enhance the gain of arterial baroreflex control of MSNA.

  2. Enhancing Three-dimensional Movement Control System for Assemblies of Machine-Building Facilities

    Science.gov (United States)

    Kuzyakov, O. N.; Andreeva, M. A.

    2018-01-01

    Aspects of enhancing three-dimensional movement control system are given in the paper. Such system is to be used while controlling assemblies of machine-building facilities, which is a relevant issue. The base of the system known is three-dimensional movement control device with optical principle of action. The device consists of multi point light emitter and light receiver matrix. The processing of signals is enhanced to increase accuracy of measurements by switching from discrete to analog signals. Light receiver matrix is divided into four areas, and the output value of each light emitter in each matrix area is proportional to its luminance level. Thus, determing output electric signal value of each light emitter in corresponding area leads to determing position of multipoint light emitter and position of object tracked. This is done by using Case-based reasoning method, the precedent in which is described as integral signal value of each matrix area, coordinates of light receivers, which luminance level is high, and decision to be made in this situation.

  3. Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae

    DEFF Research Database (Denmark)

    Haugen, P; Huss, V A; Nielsen, Henrik

    1999-01-01

    The green alga Scenedesmus pupukensis and the red alga Porphyra spiralis contain large group-IC1 introns in their nuclear small subunit ribosomal RNA genes due to the presence of open reading frames at the 5' end of the introns. The putative 555 amino-acid Scenedesmus-encoded protein harbors...... a sequence motif resembling the bacterial S9 ribosomal proteins. The Porphyra intron self-splices in vitro, and generates both ligated exons and a full-length intron RNA circle. The Porphyra intron has an unusual structural organization by encoding a potential 149 amino-acid homing-endonuclease-like protein...

  4. Learning to live together: mutualism between self-splicing introns and their hosts

    Directory of Open Access Journals (Sweden)

    Chalamcharla Venkata R

    2011-04-01

    Full Text Available Abstract Group I and II introns can be considered as molecular parasites that interrupt protein-coding and structural RNA genes in all domains of life. They function as self-splicing ribozymes and thereby limit the phenotypic costs associated with disruption of a host gene while they act as mobile DNA elements to promote their spread within and between genomes. Once considered purely selfish DNA elements, they now seem, in the light of recent work on the molecular mechanisms regulating bacterial and phage group I and II intron dynamics, to show evidence of co-evolution with their hosts. These previously underappreciated relationships serve the co-evolving entities particularly well in times of environmental stress.

  5. Phase chaos generation and security enhancement by introducing fine-controllable dispersion

    Science.gov (United States)

    Yi, Lilin; Ke, Junxiang; Xia, Guangqiong; Hu, Weisheng

    2018-01-01

    For the first time, we experimentally demonstrate phase chaos generation by introducing a fine-controllable dispersion module into the feedback-delayed loop. To study the effect of this specific nonlinearity, we demonstrate the nonlinear dynamics evolution route in terms of the dependence of dispersion and feedback gain parameters by both experiment and simulation, which show good agreement. We also investigate the synchronization error variation with the dispersion mismatch to evaluate the security level of the proposed phase chaos system. The results show that the proposed approach can simultaneously simplify the phase chaos synchronization and enhance the key space, which has potential to be used in high-speed chaotic optical communications.

  6. Enhancing the photon-extraction efficiency of site-controlled quantum dots by deterministically fabricated microlenses

    Science.gov (United States)

    Kaganskiy, Arsenty; Fischbach, Sarah; Strittmatter, André; Rodt, Sven; Heindel, Tobias; Reitzenstein, Stephan

    2018-04-01

    We report on the realization of scalable single-photon sources (SPSs) based on single site-controlled quantum dots (SCQDs) and deterministically fabricated microlenses. The fabrication process comprises the buried-stressor growth technique complemented with low-temperature in-situ electron-beam lithography for the integration of SCQDs into microlens structures with high yield and high alignment accuracy. The microlens-approach leads to a broadband enhancement of the photon-extraction efficiency of up to (21 ± 2)% and a high suppression of multi-photon events with g (2)(τ = 0) SPSs which, can be applied in photonic quantum circuits and advanced quantum computation schemes.

  7. Enhancement of Muramyldipeptide (MDP) Immunostimulatory Activity by Controlled Multimerization on Dendrimers

    DEFF Research Database (Denmark)

    Sørensen, Nanna Skall; Boas, Ulrik; Heegaard, Peter M. H.

    2011-01-01

    Peptidoglycan is a widespread bacterial PAMP molecule and a powerful initiator of innate immune responses. It consists of repeating units of MDP, which as a monomer is only weakly immunostimulatory. Here, MDP-coupled dendrimers were prepared and investigated for stimulation of pig blood mononuclear...... cells. Compared to monomeric MDP, MDP-dendrimers induced a markedly enhanced production of IL-12 p40, IL-1β and IL-6 and completely down-regulated surface expression of B7 and MHC class II. These results suggest a possible novel strategy based on controlled multimerization of minimal PAMP motifs...

  8. Connectivity-Enhanced Route Selection and Adaptive Control for the Chevrolet Volt: Preprint

    Energy Technology Data Exchange (ETDEWEB)

    Gonder, J.; Wood, E.; Rajagopalan, S.

    2014-09-01

    The National Renewable Energy Laboratory and General Motors evaluated connectivity-enabled efficiency enhancements for the Chevrolet Volt. A high-level model was developed to predict vehicle fuel and electricity consumption based on driving characteristics and vehicle state inputs. These techniques were leveraged to optimize energy efficiency via green routing and intelligent control mode scheduling, which were evaluated using prospective driving routes between tens of thousands of real-world origin/destination pairs. The overall energy savings potential of green routing and intelligent mode scheduling was estimated at 5% and 3% respectively. These represent substantial opportunities considering that they only require software adjustments to implement.

  9. The controlled pulsed laser deposition of Ag nanoparticle arrays for surface enhanced Raman scattering.

    Science.gov (United States)

    D'Andrea, C; Neri, F; Ossi, P M; Santo, N; Trusso, S

    2009-06-17

    An effective method for the production of surface enhanced Raman scattering (SERS) active substrates is presented. Nanostructured silver thin films are pulsed laser deposited in an argon atmosphere. The films consist of arrays of nanoparticles whose size is controlled by the Ar pressure. The surface morphology of the films can be tuned by the laser pulse number. Nanoparticle size is calculated by a phenomenological model taking into account the dynamics of the laser generated silver plasma. The SERS activity of the films is investigated by Raman scattering of adsorbed rhodamine 6G at different concentrations.

  10. Intronic non-CG DNA hydroxymethylation and alternative mRNA splicing in honey bees.

    Science.gov (United States)

    Cingolani, Pablo; Cao, Xiaoyi; Khetani, Radhika S; Chen, Chieh-Chun; Coon, Melissa; Sammak, Alya'a; Bollig-Fischer, Aliccia; Land, Susan; Huang, Yun; Hudson, Matthew E; Garfinkel, Mark D; Zhong, Sheng; Robinson, Gene E; Ruden, Douglas M

    2013-09-30

    Previous whole-genome shotgun bisulfite sequencing experiments showed that DNA cytosine methylation in the honey bee (Apis mellifera) is almost exclusively at CG dinucleotides in exons. However, the most commonly used method, bisulfite sequencing, cannot distinguish 5-methylcytosine from 5-hydroxymethylcytosine, an oxidized form of 5-methylcytosine that is catalyzed by the TET family of dioxygenases. Furthermore, some analysis software programs under-represent non-CG DNA methylation and hydryoxymethylation for a variety of reasons. Therefore, we used an unbiased analysis of bisulfite sequencing data combined with molecular and bioinformatics approaches to distinguish 5-methylcytosine from 5-hydroxymethylcytosine. By doing this, we have performed the first whole genome analyses of DNA modifications at non-CG sites in honey bees and correlated the effects of these DNA modifications on gene expression and alternative mRNA splicing. We confirmed, using unbiased analyses of whole-genome shotgun bisulfite sequencing (BS-seq) data, with both new data and published data, the previous finding that CG DNA methylation is enriched in exons in honey bees. However, we also found evidence that cytosine methylation and hydroxymethylation at non-CG sites is enriched in introns. Using antibodies against 5-hydroxmethylcytosine, we confirmed that DNA hydroxymethylation at non-CG sites is enriched in introns. Additionally, using a new technique, Pvu-seq (which employs the enzyme PvuRts1l to digest DNA at 5-hydroxymethylcytosine sites followed by next-generation DNA sequencing), we further confirmed that hydroxymethylation is enriched in introns at non-CG sites. Cytosine hydroxymethylation at non-CG sites might have more functional significance than previously appreciated, and in honey bees these modifications might be related to the regulation of alternative mRNA splicing by defining the locations of the introns.

  11. Learning to live together: mutualism between self-splicing introns and their hosts

    OpenAIRE

    Chalamcharla Venkata R; Edgell David R; Belfort Marlene

    2011-01-01

    Abstract Group I and II introns can be considered as molecular parasites that interrupt protein-coding and structural RNA genes in all domains of life. They function as self-splicing ribozymes and thereby limit the phenotypic costs associated with disruption of a host gene while they act as mobile DNA elements to promote their spread within and between genomes. Once considered purely selfish DNA elements, they now seem, in the light of recent work on the molecular mechanisms regulating bacter...

  12. Performance of grid connected DFIG during recurring symmetrical faults using Internal Model Controller based Enhanced Field Oriented Control

    Directory of Open Access Journals (Sweden)

    D.V.N.Ananth

    2016-06-01

    Full Text Available The modern grid rules forces DFIG to withstand and operate during single as well as multiple low voltage grid faults. The system must not lose synchronism during any type of fault for a given time period. This withstanding capacity is called low voltage ride through (LVRT. To improve performance during LVRT, enhanced field oriented control (EFOC method is adopted in rotor side converter. This method helps in improving power transfer capability during steady state and better dynamic and transient stability during abnormal conditions. In this technique, rotor flux reference change from synchronous speed to some smaller speed or zero during the fault for injecting current at the rotor slip frequency. In this process, DC-Offset component of flux is controlled beyond decomposing to a lower value during faults and maintaining it. This offset decomposition of flux will be oscillatory in conventional FOC, whereas in EFOC with internal model controller, flux can damp quickly not only for single fault but during multiple faults. This strategy can regulate stator and rotor current waveform to sinusoidal without distortion during and after fault. It has better damped torque oscillations, control in rotor speed and generator flux during and after fault. The fluctuations in DC bus voltage across capacitor are also controlled using proposed EFOC technique. The system performance with under-voltage grid fault of 30% and 60% of the rated voltage occurring at the point of common coupling during 1 to 1.25 and another fault between 1.6 to 1.85 seconds are analyzed using simulation studies.

  13. Complex group-I introns in nuclear SSU rDNA of red and green algae: evidence of homing-endonuclease pseudogenes in the Bangiophyceae

    DEFF Research Database (Denmark)

    Haugen, P; Huss, V A; Nielsen, Henrik

    1999-01-01

    The green alga Scenedesmus pupukensis and the red alga Porphyra spiralis contain large group-IC1 introns in their nuclear small subunit ribosomal RNA genes due to the presence of open reading frames at the 5' end of the introns. The putative 555 amino-acid Scenedesmus-encoded protein harbors...... a sequence motif resembling the bacterial S9 ribosomal proteins. The Porphyra intron self-splices in vitro, and generates both ligated exons and a full-length intron RNA circle. The Porphyra intron has an unusual structural organization by encoding a potential 149 amino-acid homing-endonuclease-like protein...... on the complementary strand. A comparison between related group-I introns in the Bangiophyceae revealed homing-endonuclease-like pseudogenes due to frame-shifts and deletions in Porphyra and Bangia. The Scenedesmus and Porphyra introns provide new insights into the evolution and possible novel functions of nuclear...

  14. Unusual intron conservation near tissue-regulated exons found by splicing microarrays.

    Directory of Open Access Journals (Sweden)

    Charles W Sugnet

    2006-01-01

    Full Text Available Alternative splicing contributes to both gene regulation and protein diversity. To discover broad relationships between regulation of alternative splicing and sequence conservation, we applied a systems approach, using oligonucleotide microarrays designed to capture splicing information across the mouse genome. In a set of 22 adult tissues, we observe differential expression of RNA containing at least two alternative splice junctions for about 40% of the 6,216 alternative events we could detect. Statistical comparisons identify 171 cassette exons whose inclusion or skipping is different in brain relative to other tissues and another 28 exons whose splicing is different in muscle. A subset of these exons is associated with unusual blocks of intron sequence whose conservation in vertebrates rivals that of protein-coding exons. By focusing on sets of exons with similar regulatory patterns, we have identified new sequence motifs implicated in brain and muscle splicing regulation. Of note is a motif that is strikingly similar to the branchpoint consensus but is located downstream of the 5' splice site of exons included in muscle. Analysis of three paralogous membrane-associated guanylate kinase genes reveals that each contains a paralogous tissue-regulated exon with a similar tissue inclusion pattern. While the intron sequences flanking these exons remain highly conserved among mammalian orthologs, the paralogous flanking intron sequences have diverged considerably, suggesting unusually complex evolution of the regulation of alternative splicing in multigene families.

  15. Un gene con intrones en vez de exones / Envejecimiento Prematuro de la Piel

    Directory of Open Access Journals (Sweden)

    Tobías Mojica

    1996-04-01

    Full Text Available Un gene con intrones en vez de exones. La noción de que los genes son discontinuos (compuestos de exones e intrones en forma alterna y en cuya organización los exones representan regiones presentes, por medio del código genético en las proteínas, y los intrones nadie sabe todavía que representan produjo una cierta cantidad de desasosiego entre los genetistas mayores de edad, pero hoy día es ampliamente aceptada, con poco o ningún dolor, y se ha convertido en parte del cánon científico. / Envejecimiento Prematuro de la Piel. La exposición a largo plazo de la piel a la luz ultravioleta proveniente del sol resulta en daño al colágeno de la piel y a la elastina de la matriz extracelular; se cree que este daño es responsable de la apariencia típicamente arrugadita de la piel expuesta al sol por mucho tiempo (como en los vaqueros de los comerciales de la televisión.

  16. Characterization of cryptic splicing in germline PTEN intronic variants in Cowden syndrome.

    Science.gov (United States)

    Chen, Hannah Jinlian; Romigh, Todd; Sesock, Kaitlin; Eng, Charis

    2017-10-01

    Germline mutations in the tumor-suppressor gene PTEN predispose to subsets of Cowden syndrome (CS), Bannayan-Riley-Ruvalcaba syndrome, and autism. Evidence-based classification of PTEN variants as either deleterious or benign is urgently needed for accurate molecular diagnosis and gene-informed genetic counseling. We studied 34 different germline PTEN intronic variants from 61 CS patients, characterized their PTEN mRNA processing, and analyzed PTEN expression and downstream readouts of P-AKT and P-ERK1/2. While we found that many mutations near splice junctions result in exon skipping, we also identified the presence of cryptic splicing that resulted in premature termination or a shift in isoform usage. PTEN protein expression is significantly lower in the group with splicing changes while P-AKT, but not P-ERK1/2, is significantly increased. Our observations of these PTEN intronic variants should contribute to the determination of pathogenicity of PTEN intronic variants and aid in genetic counseling. © 2017 The Authors. Human Mutation published by Wiley Periodicals, Inc.

  17. YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers.

    Science.gov (United States)

    Stein, Claudia; Bardet, Anaïs Flore; Roma, Guglielmo; Bergling, Sebastian; Clay, Ieuan; Ruchti, Alexandra; Agarinis, Claudia; Schmelzle, Tobias; Bouwmeester, Tewis; Schübeler, Dirk; Bauer, Andreas

    2015-08-01

    YAP1 is a major effector of the Hippo pathway and a well-established oncogene. Elevated YAP1 activity due to mutations in Hippo pathway components or YAP1 amplification is observed in several types of human cancers. Here we investigated its genomic binding landscape in YAP1-activated cancer cells, as well as in non-transformed cells. We demonstrate that TEAD transcription factors mediate YAP1 chromatin-binding genome-wide, further explaining their dominant role as primary mediators of YAP1-transcriptional activity. Moreover, we show that YAP1 largely exerts its transcriptional control via distal enhancers that are marked by H3K27 acetylation and that YAP1 is necessary for this chromatin mark at bound enhancers and the activity of the associated genes. This work establishes YAP1-mediated transcriptional regulation at distal enhancers and provides an expanded set of target genes resulting in a fundamental source to study YAP1 function in a normal and cancer setting.

  18. YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers.

    Directory of Open Access Journals (Sweden)

    Claudia Stein

    2015-08-01

    Full Text Available YAP1 is a major effector of the Hippo pathway and a well-established oncogene. Elevated YAP1 activity due to mutations in Hippo pathway components or YAP1 amplification is observed in several types of human cancers. Here we investigated its genomic binding landscape in YAP1-activated cancer cells, as well as in non-transformed cells. We demonstrate that TEAD transcription factors mediate YAP1 chromatin-binding genome-wide, further explaining their dominant role as primary mediators of YAP1-transcriptional activity. Moreover, we show that YAP1 largely exerts its transcriptional control via distal enhancers that are marked by H3K27 acetylation and that YAP1 is necessary for this chromatin mark at bound enhancers and the activity of the associated genes. This work establishes YAP1-mediated transcriptional regulation at distal enhancers and provides an expanded set of target genes resulting in a fundamental source to study YAP1 function in a normal and cancer setting.

  19. Three Group-I introns in 18S rDNA of Endosymbiotic Algae of Paramecium bursaria from Japan

    Science.gov (United States)

    Hoshina, Ryo; Kamako, Shin-ichiro; Imamura, Nobutaka

    2004-08-01

    In the nuclear encoded small subunit ribosomal DNA (18S rDNA) of symbiotic alga of Paramecium bursaria (F36 collected in Japan) possesses three intron-like insertions (Hoshina et al., unpubl. data, 2003). The present study confirmed these exact lengths and insertion sites by reverse transcription-PCR. Two of them were inserted at Escherichia coli 16S rRNA genic position 943 and 1512 that are frequent intron insertion positions, but another insertion position (nearly 1370) was the first finding. Their secondary structures suggested they belong to Group-I intron; one belongs to subgroup IE, others belong to subgroup IC1. Similarity search indicated these introns are ancestral ones.

  20. Mutation analysis in Duchenne and Becker muscular dystrophy patients from Bulgaria shows a peculiar distribution of breakpoints by intron

    Energy Technology Data Exchange (ETDEWEB)

    Todorova, A.; Bronzova, J.; Kremensky, I. [Univ. Hospital of Obstetrics and Gynecology, Sofia (Bulgaria)] [and others

    1996-10-02

    For the first time in Bulgaria, a deletion/duplication screening was performed on a group of 84 unrelated Duchenne/Becker muscular dystrophy patients, and the breakpoint distribution in the dystrophin gene was analyzed. Intragenic deletions were detected in 67.8% of patients, and intragenic duplications in 2.4%. A peculiar distribution of deletion breakpoints was found. Only 13.2% of the deletion breakpoints fell in the {open_quotes}classical{close_quotes} hot spot in intron 44, whereas the majority (> 54%) were located within the segment encompassing introns 45-51, which includes intron 50, the richest in breakpoints (16%) in the Bulgarian sample. Comparison with data from Greece and Turkey points at the probable existence of a deletion hot spot within intron 50, which might be a characteristic of populations of the Balkan region. 17 refs., 2 figs.

  1. A var gene promoter implicated in severe malaria nucleates silencing and is regulated by 3' untranslated region and intronic cis-elements.

    Science.gov (United States)

    Muhle, Rebecca A; Adjalley, Sophie; Falkard, Brie; Nkrumah, Louis J; Muhle, Michael E; Fidock, David A

    2009-11-01

    Questions surround the mechanism of mutually exclusive expression by which Plasmodium falciparum mediates activation and silencing of var genes. These encode PfEMP1 proteins, which function as cytoadherent and immunomodulatory molecules at the surface of parasitised erythrocytes. Current evidence suggests that promoter silencing by var introns might play a key role in var gene regulation. To evaluate the impact of cis-acting regulatory regions on var silencing, we generated P. falciparum lines in which luciferase was placed under the control of an UpsA var promoter. By utilising the Bxb1 integrase system, these reporter cassettes were targeted to a genomic region that was not in apposition to var subtelomeric domains. This eliminated possible effects from surrounding telomeric elements and removed the variability inherent in episomal systems. Studies with highly synchronised parasites revealed that the UpsA element possessed minimal activity in comparison with a heterologous (hrp3) promoter. This may result from the integrated UpsA promoter being largely silenced by the neighbouring cg6 promoter. Our analyses also revealed that the DownsA 3' untranslated region further decreased the luciferase activity from both cassettes, whereas the var A intron repressed the UpsA promoter specifically. By applying multivariate analysis over the entire cell cycle, we confirmed the significance of these cis-elements and found the parasite stage to be the major factor regulating UpsA-promoter activity. Additionally, we observed that the UpsA promoter was capable of nucleating reversible silencing that spread to a downstream promoter. We believe these studies are the first to analyse promoter activity of Group A var genes, which have been implicated in severe malaria, and support the model that var introns can further suppress var expression. These data also suggest an important suppressive role for the DownsA terminator. Our findings imply the existence of multiple levels of var

  2. Enhancement of vortex induced forces and motion through surface roughness control

    Science.gov (United States)

    Bernitsas, Michael M [Saline, MI; Raghavan, Kamaldev [Houston, TX

    2011-11-01

    Roughness is added to the surface of a bluff body in a relative motion with respect to a fluid. The amount, size, and distribution of roughness on the body surface is controlled passively or actively to modify the flow around the body and subsequently the Vortex Induced Forces and Motion (VIFM). The added roughness, when designed and implemented appropriately, affects in a predetermined way the boundary layer, the separation of the boundary layer, the level of turbulence, the wake, the drag and lift forces, and consequently the Vortex Induced Motion (VIM), and the fluid-structure interaction. The goal of surface roughness control is to increase Vortex Induced Forces and Motion. Enhancement is needed in such applications as harnessing of clean and renewable energy from ocean/river currents using the ocean energy converter VIVACE (Vortex Induced Vibration for Aquatic Clean Energy).

  3. A spinner-integrated wind lidar for enhanced wind turbine control

    DEFF Research Database (Denmark)

    Mikkelsen, Torben; Angelou, Nikolas; Hansen, Kasper Hjorth

    2013-01-01

    diameter, 59 m hub height 2.3 MW wind turbine (Vestas NM80), located at Tjæreborg Enge in western Denmark is presented. Preview wind data at two selected upwind measurement distances, acquired during two measurement periods of different wind speed and atmospheric stability conditions, are analyzed...... of the spinner lidar data, is investigated. Finally, the potential for enhancing turbine control and performance based on wind lidar preview measurements in combination with feed-forward enabled turbine controllers is discussed. Copyright © 2012 John Wiley & Sons, Ltd.......A field test with a continuous wave wind lidar (ZephIR) installed in the rotating spinner of a wind turbine for unimpeded preview measurements of the upwind approaching wind conditions is described. The experimental setup with the wind lidar on the tip of the rotating spinner of a large 80 m rotor...

  4. Pengembangan Program Aplikasi Enhanced Machine Control dengan Python untuk Metode Interpolasi Newton

    Directory of Open Access Journals (Sweden)

    Alexander A. S. Gunawan

    2012-06-01

    Full Text Available Nowadays, one of industrial main problems is the flexibility of machines to be customized since they are designed based on certain standard. This research develops software for CNC (Computer Numerically Controlled machine in order to execute the Newton Interpolation using Python. The platform used in the CNCmachine is EMC (Enhanced Machine Control and GUI (Graphical User Interface AXIS on the operating system Linux Ubuntu. The Newton interpolation is used to create a curve based on several point determined by user. By converting this curve into G-Code, which could be read by CNC machine, the machine can moveaccording to curve designed by user. This research is an initial study to customize the CNC machine and will continue to fulfill the user needs. This research obtained a program that is able to run well up to 4 input pairs. The higher number inputs will cause the oscillation in the interpolation curve.

  5. Semi-degradable poly(β-amino ester) networks with temporally controlled enhancement of mechanical properties.

    Science.gov (United States)

    Safranski, David L; Weiss, Daiana; Clark, J Brian; Taylor, W Robert; Gall, Ken

    2014-08-01

    Biodegradable polymers are clinically used in numerous biomedical applications, and classically show a loss of mechanical properties within weeks of implantation. This work demonstrates a new class of semi-degradable polymers that show an increase in mechanical properties through degradation via a controlled shift in a thermal transition. Semi-degradable polymer networks, poly(β-amino ester)-co-methyl methacrylate, were formed from a low glass transition temperature crosslinker, poly(β-amino ester), and high glass transition temperature monomer, methyl methacrylate, which degraded in a manner dependent upon the crosslinker chemical structure. In vitro and in vivo degradation revealed changes in mechanical behavior due to the degradation of the crosslinker from the polymer network. This novel polymer system demonstrates a strategy to temporally control the mechanical behavior of polymers and to enhance the initial performance of smart biomedical devices. Copyright © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  6. Suprafamilial relationships among Rodentia and the phylogenetic effect of removing fast-evolving nucleotides in mitochondrial, exon and intron fragments

    Directory of Open Access Journals (Sweden)

    Arnal Véronique

    2008-11-01

    Full Text Available Abstract Background The number of rodent clades identified above the family level is contentious, and to date, no consensus has been reached on the basal evolutionary relationships among all rodent families. Rodent suprafamilial phylogenetic relationships are investigated in the present study using ~7600 nucleotide characters derived from two mitochondrial genes (Cytochrome b and 12S rRNA, two nuclear exons (IRBP and vWF and four nuclear introns (MGF, PRKC, SPTBN, THY. Because increasing the number of nucleotides does not necessarily increase phylogenetic signal (especially if the data is saturated, we assess the potential impact of saturation for each dataset by removing the fastest-evolving positions that have been recognized as sources of inconsistencies in phylogenetics. Results Taxonomic sampling included multiple representatives of all five rodent suborders described. Fast-evolving positions for each dataset were identified individually using a discrete gamma rate category and sites belonging to the most rapidly evolving eighth gamma category were removed. Phylogenetic tree reconstructions were performed on individual and combined datasets using Parsimony, Bayesian, and partitioned Maximum Likelihood criteria. Removal of fast-evolving positions enhanced the phylogenetic signal to noise ratio but the improvement in resolution was not consistent across different data types. The results suggested that elimination of fastest sites only improved the support for nodes moderately affected by homoplasy (the deepest nodes for introns and more recent nodes for exons and mitochondrial genes. Conclusion The present study based on eight DNA fragments supports a fully resolved higher level rodent phylogeny with moderate to significant nodal support. Two inter-suprafamilial associations emerged. The first comprised a monophyletic assemblage containing the Anomaluromorpha (Anomaluridae + Pedetidae + Myomorpha (Muridae + Dipodidae as sister clade to the

  7. Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3

    Directory of Open Access Journals (Sweden)

    Kandul Nikolai P

    2009-10-01

    Full Text Available Abstract Background Alternative splicing (AS of maturing mRNA can generate structurally and functionally distinct transcripts from the same gene. Recent bioinformatic analyses of available genome databases inferred a positive correlation between intron length and AS. To study the interplay between intron length and AS empirically and in more detail, we analyzed the diversity of alternatively spliced transcripts (ASTs in the Drosophila RNA-binding Bruno-3 (Bru-3 gene. This gene was known to encode thirteen exons separated by introns of diverse sizes, ranging from 71 to 41,973 nucleotides in D. melanogaster. Although Bru-3's structure is expected to be conducive to AS, only two ASTs of this gene were previously described. Results Cloning of RT-PCR products of the entire ORF from four species representing three diverged Drosophila lineages provided an evolutionary perspective, high sensitivity, and long-range contiguity of splice choices currently unattainable by high-throughput methods. Consequently, we identified three new exons, a new exon fragment and thirty-three previously unknown ASTs of Bru-3. All exon-skipping events in the gene were mapped to the exons surrounded by introns of at least 800 nucleotides, whereas exons split by introns of less than 250 nucleotides were always spliced contiguously in mRNA. Cases of exon loss and creation during Bru-3 evolution in Drosophila were also localized within large introns. Notably, we identified a true de novo exon gain: exon 8 was created along the lineage of the obscura group from intronic sequence between cryptic splice sites conserved among all Drosophila species surveyed. Exon 8 was included in mature mRNA by the species representing all the major branches of the obscura group. To our knowledge, the origin of exon 8 is the first documented case of exonization of intronic sequence outside vertebrates. Conclusion We found that large introns can promote AS via exon-skipping and exon turnover during

  8. Implementation of an Enhanced Measurement Control Program for handling nuclear safety samples at WSRC

    International Nuclear Information System (INIS)

    Boler-Melton, C.; Holland, M.K.

    1991-01-01

    In the separation and purification of nuclear material, nuclear criticality safety (NCS) is of primary concern. The primary nuclear criticality safety controls utilized by the Savannah River Site (SRS) Separations Facilities involve administrative and process equipment controls. Additional assurance of NCS is obtained by identifying key process hold points where sampling is used to independently verify the effectiveness of production control. Nuclear safety measurements of samples from these key process locations provide a high degree of assurance that processing conditions are within administrative and procedural nuclear safety controls. An enhanced procedure management system aimed at making improvements in the quality, safety, and conduct of operation was implemented for Nuclear Safety Sample (NSS) receipt, analysis, and reporting. All procedures with nuclear safety implications were reviewed for accuracy and adequate detail to perform the analytical measurements safely, efficiently, and with the utmost quality. Laboratory personnel worked in a ''Deliberate Operating'' mode (a systematic process requiring continuous expert oversight during all phases of training, testing, and implementation) to initiate the upgrades. Thus, the effort to revise and review nuclear safety sample procedures involved a team comprised of a supervisor, chemist, and two technicians for each procedure. Each NSS procedure was upgraded to a ''Use Every Time'' (UET) procedure with sign-off steps to ensure compliance with each step for every nuclear safety sample analyzed. The upgrade program met and exceeded both the long and short term customer needs by improving measurement reliability, providing objective evidence of rigid adherence to program principles and requirements, and enhancing the system for independent verification of representative sampling from designated NCS points

  9. Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences

    OpenAIRE

    Bunawan, Hamidun; Yen, Choong Chee; Yaakop, Salmah; Noor, Normah Mohd

    2017-01-01

    Background The chloroplastic trnL intron and the nuclear internal transcribed spacer (ITS) region were sequenced for 11 Nepenthes species recorded in Peninsular Malaysia to examine their phylogenetic relationship and to evaluate the usage of trnL intron and ITS sequences for phylogenetic reconstruction of this genus. Results Phylogeny reconstruction was carried out using neighbor-joining, maximum parsimony and Bayesian analyses. All the trees revealed two major clusters, a lowland group consi...

  10. Improved CO sub 2 enhanced oil recovery -- Mobility control by in-situ chemical precipitation

    Energy Technology Data Exchange (ETDEWEB)

    Ameri, S.; Aminian, K.; Wasson, J.A.; Durham, D.L.

    1991-06-01

    The overall objective of this study has been to evaluate the feasibility of chemical precipitation to improve CO{sub 2} sweep efficiency and mobility control. The laboratory experiments have indicated that carbonate precipitation can alter the permeability of the core samples under reservoir conditions. Furthermore, the relative permeability measurements have revealed that precipitation reduces the gas permeability in favor of liquid permeability. This indicates that precipitation is occurring preferentially in the larger pores. Additional experimental work with a series of connected cores have indicated that the permeability profile can be successfully modified. However, Ph control plays a critical role in propagation of the chemical precipitation reaction. A numerical reservoir model has been utilized to evaluate the effects of permeability heterogeneity and permeability modification on the CO{sub 2} sweep efficiency. The computer simulation results indicate that the permeability profile modification can significantly enhance CO{sub 2} vertical and horizontal sweep efficiencies. The scoping studies with the model have further revealed that only a fraction of high permeability zones need to be altered to achieve sweep efficiency enhancement. 64 refs., 30 figs., 16 tabs.

  11. Coaxial PCL/PVA electrospun nanofibers: osseointegration enhancer and controlled drug release device

    International Nuclear Information System (INIS)

    Song, Wei; Shi, Tong; Ren, Weiping; Yu, Xiaowei; Markel, David C

    2013-01-01

    The failure of prosthesis after total joint replacement is mainly due to dysfunctional osseointegration and implant infection. There is a critical need for orthopedic implants that promote rapid osseointegration and prevent bacterial colonization, particularly when placed in bone compromised by disease or physiology of the patients. The aim of this study was to fabricate a novel coaxial electrospun polycaprolactone (PCL)/polyvinyl alcohol (PVA) core-sheath nanofiber (NF) blended with both hydroxyapatite nanorods (HA) and type I collagen (Col) (PCL Col /PVA HA ). Doxycycline (Doxy) and dexamethasone (Dex) were successfully incorporated into the PCL Col /PVA HA NFs for controlled release. The morphology, surface hydrophilicity and mechanical properties of the PCL/PVA NF mats were analyzed by scanning electron microscopy, water contact angle and atomic force microscopy. The PCL Col /PVA HA NFs are biocompatible and enhance the adhesion and proliferation of murine pre-osteoblastic MC3T3 cells. The release of Doxy and Dex from coaxial PCL Col /PVA HA NFs showed more controlled release compared with the blended NFs. Using an ex vivo porcine bone implantation model we found that the PCL Col /PVA HA NFs bind firmly on the titanium rod surface and the NFs coating remained intact on the surface of titanium rods after pullout. No disruption or delamination was observed after the pullout test. These findings indicate that PCL Col /PVA HA NFs encapsulating drugs have great potential in enhancing implant osseointegration and preventing implant infection. (paper)

  12. Coaxial PCL/PVA electrospun nanofibers: osseointegration enhancer and controlled drug release device.

    Science.gov (United States)

    Song, Wei; Yu, Xiaowei; Markel, David C; Shi, Tong; Ren, Weiping

    2013-09-01

    The failure of prosthesis after total joint replacement is mainly due to dysfunctional osseointegration and implant infection. There is a critical need for orthopedic implants that promote rapid osseointegration and prevent bacterial colonization, particularly when placed in bone compromised by disease or physiology of the patients. The aim of this study was to fabricate a novel coaxial electrospun polycaprolactone (PCL)/polyvinyl alcohol (PVA) core-sheath nanofiber (NF) blended with both hydroxyapatite nanorods (HA) and type I collagen (Col) (PCL(Col)/PVA(HA)). Doxycycline (Doxy) and dexamethasone (Dex) were successfully incorporated into the PCL(Col)/PVA(HA) NFs for controlled release. The morphology, surface hydrophilicity and mechanical properties of the PCL/PVA NF mats were analyzed by scanning electron microscopy, water contact angle and atomic force microscopy. The PCL(Col)/PVA(HA) NFs are biocompatible and enhance the adhesion and proliferation of murine pre-osteoblastic MC3T3 cells. The release of Doxy and Dex from coaxial PCL(Col)/PVA(HA) NFs showed more controlled release compared with the blended NFs. Using an ex vivo porcine bone implantation model we found that the PCL(Col)/PVA(HA) NFs bind firmly on the titanium rod surface and the NFs coating remained intact on the surface of titanium rods after pullout. No disruption or delamination was observed after the pullout test. These findings indicate that PCL(Col)/PVA(HA) NFs encapsulating drugs have great potential in enhancing implant osseointegration and preventing implant infection.

  13. Virtual Reality for Enhanced Ecological Validity and Experimental Control in the Clinical, Affective and Social Neurosciences

    Science.gov (United States)

    Parsons, Thomas D.

    2015-01-01

    An essential tension can be found between researchers interested in ecological validity and those concerned with maintaining experimental control. Research in the human neurosciences often involves the use of simple and static stimuli lacking many of the potentially important aspects of real world activities and interactions. While this research is valuable, there is a growing interest in the human neurosciences to use cues about target states in the real world via multimodal scenarios that involve visual, semantic, and prosodic information. These scenarios should include dynamic stimuli presented concurrently or serially in a manner that allows researchers to assess the integrative processes carried out by perceivers over time. Furthermore, there is growing interest in contextually embedded stimuli that can constrain participant interpretations of cues about a target’s internal states. Virtual reality environments proffer assessment paradigms that combine the experimental control of laboratory measures with emotionally engaging background narratives to enhance affective experience and social interactions. The present review highlights the potential of virtual reality environments for enhanced ecological validity in the clinical, affective, and social neurosciences. PMID:26696869

  14. Enhanced adhesion of osteoblastic cells on polystyrene films by independent control of surface topography and wettability

    International Nuclear Information System (INIS)

    Yang, Seung Yun; Kim, Eung-Sam; Jeon, Gumhye; Choi, Kwan Yong; Kim, Jin Kon

    2013-01-01

    We independently controlled surface topography and wettability of polystyrene (PS) films by CF 4 and oxygen plasma treatments, respectively, to evaluate the adhesion and proliferation of human fetal osteoblastic (hFOB) cells on the films. Among the CF 4 plasma-treated PS films with the average surface roughness ranging from 0.9 to 70 nm, the highest adhesion of hFOB cells was observed on a PS film with roughness of ∼ 11 nm. When this film was additionally treated by oxygen plasma to provide a hydrophilic surface with a contact angle less than 10°, the proliferation of bone-forming cell was further enhanced. Thus, the plasma-based independent modification of PS film into an optimum nanotexture for human osteoblast cells could be appplied to materials used in bone tissue engineering. Highlights: ► New approach based on plasma treatment to independently control the surface topography and wettability ► The adhesion of human fetal osteoblast (hFOB) was enhanced on a surface with an average roughness of ∼ 11 nm. ► The adhesion and proliferation of hFOB was maximized when nanotextured surface became highly hydrophilic

  15. ENHANCE: Design and rationale of a randomized controlled trial for promoting enduring happiness & well-being.

    Science.gov (United States)

    Kushlev, Kostadin; Heintzelman, Samantha J; Lutes, Lesley D; Wirtz, Derrick; Oishi, Shigehiro; Diener, Ed

    2017-01-01

    Individuals who are higher in subjective well-being not only feel happier, they are more likely have fulfilling relationships, increased work performance and income, better physical health, and longer lives. Over the past several decades, the science of subjective well-being has produced insights into these benefits of happiness, and-recognizing their importance-has begun to examine the factors that lead to greater well-being, from cultivating strong relationships to pursuing meaningful goals. However, studies to date have typically focused on improving subjective well-being by intervening with singular constructs, using primarily college student populations, and were short-term in nature. Moreover, little is understood about the impact of a well-being treatment delivered online vs. in-person. In the present article, we describe a comprehensive intervention program including 3-month initial treatment followed by a 3-month follow-up, ENHANCE: Enduring Happiness and Continued Self-Enhancement. One-hundred and sixty participants will be recruited from two different sites to participate in one of two versions of ENHANCE: in-person (n=30) vs. wait-list control (n=30); or online (n=50) vs. wait-list control (n=50). Assessments will be completed at baseline, three months and six months. Our primary outcome is change in subjective well-being across treatment (3months) and follow-up (6months). Secondary outcomes include self-report and objective measures of health, as well as a psychological mediators (e.g., psychological needs) and moderators (e.g., personality) of treatment outcomes. We hope to provide researchers, practitioners, and individuals with an evidence-based treatment to improve happiness and subjective well-being. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Using Group II Introns for Attenuating the In Vitro and In Vivo Expression of a Homing Endonuclease.

    Directory of Open Access Journals (Sweden)

    Tuhin Kumar Guha

    Full Text Available In Chaetomium thermophilum (DSM 1495 within the mitochondrial DNA (mtDNA small ribosomal subunit (rns gene a group IIA1 intron interrupts an open reading frame (ORF encoded within a group I intron (mS1247. This arrangement offers the opportunity to examine if the nested group II intron could be utilized as a regulatory element for the expression of the homing endonuclease (HEase. Constructs were generated where the codon-optimized ORF was interrupted with either the native group IIA1 intron or a group IIB type intron. This study showed that the expression of the HEase (in vivo in Escherichia coli can be regulated by manipulating the splicing efficiency of the HEase ORF-embedded group II introns. Exogenous magnesium chloride (MgCl2 stimulated the expression of a functional HEase but the addition of cobalt chloride (CoCl2 to growth media antagonized the expression of HEase activity. Ultimately the ability to attenuate HEase activity might be useful in precision genome engineering, minimizing off target activities, or where pathways have to be altered during a specific growth phase.

  17. A Novel Multiobjective Control of DVR to Enhance Power Quality of Sensitive Load

    Directory of Open Access Journals (Sweden)

    Sathish Babu Pandu

    2015-01-01

    Full Text Available The Dynamic Voltage Restorer (DVR is one of the fast, flexible, and cost effective solutions available in compensating the voltage-related power quality problems in power distribution systems. In this paper is discussed how power quality enhancement of sensitive load is achieved by applying three versions of Autonomous Group Particle Swarm Optimization like AGPSO1, AGPSO2, and AGPSO3 for tuning the Proportional-Integral DVR controller under balanced and nonlinear load conditions. A novel multiobjective function is formulated to express the control performance of the system, which is quantified using three power quality indices such as Total Harmonic Distortion (THD, voltage sag index, and RMS voltage variation. The obtained results are compared with the Proportional-Integral (PI controller tuned by Ziegler-Nichols (ZN method and also by Simple Particle Swarm Optimization based PI controlled DVR. The proposed methodology has improved the performance in terms of the considered power quality indices and the simulation has been carried out in MATLAB/Simulink environment.

  18. Might there be a link between intron 3 VNTR polymorphism in the XRCC4 DNA repair gene and the etiopathogenesis of rheumatoid arthritis?

    Science.gov (United States)

    Pehlivan, Sacide; Balci, Sibel Oguzkan; Aydeniz, Ali; Pehlivan, Mustafa; Sever, Tugce; Gursoy, Savas

    2015-01-01

    DNA repair genes are involved in several diseases such as cancers and autoimmune diseases. Previous studies indicated that a DNA repair system was involved in the development of rheumatoid arthritis (RA). In this study, we aimed to examine whether four polymorphisms in the DNA repair genes (xeroderma pigmentosum complementation group D [XPD], X-ray repair cross-complementing group 1 [XRCC1], and X-ray repair cross-complementing group 4 [XRCC4]) were associated with RA. Sixty-five patients with RA and 70 healthy controls (HCs) were examined for XPD (A-751G), XRCC1 (A399G), and XRCC4 (intron 3 VNTR and G-1394T) polymorphisms. All polymorphisms were genotyped by PCR and/or PCR-RFLP. The association between the polymorphisms and RA was analyzed using the chi-square test and de Finetti program. The intron 3 VNTR polymorphism in the XRCC4 gene showed an association with RA patients. The DI genotype was found lower in RA patients (χ(2)=8.227; p=0.0021), while the II genotype was higher in RA patients (χ(2)=5.285; p=0.010). There were deviations from the Hardy-Weinberg Equilibrium (HWE) in both intron 3 VNTR and G-1394T polymorphisms in the XRCC4 gene and in the polymorphism in the XRCC1 gene, and the observed genotype counts deviated from those expected according to the HWE (p=0.027, 0.004, and 0.002, respectively); however, there was no deviation in the other gene polymorphisms. There is no statistical difference between the RA patients and HCs for XPD (A-751G), XRCC1 (A399G), and XRCC4 (G-1394T) gene polymorphisms (p>0.05). Although XPD (A-751G), XRCC1 (A399G), and XRCC4 (G-1394T) gene polymorphisms have been extensively investigated in different clinical pictures, this is the first study to evaluate the role of these polymorphisms in the genetic etiopathogenesis of RA in Turkish patients. In conclusion, we suggested that the intron 3 VNTR polymorphism in the XRCC4 gene may be associated with the etiopathogenesis of RA as a marker of immune aging.

  19. Enhanced Control of Mercury and other HAPs by Innovative Modifications to Wet FGD Processes

    International Nuclear Information System (INIS)

    Hargrove, O.W.; Carey, T.R.; Richardson, C.F.; Skarupa, R.C.; Meserole, F.B.; Rhudy, R.G.; Brown, Thomas D.

    1997-01-01

    The overall objective of this project was to learn more about controlling emissions of hazardous air pollutants (HAPs) from coal-fired power plants that are equipped with wet flue gas desulfurization (FGD) systems. The project was included by FETC as a Phase I project in its Mega-PRDA program. Phase I of this project focused on three research areas. These areas in order of priority were: (1) Catalytic oxidation of vapor-phase elemental mercury; (2) Enhanced particulate-phase HAPs removal by electrostatic charging of liquid droplets; and (3) Enhanced mercury removal by addition of additives to FGD process liquor. Mercury can exist in two forms in utility flue gas--as elemental mercury and as oxidized mercury (predominant form believed to be HgCl 2 ). Previous test results have shown that wet scrubbers effectively remove the oxidized mercury from the gas but are ineffective in removing elemental mercury. Recent improvements in mercury speciation techniques confirm this finding. Catalytic oxidation of vapor-phase elemental mercury is of interest in cases where a wet scrubber exists or is planned for SO 2 control. If a loW--cost process could be developed to oxidize all of the elemental mercury in the flue gas, then the maximum achievable mercury removal across the existing or planned wet scrubber would increase. Other approaches for improving control of HAPs included a method for improving particulate removal across the FGD process and the use of additives to increase mercury solubility. This paper discusses results related only to catalytic oxidation of elemental mercury

  20. Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice

    Science.gov (United States)

    Badoni, Saurabh; Das, Sweta; Sayal, Yogesh K.; Gopalakrishnan, S.; Singh, Ashok K.; Rao, Atmakuri R.; Agarwal, Pinky; Parida, Swarup K.; Tyagi, Akhilesh K.

    2016-01-01

    We developed genome-wide 84634 ISM (intron-spanning marker) and 16510 InDel-fragment length polymorphism-based ILP (intron-length polymorphism) markers from genes physically mapped on 12 rice chromosomes. These genic markers revealed much higher amplification-efficiency (80%) and polymorphic-potential (66%) among rice accessions even by a cost-effective agarose gel-based assay. A wider level of functional molecular diversity (17–79%) and well-defined precise admixed genetic structure was assayed by 3052 genome-wide markers in a structured population of indica, japonica, aromatic and wild rice. Six major grain weight QTLs (11.9–21.6% phenotypic variation explained) were mapped on five rice chromosomes of a high-density (inter-marker distance: 0.98 cM) genetic linkage map (IR 64 x Sonasal) anchored with 2785 known/candidate gene-derived ISM and ILP markers. The designing of multiple ISM and ILP markers (2 to 4 markers/gene) in an individual gene will broaden the user-preference to select suitable primer combination for efficient assaying of functional allelic variation/diversity and realistic estimation of differential gene expression profiles among rice accessions. The genomic information generated in our study is made publicly accessible through a user-friendly web-resource, “Oryza ISM-ILP marker” database. The known/candidate gene-derived ISM and ILP markers can be enormously deployed to identify functionally relevant trait-associated molecular tags by optimal-resource expenses, leading towards genomics-assisted crop improvement in rice. PMID:27032371

  1. Enhancing a sustainable healthy working life: design of a clustered randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Koolhaas Wendy

    2010-08-01

    Full Text Available Abstract Background To improve a sustainable healthy working life, we have developed the intervention 'Staying healthy at work', which endeavours to enhance work participation of employees aged 45 years and older by increasing their problem-solving capacity and stimulating their awareness of their role and responsibility towards a healthy working life. This research study aims to evaluate the process and the effectiveness of the intervention compared with care as usual. Methods/design The study is a cluster-randomized controlled trial design (randomized at the supervisor level, with a 1-year follow-up. Workers aged 45 years and older have been enrolled in the study. Workers in the intervention group are receiving the intervention 'Staying healthy at work'. The main focus of the intervention is to promote a healthy working life of ageing workers by: (1 changing workers awareness and behaviour, by emphasizing their own decisive role in attaining goals; (2 improving the supervisors' ability to support workers in taking the necessary action, by means of enhancing knowledge and competence; and (3 enhancing the use of the human resource professionals and the occupational health tools available within the organization. The supervisors in the intervention group have been trained how to present themselves as a source of support for the worker. Workers in the control group are receiving care as usual; supervisors in the control group have not participated in the training. Measurements have been taken at baseline and will be followed up at 3, 6 and 12 months. The primary outcome measures are vitality, work ability and productivity. The secondary outcomes measures include fatigue, job strain, work attitude, self-efficacy and work engagement. A process evaluation will be conducted at both the supervisor and the worker levels, and satisfaction with the content of the intervention will be assessed. Discussion The intervention 'Staying healthy at work' has the

  2. Enhancing Carbon Reactivity in Mercury Control in Lignite-Fired Systems

    Energy Technology Data Exchange (ETDEWEB)

    Chad Wocken; Michael Holmes; John Pavlish; Jeffrey Thompson; Katie Brandt; Brandon Pavlish; Dennis Laudal; Kevin Galbreath; Michelle Olderbak

    2008-06-30

    This project was awarded through the U.S. Department of Energy (DOE) National Energy Technology Laboratory Program Solicitation DE-PS26-03NT41718-01. The Energy & Environmental Research Center (EERC) led a consortium-based effort to resolve mercury (Hg) control issues facing the lignite industry. The EERC team-the Electric Power Research Institute (EPRI); the URS Corporation; the Babcock & Wilcox Company; ADA-ES; Apogee; Basin Electric Power Cooperative; Otter Tail Power Company; Great River Energy; Texas Utilities; Montana-Dakota Utilities Co.; Minnkota Power Cooperative, Inc.; BNI Coal Ltd.; Dakota Westmoreland Corporation; the North American Coal Corporation; SaskPower; and the North Dakota Industrial Commission-demonstrated technologies that substantially enhanced the effectiveness of carbon sorbents to remove Hg from western fuel combustion gases and achieve a high level ({ge} 55% Hg removal) of cost-effective control. The results of this effort are applicable to virtually all utilities burning lignite and subbituminous coals in the United States and Canada. The enhancement processes were previously proven in pilot-scale and limited full-scale tests. Additional optimization testing continues on these enhancements. These four units included three lignite-fired units: Leland Olds Station Unit 1 (LOS1) and Stanton Station Unit 10 (SS10) near Stanton and Antelope Valley Station Unit 1 (AVS1) near Beulah and a subbituminous Powder River Basin (PRB)-fired unit: Stanton Station Unit 1 (SS1). This project was one of three conducted by the consortium under the DOE mercury program to systematically test Hg control technologies available for utilities burning lignite. The overall objective of the three projects was to field-test and verify options that may be applied cost-effectively by the lignite industry to reduce Hg emissions. The EERC, URS, and other team members tested sorbent injection technologies for plants equipped with electrostatic precipitators (ESPs) and

  3. Association analysis between a VNTR intron 8 polymorphism of the dopamine transporter gene (SLC6A3 and obsessive- compulsive disorder in a Brazilian sample Análise de associação entre um polimorfismo VNTR no intron 8 do gene do transportador de dopamina (SLC6A3 e transtorno obsessivo-compulsivo em uma amostra brasileira

    Directory of Open Access Journals (Sweden)

    Karen Miguita

    2007-12-01

    Full Text Available Family, twin and segregation analysis have provided evidences that genetic factors are implicated in the susceptibility for obsessive-compulsive disorder (OCD. Several lines of research suggest that the dopaminergic system may be involved in the pathophysiology of OCD. Thus, the aim of the present study was to investigate a possible association between a polymorphism located in intron 8 of the dopamine transporter gene (SLC6A3 and OCD in a Brazilian sample composed by 208 patients and 865 healthy controls. No statistically differences were observed in allelic and genotype distributions between cases and controls. No association was also observed when the sample was divided according to specific phenotypic features such as gender, presence of tic disorders co-morbidity and age at onset of obsessive-compulsive symptoms (OCS. Our results suggest that the intron 8 VNTR of the SLC6A3 investigated in this study is not related to the susceptibility for OCD in our Brazilian sample.Estudos de família, gêmeos e de segregação têm demonstrado que fatores genéticos estão envolvidos na susceptibilidade para o desenvolvimento do transtorno obsessivo-compulsivo (TOC. Várias linhas de pesquisa sugerem que o sistema dopaminérgico possa estar envolvido na fisiopatologia do TOC. Assim, o objetivo do presente estudo foi investigar uma possível associação entre o polimorfismo localizado no intron 8 do gene do transportador da dopamina (SLC6A3 e o TOC em uma amostra brasileira composta por 208 pacientes e 865 controles sadios. Nenhuma diferença estatisticamente significante foi observada nas distribuições alélicas e genotípicas entre os grupos de pacientes e controles. Nenhuma associação também foi observada quando as amostras foram divididas de acordo com características fenotípicas específicas, tais como gênero, presença de co-morbidade com tiques e idade de início dos sintomas obsessivo-compulsivo (SOC. Nossos resultados sugerem que o VNTR

  4. Predicting Bacteria Removal by Enhanced Stormwater Control Measures (SCMs) at the Watershed Scale

    Science.gov (United States)

    Wolfand, J.; Bell, C. D.; Boehm, A. B.; Hogue, T. S.; Luthy, R. G.

    2017-12-01

    Urban stormwater is a major cause of water quality impairment, resulting in surface waters that fail to meet water quality standards and support their designated uses. Fecal indicator bacteria are present in high concentrations in stormwater and are strictly regulated in receiving waters; yet, their fate and transport in urban stormwater is poorly understood. Stormwater control measures (SCMs) are often used to treat, infiltrate, and release urban runoff, but field measurements show that the removal of bacteria by these structural solutions is limited (median log removal = 0.24, n = 370). Researchers have therefore looked to improve bacterial removal by enhancing SCMs through alterations in flow regimes or adding geomedia such as biochar. The present research seeks to develop a model to predict removal of fecal indicator bacteria by enhanced SCMs at the watershed scale in a semi-arid climate. Using the highly developed Ballona Creek watershed (290 km2) located in Los Angeles County as a case study, a hydrologic model is coupled with a stochastic water quality model to predict E. coli concentration near the outfall of the Ballona Creek, Santa Monica Bay. A hydrologic model was developed using EPA SWMM, calibrated for flow from water year 1998-2006 (NSE = 0.94; R2 = 0.94), and validated from water year 2007-2015 (NSE = 0.90; R2 = 0.93). This bacterial loading model was then linked to EPA SUSTAIN and a SCM bacterial removal script to simulate log removal of bacteria by various SCMs and predict bacterial concentrations in Ballona Creek. Preliminary results suggest small enhancements to SCMs that improve bacterial removal (<0.5 log removal) may offer large benefits to surface water quality and enable communities such as Los Angeles to meet their regulatory requirements.

  5. Enhancing Congruence between Implicit Motives and Explicit Goal Commitments: Results of a Randomized Controlled Trial

    Directory of Open Access Journals (Sweden)

    Ramona M. Roch

    2017-09-01

    Full Text Available Objective: Theory and research suggest that the pursuit of personal goals that do not fit a person's affect-based implicit motives results in impaired emotional well-being, including increased symptoms of depression. The aim of this study was to evaluate an intervention designed to enhance motive-goal congruence and study its impact on well-being.Method: Seventy-four German students (mean age = 22.91, SD = 3.68; 64.9% female without current psychopathology, randomly allocated to three groups: motivational feedback (FB; n = 25; participants learned about the fit between their implicit motives and explicit goals, FB + congruence-enhancement training (CET; n = 22; participants also engaged in exercises to increase the fit between their implicit motives and goals, and a no-intervention control group (n = 27, were administered measures of implicit motives, personal goal commitments, happiness, depressive symptoms, and life satisfaction 3 weeks before (T1 and 6 weeks after (T2 treatment.Results: On two types of congruence measures derived from motive and goal assessments, treated participants showed increases in agentic (power and achievement congruence, with improvements being most consistent in the FB+CET group. Treated participants also showed a trend-level depressive symptom reduction, but no changes on other well-being measures. Although increases in overall and agentic motivational congruence were associated with increases in affective well-being, treatment-based reduction of depressive symptoms was not mediated by treatment-based agentic congruence changes.Conclusion: These findings document that motivational congruence can be effectively enhanced, that changes in motivational congruence are associated with changes in affective well-being, and they suggest that individuals' implicit motives should be considered when personal goals are discussed in the therapeutic process.

  6. A neo-strategic planning approach to enhance local tobacco control programs.

    Science.gov (United States)

    Douglas, Malinda R; Carter, Sara Sally R; Wilson, Andrew P; Chan, Andie

    2015-01-01

    Research in tobacco control demonstrating best practices is widely disseminated; however, application at the local level is often difficult. Translating research into practice requires a concerted effort to develop an understanding of the evidence and how it can be applied within diverse contexts. A strategic planning infrastructure was developed to support the translation of evidence-based interventions into community practice. This paper highlights the strategic process of turning "know-what" into "know-how" to facilitate the strategic planning and implementation of tobacco control best practices at the local level. The purpose, people, process, and product strategies of knowledge management and translation provided a framework for the strategic planning infrastructure. The knowledge translation concepts of audience, motivations, and mechanisms were synergized in the neo-strategic planning component design. The participants were 20 community coalitions funded to implement local tobacco control programs. From 2004 to 2011, the strategic planners facilitated a cyclical process to translate research into practice using a trio of integrated tools, skill-building workshops on strategic planning, and grantee-driven technical assistance and consultation. In the short term, the usefulness of the strategic planning components to the programs was measured. The intermediate outcome was the successful movement of the community programs from the planning stage to the implementation stage. The achievement of community-level changes in planned tobacco control efforts was the overall outcome measure for the success of the local coalitions. Seventeen of 20 communities that began the planning process implemented strategic plans. All 17 of the programs implemented evidence-based practices, resulting in numerous tobacco-free policies, increased cessation, and increased support from the media and community. Bridging the gap between research and practice can enhance the practicality

  7. Constraining the optimization of a fuzzy logic controller using an enhanced genetic algorithm.

    Science.gov (United States)

    Cheong, F; Lai, R

    2000-01-01

    Fuzzy logic controllers (FLCs) are gaining in popularity across a broad array of disciplines because they allow a more human approach to control. Recently, the design of the fuzzy sets and the rule base has been automated by the use of genetic algorithms (GAs) which are powerful search techniques. Though the use of GAs can produce near optimal FLCs, it raises problems such as messy overlapping of fuzzy sets and rules not in agreement with common sense. This paper describes an enhanced genetic algorithm which constrains the optimization of FLCs to produce well-formed fuzzy sets and rules which can be better understood by human beings. To achieve the above, we devised several new genetic operators and used a parallel GA with three populations for optimizing FLCs with 3x3, 5x5, and 7x7 rule bases, and we also used a novel method for creating migrants between the three populations of the parallel GA to increase the chances of optimization. In this paper, we also present the results of applying our GA to designing FLCs for controlling three different plants and compare the performance of these FLC's with their unconstrained counterparts.

  8. Power system stability enhancement employing controllers based on a versatile modeling

    Science.gov (United States)

    Chung, Chi Yung

    Rapid advances in power electronics have made it both practicable and economic to design powerful thyristor-controlled devices, such as Flexible AC Transmission Systems (FACTS), for stability enhancements. The discrepancies of existing modeling approaches have limited the feasibility of handling these devices or designing its damping controller. In this thesis, a versatile and generalized approach to model standard power system components is proposed. The more systematic and realistic representation, accompanied by the development of powerful eigenvalue-analysis techniques, facilitates the study of small signal stability (monotonic and oscillatory) of the power systems. In monotonic stability study, the effect of exciter and governor is critically reviewed based on the exploitation of eigenvalues, modal and sensitivity analyses over a wide range of operating conditions. In oscillatory stability study, a common FACTS device, the static var compensator (SVC), is used to improve system damping. This study reveals the inadequacy of many conventional methodologies in SVC design since they have ignored (or cannot handle) some important factors such as SVC mode instability and robustness of the power system. Two approaches, combined sensitivities and Hinfinity algorithms, are introduced to solve these limitations. Finally, an extended Hinfinity algorithm, which is applied to PSS design and successfully solves certain limitations of the existing H infinity based PSS design, is also presented. Although these studies are developed on selected controller devices or typical systems for convenience of discussion, extension to more complex systems can be dealt with in a similar way because of the versatility of the proposed modeling methodology.

  9. Touch HDR: photograph enhancement by user controlled wide dynamic range adaptation

    Science.gov (United States)

    Verrall, Steve; Siddiqui, Hasib; Atanassov, Kalin; Goma, Sergio; Ramachandra, Vikas

    2013-03-01

    High Dynamic Range (HDR) technology enables photographers to capture a greater range of tonal detail. HDR is typically used to bring out detail in a dark foreground object set against a bright background. HDR technologies include multi-frame HDR and single-frame HDR. Multi-frame HDR requires the combination of a sequence of images taken at different exposures. Single-frame HDR requires histogram equalization post-processing of a single image, a technique referred to as local tone mapping (LTM). Images generated using HDR technology can look less natural than their non- HDR counterparts. Sometimes it is only desired to enhance small regions of an original image. For example, it may be desired to enhance the tonal detail of one subject's face while preserving the original background. The Touch HDR technique described in this paper achieves these goals by enabling selective blending of HDR and non-HDR versions of the same image to create a hybrid image. The HDR version of the image can be generated by either multi-frame or single-frame HDR. Selective blending can be performed as a post-processing step, for example, as a feature of a photo editor application, at any time after the image has been captured. HDR and non-HDR blending is controlled by a weighting surface, which is configured by the user through a sequence of touches on a touchscreen.

  10. Mobile phone SMS messages can enhance healthy behaviour: a meta-analysis of randomised controlled trials.

    Science.gov (United States)

    Orr, Jayne A; King, Robert J

    2015-01-01

    Healthy behaviour, such as smoking cessation and adherence to prescribed medications, mitigates illness risk factors but health behaviour change can be challenging. Mobile phone short-message service (SMS) messages are increasingly used to deliver interventions designed to enhance healthy behaviour. This meta-analysis used a random-effects model to synthesise 38 randomised controlled trials that investigated the efficacy of SMS messages to enhance healthy behaviour. Participants (N = 19,641) lived in developed and developing countries and were diverse with respect to age, ethnicity, socioeconomic background and health behaviours targeted for change. SMS messages had a small, positive, significant effect (g = 0.291) on a broad range of healthy behaviour. This effect was maximised when multiple SMS messages per day were used (g = 0.395) compared to using lower frequencies (daily, multiple per week and once-off) (g = 0.244). The low heterogeneity in this meta-analysis (I (2) = 38.619) supports reporting a summary effect size and implies that the effect of SMS messaging is robust, regardless of population characteristics or healthy behaviour targeted. SMS messaging is a simple, cost-effective intervention that can be automated and can reach any mobile phone owner. While the effect size is small, potential health benefits are well worth achieving.

  11. Enhanced Tobacco Control Initiative at Johns Hopkins Health System: Employee Fairness Perception.

    Science.gov (United States)

    Durrani, Shabnum; Lucik, Meg; Safeer, Richard

    2018-02-01

    Organizations often fail to establish a clear awareness of what employees consider fair when implementing changes to employee benefits in the workplace. In 2016, the Johns Hopkins Health System (JHHS) enhanced their tobacco control efforts. In addition to enhanced smoking cessation benefits, employees were offered an increased reduction in their insurance premiums if they were nonsmokers. To qualify for the reduction, employees participated in testing rather than relying on self-reporting as had been done in the past. The shift to testing prompted a concern by some senior management at JHHS who did not want employees to feel they were not trusted. As the program unfolded at JHHS, the four-component model of procedural justice was applied to provide a framework for reviewing the implementation of the new voluntary tobacco testing at JHHS from a fairness lens. The purpose of this article is to illustrate the application of the four-component procedural model of justice to the tobacco testing process at JHHS. As approximately 75% of employees participated in the program, the experience at JHHS can be instructive to other employers who are looking to implement changes in their workplaces and how to minimize unintended consequences with their employees.

  12. Controlled biomineralization of electrospun poly(ε-caprolactone) fibers to enhance their mechanical properties.

    Science.gov (United States)

    Xie, Jingwei; Zhong, Shaoping; Ma, Bing; Shuler, Franklin D; Lim, Chwee Teck

    2013-03-01

    Electrospun polymeric fibers have been investigated as scaffolding materials for bone tissue engineering. However, their mechanical properties, and in particular stiffness and ultimate tensile strength, cannot match those of natural bones. The objective of the study was to develop novel composite nanofiber scaffolds by attaching minerals to polymeric fibers using an adhesive material - the mussel-inspired protein polydopamine - as a "superglue". Herein, we report for the first time the use of dopamine to regulate mineralization of electrospun poly(ε-caprolactone) (PCL) fibers to enhance their mechanical properties. We examined the mineralization of the PCL fibers by adjusting the concentration of HCO(3)(-) and dopamine in the mineralized solution, the reaction time and the surface composition of the fibers. We also examined mineralization on the surface of polydopamine-coated PCL fibers. We demonstrated the control of morphology, grain size and thickness of minerals deposited on the surface of electrospun fibers. The obtained mineral coatings render electrospun fibers with much higher stiffness, ultimate tensile strength and toughness, which could be closer to the mechanical properties of natural bone. Such great enhancement of mechanical properties for electrospun fibers through mussel protein-mediated mineralization has not been seen previously. This study could also be extended to the fabrication of other composite materials to better bridge the interfaces between organic and inorganic phases. Copyright © 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  13. Enhancing the Mechanical Properties of Electrospun Nanofiber Mats through Controllable Welding at the Cross Points.

    Science.gov (United States)

    Li, Haoxuan; Zhu, Chunlei; Xue, Jiajia; Ke, Qinfei; Xia, Younan

    2017-05-01

    This communication describes a simple and effective method for welding electrospun nanofibers at the cross points to enhance the mechanical properties of their nonwoven mats. The welding is achieved by placing a nonwoven mat of the nanofibers in a capped vial with the vapor of a proper solvent. For polycaprolactone (PCL) nanofibers, the solvent is dichloromethane (DCM). The welding can be managed in a controllable fashion by simply varying the partial pressure of DCM and/or the exposure time. Relative to the pristine nanofiber mat, the mechanical strength of the welded PCL nanofiber mat can be increased by as much as 200%. Meanwhile, such a treatment does not cause any major structural changes, including morphology, fiber diameter, and pore size. This study provides a generic method for improving the mechanical properties of nonwoven nanofiber mats, holding great potential in various applications. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Enhanced signaling scheme with admission control in the hybrid optical wireless (HOW) networks

    DEFF Research Database (Denmark)

    Yan, Ying; Yu, Hao; Wessing, Henrik

    2009-01-01

    that it can support stringent Quality of Service (QoS) requirements. In this paper, we describe and evaluate a resource management framework designed for the HOW networks. There are two parts in the resource management framework The first part is the Enhanced MPCP (E-MPCP) scheme aiming at improving signaling......The hybrid optical wireless (HOW) network has been viewed as a promising solution to meet the increasing user bandwidth and mobility demands. Due to the basic differences in the optical and wireless technologies, a challenging problem lies in the Media Access Control (MAC) protocol design so...... dropping probability depend on several factors. These factors include the frame duration, the traffic load and the total number of shared users. The results also highlight that our proposed system achieves significant improvements over the traditional approach in terms of user QoS guarantee and network...

  15. Enhancing Piezoelectric Performance of CaBi2Nb2O9 Ceramics Through Microstructure Control

    Science.gov (United States)

    Chen, Huanbei; Zhai, Jiwei

    2012-08-01

    Calcium bismuth niobate (CaBi2Nb2O9, CBN) is a high-Curie-temperature ( T C) piezoelectric material with relatively poor piezoelectric performance. Attempts were made to enhance the piezoelectric and direct-current (DC) resistive properties of CBN ceramics by increasing their density and controlling their microstructural texture, which were achieved by combining the templated grain growth and hot pressing methods. The modified CBN ceramics with 97.5% relative density and 90.5% Lotgering factor had much higher piezoelectric constant ( d 33 = 20 pC/N) than those prepared by the normal sintering process ( d 33 = 6 pC/N). High-temperature alternating-current (AC) impedance spectroscopy of the CBN ceramics was measured by using an impedance/gain-phase analyzer. Their electrical resistivity was approximately 6.5 × 104 Ω cm at 600°C. Therefore, CBN ceramics can be used for high-temperature piezoelectric applications.

  16. Admixture enhanced controlled low-strength material for direct underwater injection with minimal cross-contamination

    International Nuclear Information System (INIS)

    Hepworth, H.K.; Davidson, J.S.; Hooyman, J.L.

    1997-01-01

    Commercially available admixtures have been developed for placing traditional concrete products under water. This paper evaluates adapting anti-washout admixture (AWA) and high range water reducing admixture (HRWRA) products to enhance controlled low-strength materials (CLSMs) for underwater placement. A simple experimental scale model (based on dynamic and geometric similitude) of typical grout pump emplacement equipment has been developed to determine the percentage of cementing material washed out. The objective of this study was to identify proportions of admixtures and underwater CLSM emplacement procedures which would minimize the cross-contamination of the displaced water while maintaining the advantages of CLSM. Since the displaced water from radioactively contaminated systems must be subsequently treated prior to release to the environment, the amount of cross-contamination is important for cases in which cementing material could form hard sludges in a water treatment facility and contaminate the in-place CLSM stabilization medium

  17. Enhanced control of DFIG wind turbine based on stator flux decay compensation

    DEFF Research Database (Denmark)

    Zhu, Rongwu; Deng, Fujin; Chen, Zhe

    2016-01-01

    For the doubly-fed induction generator (DFIG)- based wind energy conversion system (WECS), the decaying flux and negative flux are the main reasons to cause the DFIG rotor overcurrent, during grid faults. The stator decaying flux characteristics versus the depth and instant of the stator voltage...... variation are analyzed firstly. On the basis of the stator flux performances, the enhanced control strategy is proposed to limit the decaying flux approximately into zero in half fundamental period by changing the stator voltage drop and recovery mode, and consequently the rotor transient current pulse...... is significantly reduced during grid faults. The experimental results based on the 7.5 kW DFIG setup is carried to validate the correctness and feasibility of the proposed strategy. Dynamic voltage restorer (DVR) can be one of the applications. With the proposed strategy, the DVR only works in a half fundamental...

  18. Controlled Thermal-Mechanical Processing of Tubes and Pipes for Enhanced Manufacturing and Performance

    Energy Technology Data Exchange (ETDEWEB)

    Kolarik, Robert V.

    2005-11-11

    The Alloy Steel Business of The Timken Company won an award for the controlled thermo-mechanical processing (CTMP) project and assembled a strong international public/private partnership to execute the project. The premise of the CTMP work was to combine Timken's product understanding with its process expertise and knowledge of metallurgical and deformation fundamentals developed during the project to build a predictive process design capability. The CTMP effort succeeded in delivering a pc-based capability in the tube optimization model, with a virtual pilot plant (VPP) feature to represent the desired tube making process to predict the resultant microstructure tailored for the desired application. Additional tasks included a system for direct, online measurement of grain size and demonstration of application of CTMP via robotically enhanced manufacturing.

  19. Heteropoly acid catalytic treatment for reactivity enhancement and viscosity control of dissolving pulp.

    Science.gov (United States)

    Wang, Xinqi; Duan, Chao; Zhao, Chengxin; Meng, Jingru; Qin, Xiaoyu; Xu, Yongjian; Ni, Yonghao

    2018-04-01

    The reactivity enhancement and viscosity control are of practical importance during the manufacture of high-quality cellulose (also known as dissolving pulp). In the study, the concept of using phosphotungstic acid (HPW) for this purpose was demonstrated. The Fock reactivity of resultant pulp increased from 49.1% to 74.1% after the HPW catalytic treatment at a dosage of 86.4 mg HPW/g odp. The improved results can be attributed to the increased fiber accessibility, thanks to the favorable fiber morphologic changes, such as increased pore volume/size, water retention value and specific surface area. HPW can be readily recycled/reused by evaporating method, where maintaining 87.1% catalytic activity after six recycle times. The HPW catalytic treatment concept may provide a green alternative for the manufacture of high-quality dissolving pulp. Copyright © 2018 Elsevier Ltd. All rights reserved.

  20. Dendrimer-assisted controlled growth of carbon nanotubes for enhanced thermal interface conductance

    International Nuclear Information System (INIS)

    Amama, Placidus B; Cola, Baratunde A; Sands, Timothy D; Xu, Xianfan; Fisher, Timothy S

    2007-01-01

    Multi-walled carbon nanotubes (MWCNTs) with systematically varied diameter distributions and defect densities were reproducibly grown from a modified catalyst structure templated in an amine-terminated fourth-generation poly(amidoamine) (PAMAM) dendrimer by microwave plasma-enhanced chemical vapor deposition. Thermal interface resistances of the vertically oriented MWCNT arrays as determined by a photoacoustic technique reveal a strong correlation with the quality as assessed by Raman spectroscopy. This study contributes not only to the development of an active catalyst via a wet chemical route for structure-controlled MWCNT growth, but also to the development of efficient and low-cost MWCNT-based thermal interface materials with thermal interface resistances ≤10 mm 2 K W -1

  1. Microsystems for enhanced control of cell behavior fundamentals, design and manufacturing strategies, applications and challenges

    CERN Document Server

    2016-01-01

    This handbook focuses on the entire development process of biomedical microsystems that promote special interactions with cells. Fundamentals of cell biology and mechanobiology are described as necessary preparatory input for design tasks. Advanced design, simulation, and micro/nanomanufacturing resources, whose combined use enables the development of biomedical microsystems capable of interacting at a cellular level, are covered in depth. A detailed series of chapters is then devoted to applications based on microsystems that offer enhanced cellular control, including microfluidic devices for diagnosis and therapy, cell-based sensors and actuators (smart biodevices), microstructured prostheses for improvement of biocompatibility, microstructured and microtextured cell culture matrices for promotion of cell growth and differentiation, electrophoretic microsystems for study of cell mechanics, microstructured and microtextured biodevices for study of cell adhesion and dynamics, and biomimetic microsystems (incl...

  2. Environmental controls on stable isotopes of precipitation in Lanzhou, China: An enhanced network at city scale.

    Science.gov (United States)

    Chen, Fenli; Zhang, Mingjun; Wang, Shengjie; Qiu, Xue; Du, Mingxia

    2017-12-31

    Stable hydrogen and oxygen isotopes in precipitation are very sensitive to environmental changes, and can record evolution of water cycle. The Lanzhou city in northwestern China is jointly influenced by the monsoon and westerlies, which is considered as a vital platform to investigate the moisture regime for this region. Since 2011, an observation network of stable isotopes in precipitation was established across the city, and four stations were included in the network. In 2013, six more sampling stations were added, and the enhanced network might provide more meaningful information on spatial incoherence and synoptic process. This study focused on the variations of stable isotopes (δ 18 O and δD) in precipitation and the environmental controls based on the 1432 samples in this enhanced network from April 2011 to October 2014. The results showed that the precipitation isotopes had great spatial diversity, and the neighboring stations may present large difference in δD and δ 18 O. Based on the observation at ten sampling sites, an isoscape in precipitation was calculated, and the method is useful to produce isoscape for small domains. The temperature effect and amount effect was reconsidered based on the dataset. Taking meteorological parameters (temperature, precipitation amount, relative humidity, water vapor pressure and dew point temperature) as variables in a multi-linear regression, the result of coefficients for these meteorological parameters were calculated. Some cases were also involved in this study, and the isotopic characteristics during one event or continuous days were used to understand the environmental controls on precipitation isotopes. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. The evaluation of angiotensin-converting enzyme (ACE) gene I/D and IL-4 gene intron 3 VNTR polymorphisms in coronary artery disease.

    Science.gov (United States)

    Basol, Nursah; Celik, Atac; Karakus, Nevin; Ozturk, Sibel Demir; Ozsoy, Sibel Demir; Yigit, Serbulent

    2014-01-01

    Genetic polymorphism is a strong risk factor for coronary artery disease (CAD). In the present study, our aim was to evaluate angiotensin-converting enzyme (ACE) gene I/D polymorphism and interleukin-4 (IL-4) gene Intron 3 variable number of tandem repeat (VNTR) polymorphism in CAD. One hundred and twenty-four CAD patients and one hundred and twenty-three controls were enrolled. Genomic DNA was isolated and genotyped using polymerase chain reaction (PCR) analyses. The risk associated with inheriting the combined genotypes for the two polymorphisms were evaluated and it was found that the individuals who were P2P2-homozygous at IL-4 gene intron 3 VNTR and DD-homozygous at ACE gene I/D have a higher risk of developing CAD. Although, there is no correlation between IL4 VNTR polymorphism and ACE gene polymorphism and CAD, there is a strong association between CAD and co-existence of IL-4 VNTR and ACE gene polymorphisms in the Turkish population. Copyright © 2014 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

  4. A native promoter and inclusion of an intron is necessary for efficient expression of GFP or mRFP in Armillaria mellea.

    Science.gov (United States)

    Ford, Kathryn L; Baumgartner, Kendra; Henricot, Béatrice; Bailey, Andy M; Foster, Gary D

    2016-07-07

    Armillaria mellea is a significant pathogen that causes Armillaria root disease on numerous hosts in forests, gardens and agricultural environments worldwide. Using a yeast-adapted pCAMBIA0380 Agrobacterium vector, we have constructed a series of vectors for transformation of A. mellea, assembled using yeast-based recombination methods. These have been designed to allow easy exchange of promoters and inclusion of introns. The vectors were first tested by transformation into basidiomycete Clitopilus passeckerianus to ascertain vector functionality then used to transform A. mellea. We show that heterologous promoters from the basidiomycetes Agaricus bisporus and Phanerochaete chrysosporium that were used successfully to control the hygromycin resistance cassette were not able to support expression of mRFP or GFP in A. mellea. The endogenous A. mellea gpd promoter delivered efficient expression, and we show that inclusion of an intron was also required for transgene expression. GFP and mRFP expression was stable in mycelia and fluorescence was visible in transgenic fruiting bodies and GFP was detectable in planta. Use of these vectors has been successful in giving expression of the fluorescent proteins GFP and mRFP in A. mellea, providing an additional molecular tool for this pathogen.

  5. Numerical analysis of the effect of plasma flow control on enhancing the aerodynamic characteristics of stratospheric screw propeller

    International Nuclear Information System (INIS)

    Cheng Yufeng; Nie Wansheng

    2012-01-01

    Based on the body force aerodynamic actuation mechanism of dielectric barrier discharge (DBD) plasma, the effect of plasma flow control on enhancing the aerodynamic characteristics of ten blade elements equably along the stratospheric screw propeller blade was numerical studied. Then the effect of plasma flow control enhancing the aerodynamic characteristics of stratospheric screw propeller was compared that by the blade element theory method. The results show that the flow separate phenomena will easily happen in the root region and top end region of screw propeller, and the blade elements in the root region of screw propeller may work on the negative attack angle condition. DBD plasma flow control can entirely restrain the faintish flow separate phenomena in middle region of screw propeller. Although DBD plasma flow control can not entirely restrain the badly flow separate phenomena in top end region of screw propeller, it also can enhance the aerodynamic characteristics of blade elements in these regions in same degree. But effect of DBD plasma flow control on enhancing the aerodynamic characteristics of the blade elements working on the negative attack angle condition is ineffectively. It can be concluded that DBD plasma flow control can enhance the aerodynamic characteristics of stratospheric screw propeller, the thrust of the whole propeller and the propeller efficiency in the case of plasma on will increases by a factor of 28.27% and 12.3% respectively compared with that in the case of plasma off studied. (authors)

  6. An Enhanced State Observer for DC-Link Voltage Control of Three- Phase AC/DC Converters

    DEFF Research Database (Denmark)

    Lu, Jinghang; Golestan, Saeed; Savaghebi, Mehdi

    2018-01-01

    To regulate the DC-link voltage of three-phase AC/DC converters, an enhanced state observer (ESO)-based controller is presented in this letter. The proposed controller, contrary to the traditional ones, does not require the DClink current measurement and offers a “plug and play” capability, a rat...

  7. Synthesis and photoluminescence enhancement of nano-PAA-ZnCl2 with controllable dimension and morphology

    International Nuclear Information System (INIS)

    Wu, Jianguo; Wang, Kaige; Zhou, Yukun; Wang, Shuang; Zhang, Chen; Wang, Guiren

    2016-01-01

    Highlights: • One kind of large area nano-PAA-ZnCl 2 composite film is fabricated, its dimension and morphology is controllable. The properties of nano-composite films have been heavily influenced by the concentration of initial ZnCl 2 solution, the depth of nano-PAAM substrate and the growth time of ZnCl 2 crystals. • At room temperature, the nano-PAA-ZnCl 2 film has the same excitation center (335 nm) and emission center (430 nm) as the nano-PAAM substrate, and the PL intensities can be doubly enhanced. • After annealing at 500 °C, the emission peak spectra of the nano-composite films stabilized at 385 nm, 402 nm, and 430 nm. - Abstract: One kind of ZnCl 2 nano-films with controllable dimension and morphology is successfully synthesized on the top surface of nano-porous anodic alumina membrane (nano-PAAM) by self-organized method. The nano-PAA-ZnCl 2 composite films are characterized by field emission scanning electron microscopy, energy dispersive spectrometer, and laser confocal Raman spectroscopy. The results indicate that the concentration of initial ZnCl 2 solution, the depth of nano-PAAM substrate and the growth time of ZnCl 2 crystals have important influences on the properties of nano-composite films. Furthermore, the characteristics of nano-composites such as the photoluminescence (PL) spectra are investigated. Compared with the nano-PAAM substrate, at room temperature, all of the nano-PAA-ZnCl 2 composite films have both the same excitation center (335 nm) and emission center (430 nm), no matter what the nano-composite morphologies being; and the PL intensity of nano-PAA-ZnCl 2 composite films are all enhanced and the maximum enhancement is two times; after annealing at 500 °C, the emission spectra of the nano-composite films stabilized at the 385 nm, 402 nm and 430 nm. The research provides a new, simple, economical and practical technology to fabricate nano-PAA composite films with higher luminousintensity.

  8. A systematic review of randomized controlled trials on curative and health enhancement effects of forest therapy

    Directory of Open Access Journals (Sweden)

    Kamioka H

    2012-07-01

    Full Text Available Hiroharu Kamioka,1 Kiichiro Tsutani,2 Yoshiteru Mutoh,3 Takuya Honda,4 Nobuyoshi Shiozawa,5 Shinpei Okada,6 Sang-Jun Park,6 Jun Kitayuguchi,7 Masamitsu Kamada,8 Hiroyasu Okuizumi,9 Shuichi Handa91Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo, 2Department of Drug Policy and Management, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 3Todai Policy Alternatives Research Institute, The University of Tokyo, Tokyo, 4Japanese Society for the Promotion of Science, Tokyo, 5Food Labeling Division, Consumer Affairs Agency, Cabinet Office, Government of Japan, Tokyo, 6Physical Education and Medicine Research Foundation, Nagano, 7Physical Education and Medicine Research Center Unnan, Shimane, 8Department of Environmental and Preventive Medicine, Shimane University School of Medicine, Shimane, 9Mimaki Onsen (Spa Clinic, Tomi City, Nagano, JapanObjective: To summarize the evidence for curative and health enhancement effects through forest therapy and to assess the quality of studies based on a review of randomized controlled trials (RCTs.Study design: A systematic review based on RCTs.Methods: Studies were eligible if they were RCTs. Studies included one treatment group in which forest therapy was applied. The following databases – from 1990 to November 9, 2010 – were searched: MEDLINE via PubMed, CINAHL, Web of Science, and Ichushi-Web. All Cochrane databases and Campbell Systematic Reviews were also searched up to November 9, 2010.Results: Two trials met all inclusion criteria. No specific diseases were evaluated, and both studies reported significant effectiveness in one or more outcomes for health enhancement. However, the results of evaluations with the CONSORT (Consolidated Standards of Reporting Trials 2010 and CLEAR NPT (A Checklist to Evaluate a Report of a Nonpharmacological Trial checklists generally showed a remarkable lack of description in the studies. Furthermore, there was a

  9. Treating the invisible: Gaps and opportunities for enhanced TB control along the Thailand-Myanmar border.

    Science.gov (United States)

    Tschirhart, Naomi; Thi, Sein Sein; Swe, Lei Lei; Nosten, Francois; Foster, Angel M

    2017-01-13

    In Thailand's northwestern Tak province, contextual conditions along the border with Myanmar pose difficulties for TB control among migrant populations. Incomplete surveillance data, migrant patient mobility, and loss to follow-up make it difficult to estimate the TB burden and implement effective TB control measures. This multi-methods study examined tuberculosis, tuberculosis and human immunodeficiency virus co-infection, and multidrug-resistant tuberculosis treatment accessibility for migrants and refugees in Tak province, health system response, and public health surveillance. In this study we conducted 13 interviews with key informants working in public health or TB treatment provision to elicit information on TB treatment availability and TB surveillance practices. In addition we organized 15 focus group discussions with refugee and migrant TB, TB/HIV, and MDR-TB patients and non-patients to discuss treatment access. We analyzed the data using thematic analysis and created treatment availability maps with Google maps. The study identified surveillance, treatment, and funding gaps. Migrant TB cases are underreported in the provincial statistics due to jurisdictional interpretations and resource barriers. Our results suggest that TB/HIV and MDR-TB treatment options are limited for migrants and a heavy reliance on donor funding may lead to potential funding gaps for migrant TB services. We identified several opportunities that positively contribute to TB control in Tak province: improved diagnostics, comprehensive care, and collaboration through data sharing, planning, and patient referrals. The various organizations providing TB treatment to migrant and refugee populations along the border and the Tak Provincial Public Health Office are highly collaborative which offers a strong foundation for future TB control initiatives. Our findings suggest the need to enhance the surveillance system to include all migrant TB patients who seek treatment in Tak province and

  10. The effect of gamma-enhancing binaural beats on the control of feature bindings.

    Science.gov (United States)

    Colzato, Lorenza S; Steenbergen, Laura; Sellaro, Roberta

    2017-07-01

    Binaural beats represent the auditory experience of an oscillating sound that occurs when two sounds with neighboring frequencies are presented to one's left and right ear separately. Binaural beats have been shown to impact information processing via their putative role in increasing neural synchronization. Recent studies of feature-repetition effects demonstrated interactions between perceptual features and action-related features: repeating only some, but not all features of a perception-action episode hinders performance. These partial-repetition (or binding) costs point to the existence of temporary episodic bindings (event files) that are automatically retrieved by repeating at least one of their features. Given that neural synchronization in the gamma band has been associated with visual feature bindings, we investigated whether the impact of binaural beats extends to the top-down control of feature bindings. Healthy adults listened to gamma-frequency (40 Hz) binaural beats or to a constant tone of 340 Hz (control condition) for ten minutes before and during a feature-repetition task. While the size of visuomotor binding costs (indicating the binding of visual and action features) was unaffected by the binaural beats, the size of visual feature binding costs (which refer to the binding between the two visual features) was considerably smaller during gamma-frequency binaural beats exposure than during the control condition. Our results suggest that binaural beats enhance selectivity in updating episodic memory traces and further strengthen the hypothesis that neural activity in the gamma band is critically associated with the control of feature binding.

  11. Error-enhancing robot therapy to induce motor control improvement in childhood onset primary dystonia

    Directory of Open Access Journals (Sweden)

    Casellato Claudia

    2012-07-01

    Full Text Available Abstract Background Robot-generated deviating forces during multijoint reaching movements have been applied to investigate motor control and to tune neuromotor adaptation. Can the application of force to limbs improve motor learning? In this framework, the response to altered dynamic environments of children affected by primary dystonia has never been studied. Methods As preliminary pilot study, eleven children with primary dystonia and eleven age-matched healthy control subjects were asked to perform upper limb movements, triangle-reaching (three directions and circle-writing, using a haptic robot interacting with ad-hoc developed task-specific visual interfaces. Three dynamic conditions were provided, null additive external force (A, constant disturbing force (B and deactivation of the additive external force again (C. The path length for each trial was computed, from the recorded position data and interaction events. Results The results show that the disturbing force affects significantly the movement outcomes in healthy but not in dystonic subjects, already compromised in the reference condition: the external alteration uncalibrates the healthy sensorimotor system, while the dystonic one is already strongly uncalibrated. The lack of systematic compensation for perturbation effects during B condition is reflected into the absence of after-effects in C condition, which would be the evidence that CNS generates a prediction of the perturbing forces using an internal model of the environment. The most promising finding is that in dystonic population the altered dynamic exposure seems to induce a subsequent improvement, i.e. a beneficial after-effect in terms of optimal path control, compared with the correspondent reference movement outcome. Conclusions The short-time error-enhancing training in dystonia could represent an effective approach for motor performance improvement, since the exposure to controlled dynamic alterations induces a refining

  12. Deep intronic GBE1 mutation in manifesting heterozygous patients with adult polyglucosan body disease.

    Science.gov (United States)

    Akman, H Orhan; Kakhlon, Or; Coku, Jorida; Peverelli, Lorenzo; Rosenmann, Hanna; Rozenstein-Tsalkovich, Lea; Turnbull, Julie; Meiner, Vardiella; Chama, Liat; Lerer, Israela; Shpitzen, Shoshi; Leitersdorf, Eran; Paradas, Carmen; Wallace, Mary; Schiffmann, Raphael; DiMauro, Salvatore; Lossos, Alexander; Minassian, Berge A

    2015-04-01

    We describe a deep intronic mutation in adult polyglucosan body disease. Similar mechanisms can also explain manifesting heterozygous cases in other inborn metabolic diseases. To explain the genetic change consistently associated with manifesting heterozygous patients with adult polyglucosan body disease. This retrospective study took place from November 8, 2012, to November 7, 2014. We studied 35 typical patients with adult polyglucosan body disease, of whom 16 were heterozygous for the well-known c.986A>C mutation in the glycogen branching enzyme gene (GBE1) but harbored no other known mutation in 16 exons. All 16 manifesting heterozygous patients had lower glycogen branching activity compared with homozygous patients, which showed inactivation of the apparently normal allele. We studied the messenger ribonucleic acid (mRNA) structure and the genetic change due to the elusive second mutation. When we reverse transcribed and sequenced the mRNA of GBE1, we found that all manifesting heterozygous patients had the c.986A>C mutant mRNA and complete lack of mRNA encoded by the second allele. We identified a deep intronic mutation in this allele, GBE1-IVS15+5289_5297delGTGTGGTGGinsTGTTTTTTACATGACAGGT, which acts as a gene trap, creating an ectopic last exon. The mRNA transcript from this allele missed the exon 16 and 3'UTR and encoded abnormal GBE causing further decrease of enzyme activity from 18% to 8%. We identified the deep intronic mutation, which acts as a gene trap. This second-most common adult polyglucosan body disease mutation explains another founder effect in all Ashkenazi-Jewish cases.

  13. Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

    Directory of Open Access Journals (Sweden)

    Yan Ding

    Full Text Available Previously, a candidate gene linkage approach on brother pairs affected with prostate cancer identified a locus of prostate cancer susceptibility at D3S1234 within the fragile histidine triad gene (FHIT, a tumor suppressor that induces apoptosis. Subsequent association tests on 16 SNPs spanning approximately 381 kb surrounding D3S1234 in Americans of European descent revealed significant evidence of association for a single SNP within intron 5 of FHIT. In the current study, re-sequencing and genotyping within a 28.5 kb region surrounding this SNP further delineated the association with prostate cancer risk to a 15 kb region. Multiple SNPs in sequences under evolutionary constraint within intron 5 of FHIT defined several related haplotypes with an increased risk of prostate cancer in European-Americans. Strong associations were detected for a risk haplotype defined by SNPs 138543, 142413, and 152494 in all cases (Pearson's chi(2 = 12.34, df 1, P = 0.00045 and for the homozygous risk haplotype defined by SNPs 144716, 142413, and 148444 in cases that shared 2 alleles identical by descent with their affected brothers (Pearson's chi(2 = 11.50, df 1, P = 0.00070. In addition to highly conserved sequences encompassing SNPs 148444 and 152413, population studies revealed strong signatures of natural selection for a 1 kb window covering the SNP 144716 in two human populations, the European American (pi = 0.0072, Tajima's D = 3.31, 14 SNPs and the Japanese (pi = 0.0049, Fay & Wu's H = 8.05, 14 SNPs, as well as in chimpanzees (Fay & Wu's H = 8.62, 12 SNPs. These results strongly support the involvement of the FHIT intronic region in an increased risk of prostate cancer.

  14. The relationship between polymorphisms in intron 8 of vitamin D receptor gene and occult HBV infection

    Directory of Open Access Journals (Sweden)

    Rezvani ME

    2009-08-01

    Full Text Available "n Normal 0 false false false EN-US X-NONE AR-SA MicrosoftInternetExplorer4 Background: Occult hepatitis B infection (OBI is a form of hepatitis in which despite absence of detectable HBsAg, HBV-DNA is present in peripheral blood of patients. The responsible mechanisms for progression of OBI yet to be clarified, but some investigators believed that the genetics and immunological parameters are different in resistant individuals and patients. Vitamin D3 and its receptor interaction could be involved in anti-viral immune response. The aim of this study was to investigate the association between polymorphisms in intron 8 of VDR with OBI."n"n Methods: In this experimental study, the plasma samples of 3700 blood donors were collected and tested for HBsAg and anti-HBs by ELISA. The HBsAg negative and anti-HBc positive samples were selected and screened for HBV-DNA using PCR. HBV-DNA positive samples were assigned as OBI cases and PCR-RFLP was performed to examine the polymorphisms in intron 8 of VDR genes."n"n Results: Results of current study indicated that 352 (9.5% of 3700 blood samples were HBsAg- and anti-HBc+. HBV-DNA was detected in 57/352 (16.1% of HBsAg- and anti-HBc+ samples. Our results showed that no significant difference was observed in Apa-1 polymorphisms of intron 8 of VDR and OBI patients."n"n Conclusion: Our results demonstrated that there are not any association between Apa-1 detected alleles and OBI, hence, it can be concluded that these alleles are not associated with OBI and other researchers should evaluate relation between other polymorphisms of VDR with OBI.

  15. Novel pre-mRNA splicing of intronically integrated HBV generates oncogenic chimera in hepatocellular carcinoma.

    Science.gov (United States)

    Chiu, Yung-Tuen; Wong, John K L; Choi, Shing-Wan; Sze, Karen M F; Ho, Daniel W H; Chan, Lo-Kong; Lee, Joyce M F; Man, Kwan; Cherny, Stacey; Yang, Wan-Ling; Wong, Chun-Ming; Sham, Pak-Chung; Ng, Irene O L

    2016-06-01

    Hepatitis B virus (HBV) integration is common in HBV-associated hepatocellular carcinoma (HCC) and may play an important pathogenic role through the production of chimeric HBV-human transcripts. We aimed to screen the transcriptome for HBV integrations in HCCs. Transcriptome sequencing was performed on paired HBV-associated HCCs and corresponding non-tumorous liver tissues to identify viral-human chimeric sites. Validation was further performed in an expanded cohort of human HCCs. Here we report the discovery of a novel pre-mRNA splicing mechanism in generating HBV-human chimeric protein. This mechanism was exemplified by the formation of a recurrent HBV-cyclin A2 (CCNA2) chimeric transcript (A2S), as detected in 12.5% (6 of 48) of HCC patients, but in none of the 22 non-HCC HBV-associated cirrhotic liver samples examined. Upon the integration of HBV into the intron of the CCNA2 gene, the mammalian splicing machinery utilized the foreign splice sites at 282nt. and 458nt. of the HBV genome to generate a pseudo-exon, forming an in-frame chimeric fusion with CCNA2. The A2S chimeric protein gained a non-degradable property and promoted cell cycle progression, demonstrating its potential oncogenic functions. A pre-mRNA splicing mechanism is involved in the formation of HBV-human chimeric proteins. This represents a novel and possibly common mechanism underlying the formation of HBV-human chimeric transcripts from intronically integrated HBV genome with functional impact. HBV is involved in the mammalian pre-mRNA splicing machinery in the generation of potential tumorigenic HBV-human chimeras. This study also provided insight on the impact of intronic HBV integration with the gain of splice sites in the development of HBV-associated HCC. Copyright © 2016 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

  16. Emotional and uncontrolled eating styles and chocolate chip cookie consumption. A controlled trial of the effects of positive mood enhancement.

    Science.gov (United States)

    Turner, Sally Ann; Luszczynska, Aleksandra; Warner, Lisa; Schwarzer, Ralf

    2010-02-01

    The study tested the effects of positive mood enhancement on chocolate chip cookie consumption in the context of emotional and uncontrolled eating styles. The relationship between emotional eating style and chocolate chip cookie intake was assumed to be mediated by uncontrolled eating style. Further, it was hypothesized that the effectiveness of the positive mood enhancement may be more salient among those who have effective control of their eating. In this experimental study, respondents (N=106, 70% women, aged 16-45 years old) were assigned by means of cluster randomization to the control or positive mood enhancement condition (a comedy movie clip). Compared to the control condition, positive mood enhancement resulted in consuming on average 53.86 kcal less. Relationships between emotional eating style and cookie intake were mediated by uncontrolled eating. Moderated mediation analysis indicated that the effect of a mediator (uncontrolled eating) on cookie intake was moderated by the group assignment. Positive mood enhancement resulted in eating on average 3.3 cookies less among individuals with a more controlled eating style. By contrast, among those who presented uncontrolled eating, positive mood enhancement led to consuming an average of 1.7 cookies more. 2009 Elsevier Ltd. All rights reserved.

  17. Association of eNOS gene intron 4 a/b VNTR polymorphisms in children with nephrotic syndrome.

    Science.gov (United States)

    Dursun, Hasan; Noyan, Aytul; Matyar, Selcuk; Buyukcelik, Mithat; Soran, Mustafa; Cengiz, Nurcan; Bayazit, Aysun K; Seydaoglu, Gulsah; Attila, Gulen; Anarat, Ali

    2013-06-15

    To investigate the association of endothelial nitric oxide synthase gene intron 4 (eNOS4) polymorphisms with nephrotic syndrome, the eNOS4 genotypes were assessed in 161 children with nephrotic syndrome in comparison with 78 healthy subjects. We classified the children with nephritic syndrome into 2 groups: as steroid-sensitive nephrotic syndrome (SSNS) (n=125) and steroid-resistant nephrotic syndrome (SRNS) (n=36). The eNOS4 polymorphisms were analyzed by polymerase chain reaction. The frequencies of eNOS4 aa, ab and bb genotypes were 3%, 31%, and 66% in all the nephrotic syndrome groups, and 1%, 23%, and 76% in the control group (x(2)=2.87, p>0.05). In addition, the frequencies of eNOS4 aa, ab and bb genotypes were 2%, 33%, and 65% in SSNS group, and 5%, 28%, and 67% in the SRNS group (x(2)=1.13, p=0.567). The present study is the first to investigate eNOS4 gene polymorphisms in children with SSNS and SRNS. Our data show that the eNOS4 gene polymorphisms were not associated with the development, frequent relapse and response to steroid in nephritic syndrome. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

    Energy Technology Data Exchange (ETDEWEB)

    Smith, David R.; Lee, Robert W.; Cushman, John C.; Magnuson, Jon K.; Tran, Duc; Polle, Juergen E.

    2010-05-07

    Abstract Background: Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. Results: The D. salina organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA) sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA. Conclusions: These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the development of a viable

  19. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

    Directory of Open Access Journals (Sweden)

    Tran Duc

    2010-05-01

    Full Text Available Abstract Background Dunaliella salina Teodoresco, a unicellular, halophilic green alga belonging to the Chlorophyceae, is among the most industrially important microalgae. This is because D. salina can produce massive amounts of β-carotene, which can be collected for commercial purposes, and because of its potential as a feedstock for biofuels production. Although the biochemistry and physiology of D. salina have been studied in great detail, virtually nothing is known about the genomes it carries, especially those within its mitochondrion and plastid. This study presents the complete mitochondrial and plastid genome sequences of D. salina and compares them with those of the model green algae Chlamydomonas reinhardtii and Volvox carteri. Results The D. salina organelle genomes are large, circular-mapping molecules with ~60% noncoding DNA, placing them among the most inflated organelle DNAs sampled from the Chlorophyta. In fact, the D. salina plastid genome, at 269 kb, is the largest complete plastid DNA (ptDNA sequence currently deposited in GenBank, and both the mitochondrial and plastid genomes have unprecedentedly high intron densities for organelle DNA: ~1.5 and ~0.4 introns per gene, respectively. Moreover, what appear to be the relics of genes, introns, and intronic open reading frames are found scattered throughout the intergenic ptDNA regions -- a trait without parallel in other characterized organelle genomes and one that gives insight into the mechanisms and modes of expansion of the D. salina ptDNA. Conclusions These findings confirm the notion that chlamydomonadalean algae have some of the most extreme organelle genomes of all eukaryotes. They also suggest that the events giving rise to the expanded ptDNA architecture of D. salina and other Chlamydomonadales may have occurred early in the evolution of this lineage. Although interesting from a genome evolution standpoint, the D. salina organelle DNA sequences will aid in the

  20. Use of a Fluorescent Aptamer RNA as an Exonic Sequence to Analyze Self-Splicing Ability of a Group I Intron from Structured RNAs

    Directory of Open Access Journals (Sweden)

    Airi Furukawa

    2016-11-01

    Full Text Available Group I self-splicing intron constitutes an important class of functional RNA molecules that can promote chemical transformation. Although the fundamental mechanism of the auto-excision from its precursor RNA has been established, convenient assay systems for its splicing activity are still useful for a further understanding of its detailed mechanism and of its application. Because some host RNA sequences, to which group I introns inserted form stable three-dimensional (3D structures, the effects of the 3D structures of exonic elements on the splicing efficiency of group I introns are important but not a fully investigated issue. We developed an assay system for group I intron self-splicing by employing a fluorescent aptamer RNA (spinach RNA as a model exonic sequence inserted by the Tetrahymena group I intron. We investigated self-splicing of the intron from spinach RNA, serving as a model exonic sequence with a 3D structure.

  1. EMPRESS: A European Project to Enhance Process Control Through Improved Temperature Measurement

    Science.gov (United States)

    Pearce, J. V.; Edler, F.; Elliott, C. J.; Rosso, L.; Sutton, G.; Andreu, A.; Machin, G.

    2017-08-01

    A new European project called EMPRESS, funded by the EURAMET program `European Metrology Program for Innovation and Research,' is described. The 3 year project, which started in the summer of 2015, is intended to substantially augment the efficiency of high-value manufacturing processes by improving temperature measurement techniques at the point of use. The project consortium has 18 partners and 5 external collaborators, from the metrology sector, high-value manufacturing, sensor manufacturing, and academia. Accurate control of temperature is key to ensuring process efficiency and product consistency and is often not achieved to the level required for modern processes. Enhanced efficiency of processes may take several forms including reduced product rejection/waste; improved energy efficiency; increased intervals between sensor recalibration/maintenance; and increased sensor reliability, i.e., reduced amount of operator intervention. Traceability of temperature measurements to the International Temperature Scale of 1990 (ITS-90) is a critical factor in establishing low measurement uncertainty and reproducible, consistent process control. Introducing such traceability in situ (i.e., within the industrial process) is a theme running through this project.

  2. Regulatory Initiatives for Control and Release of Technologically Enhanced Naturally-Occurring Radioactive Materials

    Energy Technology Data Exchange (ETDEWEB)

    Egidi, P.V.

    1999-03-02

    Current drafts of proposed standards and suggested State regulations for control and release of technologically-enhanced naturally-occurring radioactive material (TENORM), and standards for release of volumetrically-contaminated material in the US are reviewed. These are compared to the recommendations of the International Atomic Energy Association (IAEA) Safety Series and the European Commission (EC) proposals. Past regulatory efforts with respect to TENORM in the US dealt primarily with oil-field related wastes. Currently, nine states (AK, GA, LA, MS, NM, OH, OR SC, TX) have specific regulations pertaining to TENORM, mostly based on uranium mill tailings cleanup criteria. The new US proposals are dose- or risk-based, as are the IAEA and EC recommendations, and are grounded in the linear no threshold hypothesis (LNT). TENORM wastes involve extremely large volumes, particularly scrap metal and mine wastes. Costs to control and dispose of these wastes can be considerable. The current debate over the validity of LNT at low doses and low dose rates is particularly germane to this discussion. Most standards setting organizations and regulatory agencies base their recommendations on the LNT. The US Environmental Protection Agency has released a draft Federal Guidance Report that recommends calculating health risks from low-level exposure to radionuclides based on the LNT. However, some scientific and professional organizations are openly questioning the validity of LNT and its basis for regulations, practices, and costs to society in general. It is not clear at this time how a non-linear regulatory scheme would be implemented.

  3. Regulatory Initiatives for Control and Release of Technologically Enhanced Naturally-Occurring Radioactive Material

    International Nuclear Information System (INIS)

    Egidi, P.V.

    1999-01-01

    Current drafts of proposed standards and suggested State regulations for control and release of technologically-enhanced naturally-occurring radioactive material (TENORM), and standards for release of volumetrically-contaminated material in the US are reviewed. These are compared to the recommendations of the International Atomic Energy Association (IAEA) Safety Series and the European Commission (EC) proposals. Past regulatory efforts with respect to TENORM in the US dealt primarily with oil-field related wastes. Currently, nine states (AK, GA, LA, MS, NM, OH, OR SC, TX) have specific regulations pertaining to TENORM, mostly based on uranium mill tailings cleanup criteria. The new US proposals are dose- or risk-based, as are the IAEA and EC recommendations, and are grounded in the linear no threshold hypothesis (LNT). TENORM wastes involve extremely large volumes, particularly scrap metal and mine wastes. Costs to control and dispose of these wastes can be considerable. The current debate over the validity of LNT at low doses and low dose rates is particularly germane to this discussion. Most standards setting organizations and regulatory agencies base their recommendations on the LNT. The US Environmental Protection Agency has released a draft Federal Guidance Report that recommends calculating health risks from low-level exposure to radionuclides based on the LNT. However, some scientific and professional organizations are openly questioning the validity of LNT and its basis for regulations, practices, and costs to society in general. It is not clear at this time how a non-linear regulatory scheme would be implemented

  4. Performance enhancement of adaptive Active Noise Control systems for FMRI machines.

    Science.gov (United States)

    Kannan, Govind; Milani, Ali A; Panahi, Issa M S; Kehtarnavaz, Nasser

    2010-01-01

    Active Noise Control (ANC) of fMRI acoustic noise using the conventional Filtered-X LMS (FXLMS) approach results in poor cancelation performance and slow convergence due to its broadband nature and the need for high order adaptive filters. High order adaptive filters are needed to effectively model the long acoustic impulse responses. Existing methods to improve the performance of FXLMS based broadband ANC systems are either computationally expensive or need elaborate implementation. In this paper we show a practical method to enhance the performance of FXLMS based algorithms, by deriving a crude estimate of the causalWiener filter and initializing the adaptive filter with the estimated Wiener filter. We observe that very fast convergence to the global minimum can be achieved along with huge gains in the noise cancelation performance. We call this method Wiener initialized FXLMS (WI-FXLMS).We show the effectiveness of the proposed approach for the active noise control of functional MRI acoustic noise and several other realistic noise sources.

  5. Is DBM Beneficial for the Enhancement of Bony Consolidation in Distraction Osteogenesis? A Randomized Controlled Trial

    Directory of Open Access Journals (Sweden)

    Sang-Heon Song

    2015-01-01

    Full Text Available The aim of the present study was to compare the radiographic and clinical outcomes of DBM injection and conventional treatment during tibial lengthening over an intramedullary nail in adult patients with short stature. Twenty-nine patients were randomized to receive DBM injection (n=14 or conventional treatment without any injection (n=15 and evaluated. The outcome was measured on the basis of the pixel value ratio (PVR in the digital radiographs during the consolidation period; healing index; clinical assessment; and the rate of complications. In the DBM group, the mean PVR of 1 (mineral density of the callus is comparable to the adjacent bone was reached by 40 weeks in anterior and medial cortices which was significantly different than that in the control group (P=0.03 for anterior cortex; P=0.04 for medial cortex. The average healing index in the DBM group was 39.8 ± 5.3 days/cm compared to 44.3 ± 5.8 days/cm in the control group (P=0.05. There were no significant differences in clinical outcomes (P=0.23 and functional status (P=0.47 including complications (P=0.72 between two groups. In this randomized clinical trial, injection of DBM at the time of initial operation enhanced consolidation of regenerate callus without interfering with clinical outcomes compared to that with conventional treatment.

  6. Faces presenting sadness enhance self-control abilities in gifted adolescents.

    Science.gov (United States)

    Urben, Sébastien; Camos, Valérie; Habersaat, Stéphanie; Stéphan, Philippe

    2018-02-23

    Self-regulation skills refer to processes allowing emotional and cognitive adaptation of the individual. Some gifted adolescents are known for their imbalance between high intellectual abilities and low emotional skills. Thus, this study aimed at examining the interplay between emotion and cognition in gifted and non-gifted adolescents. A stop-signal task, a response inhibition task including neutral, happy, or sad faces as signal triggering inhibition, was administered to 19 gifted and 20 typically developing male adolescents (12-18 years old). Gifted adolescents showed lower response inhibition abilities than non-gifted adolescents in the neutral and happy face conditions. Sad faces in gifted adolescents were associated with higher response inhibition compared to happy condition. In typically developing adolescents, emotional information (happy or sad faces) was related to lower response inhibition compared to neutral face condition. This study highlights that gifted adolescents present different self-regulation skills than their typically developing peers. Statement of contribution What is already known on this subject? Some gifted adolescents present higher intellectual abilities alongside with lower socio-emotional skills. Self-regulation skills refer to processes allowing emotional and cognitive adaptation. Self-regulation skills might help to understand gifted adolescents, but remain scarcely studied. What does this study adds? Task-relevant emotional information impaired cognitive control in typically developing adolescents. Gifted adolescents are able to use sad faces to enhance their cognitive control abilities. © 2018 The British Psychological Society.

  7. Increased reward in ankle robotics training enhances motor control and cortical efficiency in stroke.

    Science.gov (United States)

    Goodman, Ronald N; Rietschel, Jeremy C; Roy, Anindo; Jung, Brian C; Diaz, Jason; Macko, Richard F; Forrester, Larry W

    2014-01-01

    Robotics is rapidly emerging as a viable approach to enhance motor recovery after disabling stroke. Current principles of cognitive motor learning recognize a positive relationship between reward and motor learning. Yet no prior studies have established explicitly whether reward improves the rate or efficacy of robotics-assisted rehabilitation or produces neurophysiologic adaptations associated with motor learning. We conducted a 3 wk, 9-session clinical pilot with 10 people with chronic hemiparetic stroke, randomly assigned to train with an impedance-controlled ankle robot (anklebot) under either high reward (HR) or low reward conditions. The 1 h training sessions entailed playing a seated video game by moving the paretic ankle to hit moving onscreen targets with the anklebot only providing assistance as needed. Assessments included paretic ankle motor control, learning curves, electroencephalograpy (EEG) coherence and spectral power during unassisted trials, and gait function. While both groups exhibited changes in EEG, the HR group had faster learning curves (p = 0.05), smoother movements (p

  8. Is DBM beneficial for the enhancement of bony consolidation in distraction osteogenesis? A randomized controlled trial.

    Science.gov (United States)

    Song, Sang-Heon; Kim, Sang-Gyun; Kim, Sung-Eun; Song, Hae-Ryong

    2015-01-01

    The aim of the present study was to compare the radiographic and clinical outcomes of DBM injection and conventional treatment during tibial lengthening over an intramedullary nail in adult patients with short stature. Twenty-nine patients were randomized to receive DBM injection (n = 14) or conventional treatment without any injection (n = 15) and evaluated. The outcome was measured on the basis of the pixel value ratio (PVR) in the digital radiographs during the consolidation period; healing index; clinical assessment; and the rate of complications. In the DBM group, the mean PVR of 1 (mineral density of the callus is comparable to the adjacent bone) was reached by 40 weeks in anterior and medial cortices which was significantly different than that in the control group (P = 0.03 for anterior cortex; P = 0.04 for medial cortex). The average healing index in the DBM group was 39.8 ± 5.3 days/cm compared to 44.3 ± 5.8 days/cm in the control group (P = 0.05). There were no significant differences in clinical outcomes (P = 0.23) and functional status (P = 0.47) including complications (P = 0.72) between two groups. In this randomized clinical trial, injection of DBM at the time of initial operation enhanced consolidation of regenerate callus without interfering with clinical outcomes compared to that with conventional treatment.

  9. Transient stability enhancement of modern power grid using predictive Wide-Area Monitoring and Control

    Science.gov (United States)

    Yousefian, Reza

    This dissertation presents a real-time Wide-Area Control (WAC) designed based on artificial intelligence for large scale modern power systems transient stability enhancement. The WAC using the measurements available from Phasor Measurement Units (PMUs) at generator buses, monitors the global oscillations in the system and optimally augments the local excitation system of the synchronous generators. The complexity of the power system stability problem along with uncertainties and nonlinearities makes the conventional modeling non-practical or inaccurate. In this work Reinforcement Learning (RL) algorithm on the benchmark of Neural Networks (NNs) is used to map the nonlinearities of the system in real-time. This method different from both the centralized and the decentralized control schemes, employs a number of semi-autonomous agents to collaborate with each other to perform optimal control theory well-suited for WAC applications. Also, to handle the delays in Wide-Area Monitoring (WAM) and adapt the RL toward the robust control design, Temporal Difference (TD) is proposed as a solver for RL problem or optimal cost function. However, the main drawback of such WAC design is that it is challenging to determine if an offline trained network is valid to assess the stability of the power system once the system is evolved to a different operating state or network topology. In order to address the generality issue of NNs, a value priority scheme is proposed in this work to design a hybrid linear and nonlinear controllers. The algorithm so-called supervised RL is based on mixture of experts, where it is initialized by linear controller and as the performance and identification of the RL controller improves in real-time switches to the other controller. This work also focuses on transient stability and develops Lyapunov energy functions for synchronous generators to monitor the stability stress of the system. Using such energies as a cost function guarantees the convergence

  10. Vestibular control of standing balance is enhanced with increased cognitive load.

    Science.gov (United States)

    McGeehan, Michael A; Woollacott, Marjorie H; Dalton, Brian H

    2017-04-01

    When cognitive load is elevated during a motor task, cortical inhibition and reaction time are increased; yet, standing balance control is often unchanged. This disconnect is likely explained by compensatory mechanisms within the balance system such as increased sensitivity of the vestibulomotor pathway. This study aimed to determine the effects of increased cognitive load on the vestibular control of standing balance. Participants stood blindfolded on a force plate with their head facing left and arms relaxed at their sides for two trials while exposed to continuous electrical vestibular stimulation (EVS). Participants either stood quietly or executed a cognitive task (double-digit arithmetic). Surface electromyography (EMG) and anterior-posterior ground-body forces (APF) were measured in order to evaluate vestibular-evoked balance responses in the frequency (coherence and gain) and time (cumulant density) domains. Total distance traveled for anterior-posterior center of pressure (COP) was assessed as a metric of balance variability. Despite similar distances traveled for COP, EVS-medial gastrocnemius (MG) EMG and EVS-APF coherence and EVS-TA EMG and EVS-MG EMG gain were elevated for multiple frequencies when standing with increased cognitive load. For the time domain, medium-latency peak amplitudes increased by 13-54% for EVS-APF and EVS-EMG relationships with the cognitive task compared to without. Peak short-latency amplitudes were unchanged. These results indicate that reliance on vestibular control of balance is enhanced when cognitive load is elevated. This augmented neural strategy may act to supplement divided cortical processing resources within the balance system and compensate for the acute neuromuscular modifications associated with increased cognitive demand.

  11. Length and GC content variability of introns among teleostean genomes in the light of the metabolic rate hypothesis.

    Directory of Open Access Journals (Sweden)

    Ankita Chaurasia

    Full Text Available A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi. An inter-genome approach using orthologous intronic sequences was carried out, analyzing independently both variables in pairwise comparisons. An average length shortening of introns was observed at increasing average GCi values. The result was not affected by masking transposable and repetitive elements harbored in the intronic sequences. The routine metabolic rate (mass specific temperature-corrected using the Boltzmann's factor was measured for each species. A significant correlation held between average differences of metabolic rate, length and GC content, while environmental temperature of fish habitat was not correlated with bpi and GCi. Analyzing the concomitant effect of both variables, i.e., bpi and GCi, at increasing genomic GC content, a decrease of bpi and an increase of GCi was observed for the significant majority of the intronic sequences (from ∼ 40% to ∼ 90%, in each pairwise comparison. The opposite event, concomitant increase of bpi and decrease of GCi, was counter selected (from <1% to ∼ 10%, in each pairwise comparison. The results further support the hypothesis that the metabolic rate plays a key role in shaping genome architecture and evolution of vertebrate genomes.

  12. Length and GC content variability of introns among teleostean genomes in the light of the metabolic rate hypothesis.

    Science.gov (United States)

    Chaurasia, Ankita; Tarallo, Andrea; Bernà, Luisa; Yagi, Mitsuharu; Agnisola, Claudio; D'Onofrio, Giuseppe

    2014-01-01

    A comparative analysis of five teleostean genomes, namely zebrafish, medaka, three-spine stickleback, fugu and pufferfish was performed with the aim to highlight the nature of the forces driving both length and base composition of introns (i.e., bpi and GCi). An inter-genome approach using orthologous intronic sequences was carried out, analyzing independently both variables in pairwise comparisons. An average length shortening of introns was observed at increasing average GCi values. The result was not affected by masking transposable and repetitive elements harbored in the intronic sequences. The routine metabolic rate (mass specific temperature-corrected using the Boltzmann's factor) was measured for each species. A significant correlation held between average differences of metabolic rate, length and GC content, while environmental temperature of fish habitat was not correlated with bpi and GCi. Analyzing the concomitant effect of both variables, i.e., bpi and GCi, at increasing genomic GC content, a decrease of bpi and an increase of GCi was observed for the significant majority of the intronic sequences (from ∼ 40% to ∼ 90%, in each pairwise comparison). The opposite event, concomitant increase of bpi and decrease of GCi, was counter selected (from hypothesis that the metabolic rate plays a key role in shaping genome architecture and evolution of vertebrate genomes.

  13. Regulation of mRNA Levels by Decay-Promoting Introns that Recruit the Exosome Specificity Factor Mmi1

    Directory of Open Access Journals (Sweden)

    Cornelia Kilchert

    2015-12-01

    Full Text Available In eukaryotic cells, inefficient splicing is surprisingly common and leads to the degradation of transcripts with retained introns. How pre-mRNAs are committed to nuclear decay is unknown. Here, we uncover a mechanism by which specific intron-containing transcripts are targeted for nuclear degradation in fission yeast. Sequence elements within these “decay-promoting” introns co-transcriptionally recruit the exosome specificity factor Mmi1, which induces degradation of the unspliced precursor and leads to a reduction in the levels of the spliced mRNA. This mechanism negatively regulates levels of the RNA helicase DDX5/Dbp2 to promote cell survival in response to stress. In contrast, fast removal of decay-promoting introns by co-transcriptional splicing precludes Mmi1 recruitment and relieves negative expression regulation. We propose that decay-promoting introns facilitate the regulation of gene expression. Based on the identification of multiple additional Mmi1 targets, including mRNAs, long non-coding RNAs, and sn/snoRNAs, we suggest a general role in RNA regulation for Mmi1 through transcript degradation.

  14. Multi-scale Control and Enhancement of Reactor Boiling Heat Flux by Reagents and Nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Manglik, R M; Athavale, A; Kalaikadal, D S; Deodhar, A; Verma, U

    2011-09-02

    The phenomenological characterization of the use of non-invasive and passive techniques to enhance the boiling heat transfer in water has been carried out in this extended study. It provides fundamental enhanced heat transfer data for nucleate boiling and discusses the associated physics with the aim of addressing future and next-generation reactor thermal-hydraulic management. It essentially addresses the hypothesis that in phase-change processes during boiling, the primary mechanisms can be related to the liquid-vapor interfacial tension and surface wetting at the solidliquid interface. These interfacial characteristics can be significantly altered and decoupled by introducing small quantities of additives in water, such as surface-active polymers, surfactants, and nanoparticles. The changes are fundamentally caused at a molecular-scale by the relative bulk molecular dynamics and adsorption-desorption of the additive at the liquid-vapor interface, and its physisorption and electrokinetics at the liquid-solid interface. At the micro-scale, the transient transport mechanisms at the solid-liquid-vapor interface during nucleation and bubblegrowth can be attributed to thin-film spreading, surface-micro-cavity activation, and micro-layer evaporation. Furthermore at the macro-scale, the heat transport is in turn governed by the bubble growth and distribution, macro-layer heat transfer, bubble dynamics (bubble coalescence, collapse, break-up, and translation), and liquid rheology. Some of these behaviors and processes are measured and characterized in this study, the outcomes of which advance the concomitant fundamental physics, as well as provide insights for developing control strategies for the molecular-scale manipulation of interfacial tension and surface wetting in boiling by means of polymeric reagents, surfactants, and other soluble surface-active additives.

  15. Enhanced control and sensing for the REMOTEC ANDROS Mk VI robot. CRADA final report

    International Nuclear Information System (INIS)

    Spelt, P.F.; Harvey, H.W.

    1998-01-01

    This Cooperative Research and Development Agreement (CRADA) between Lockheed Martin Energy Systems, Inc., and REMOTEC, Inc., explored methods of providing operator feedback for various work actions of the ANDROS Mk VI teleoperated robot. In a hazardous environment, an extremely heavy workload seriously degrades the productivity of teleoperated robot operators. This CRADA involved the addition of computer power to the robot along with a variety of sensors and encoders to provide information about the robot's performance in and relationship to its environment. Software was developed to integrate the sensor and encoder information and provide control input to the robot. ANDROS Mk VI robots are presently used by numerous electric utilities to perform tasks in reactors where substantial exposure to radiation exists, as well as in a variety of other hazardous environments. Further, this platform has potential for use in a number of environmental restoration tasks, such as site survey and detection of hazardous waste materials. The addition of sensors and encoders serves to make the robot easier to manage and permits tasks to be done more safely and inexpensively (due to time saved in the completion of complex remote tasks). Prior research on the automation of mobile platforms with manipulators at Oak Ridge National Laboratory's Center for Engineering Systems Advanced Research (CESAR, B ampersand R code KC0401030) Laboratory, a BES-supported facility, indicated that this type of enhancement is effective. This CRADA provided such enhancements to a successful working teleoperated robot for the first time. Performance of this CRADA used the CESAR laboratory facilities and expertise developed under BES funding

  16. Enhancing the Frequency Adaptability of Periodic Current Controllers with a Fixed Sampling Rate for Grid-Connected Power Converters

    DEFF Research Database (Denmark)

    Yang, Yongheng; Zhou, Keliang; Blaabjerg, Frede

    2016-01-01

    for the periodic signal controllers (e.g., PR and RC) with a fixed sampling rate. In this paper, the impacts of frequency deviations induced by the PLL and/or the grid disturbances on the selected current controllers are investigated by analyzing the frequency adaptability of these current controllers....... Subsequently, strategies to enhance the frequency adaptability of the current controllers are proposed for the power converters to produce high quality feed-in currents even in the presence of grid frequency deviations. Specifically, by feeding back the PLL estimated frequency to update the center frequencies......, which have verified the discussions and the effectiveness of the frequency adaptive current controllers....

  17. Applying Space Technology to Enhance Control of an Artificial Arm for Children and Adults With Amputations

    Science.gov (United States)

    Atkins, Diane J.

    1998-01-01

    The first single function myoelectric prosthetic hand was introduced in the 1960's. This hand was controlled by the electric fields generated by muscle contractions in the residual limb of the amputee user. Electrodes and amplifiers, embedded in the prosthetic socket, measured these electric fields across the skin, which increase in amplitude as the individual contracts their muscle. When the myoelectric signal reached a certain threshold amplitude, the control unit activated a motor which opened or closed a hand-like prosthetic terminal device with a pincher grip. Late in the 1990's, little has changed. Most current myoelectric prostheses still operate in this same, single-function way. To better understand the limitations of the current single-function myoelectric hand and the needs of those who use them, The Institute for Rehabilitation and Research (TIRR), sponsored by the National Institutes of Health (NUH), surveyed approximately 2,500 individuals with upper limb loss [1]. When asked to identify specific features of their current myoelectric prostheses that needed improvement, the survey respondents overwhelmingly identified the lack of wrist and finger movement, as well as poor control capability. However, simply building a mechanism with individual finger and wrist motion is not enough. In the 1960's and 1970's, engineers built a number of more dexterous prosthetic hands. Unfortunately, these were rejected during clinical trials due to a difficult and distracting control interface. The goal of this project, "Applying Space Technology to Enhance Control of an Artificial Arm for Children and Adults with Amputations," was to lay the foundation for a multi-function, intuitive myoelectric control system which requires no conscious thought to move the hand. We built an extensive myoelectric signal database for six motions from ten amputee volunteers, We also tested a control system based on new artificial intelligence techniques on the data from two of these

  18. High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases.

    Science.gov (United States)

    Qin, Yidan; Yao, Jun; Wu, Douglas C; Nottingham, Ryan M; Mohr, Sabine; Hunicke-Smith, Scott; Lambowitz, Alan M

    2016-01-01

    Next-generation RNA-sequencing (RNA-seq) has revolutionized transcriptome profiling, gene expression analysis, and RNA-based diagnostics. Here, we developed a new RNA-seq method that exploits thermostable group II intron reverse transcriptases (TGIRTs) and used it to profile human plasma RNAs. TGIRTs have higher thermostability, processivity, and fidelity than conventional reverse transcriptases, plus a novel template-switching activity that can efficiently attach RNA-seq adapters to target RNA sequences without RNA ligation. The new TGIRT-seq method enabled construction of RNA-seq libraries from RNA in RNA in 1-mL plasma samples from a healthy individual revealed RNA fragments mapping to a diverse population of protein-coding gene and long ncRNAs, which are enriched in intron and antisense sequences, as well as nearly all known classes of small ncRNAs, some of which have never before been seen in plasma. Surprisingly, many of the small ncRNA species were present as full-length transcripts, suggesting that they are protected from plasma RNases in ribonucleoprotein (RNP) complexes and/or exosomes. This TGIRT-seq method is readily adaptable for profiling of whole-cell, exosomal, and miRNAs, and for related procedures, such as HITS-CLIP and ribosome profiling. © 2015 Qin et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  19. Ultra-high enhancement of light focusing through disordered media controlled by mega-pixel modes (Conference Presentation)

    Science.gov (United States)

    Yu, Hyeonseung; Lee, KyeoReh; Park, YongKeun

    2017-02-01

    Developing an efficient strategy for light focusing through scattering media is an important topic in the study of multiple light scattering. The enhancement factor of the light focusing, defined as the ratio between the optimized intensity and the background intensity is proportional to the number of controlling modes in a spatial light modulator (SLM). The demonstrated enhancement factors in previous studies are typically less than 1,000 due to several limiting factors, such as the slow refresh rate of a LCoS SLM, long optimization time, and lack of an efficient algorithm for high controlling modes. A digital micro-mirror device is an amplitude modulator, which is recently widely used for fast optimization through dynamic biological tissues. The fast frame rate of the DMD up to 16 kHz can also be exploited for increasing the number of controlling modes. However, the manipulation of large pattern data and efficient calculation of the optimized pattern remained as an issue. In this work, we demonstrate the enhancement factor more than 100,000 in focusing through scattering media by using 1 Mega controlling modes of a DMD. Through careful synchronization between a DMD, a photo-detector and an additional computer for parallel optimization, we achieved the unprecedented enhancement factor with 75 mins of the optimization time. We discuss the design principles of the system and the possible applications of the enhanced light focusing.

  20. "Killing Two Birds with One Stone": Alcohol Use Reduction Interventions with Potential Efficacy in Enhancing Self-Control.

    Science.gov (United States)

    Leeman, Robert F; Bogart, Devorah; Fucito, Lisa M; Boettiger, Charlotte A

    2014-03-01

    We review interventions with empirical support for reducing alcohol use and enhancing self-control. While any intervention that decreases drinking could improve self-control, we focus here on interventions with evidence of direct benefit for both indications. Although no intervention yet shows strong evidence for dual efficacy, multiple interventions have strong evidence for one indication and solid or suggestive evidence for the other. Among pharmacotherapies, opioid antagonists currently have the best evidence for reducing alcohol use and enhancing self-control. Nicotinic partial agonist varenicline also appears to be efficacious for alcohol use and self-control. Many psychosocial and behavioral interventions (e.g., cognitive behavioral therapy, contingency management, mindfulness training) may have efficacy for both indications based on purported mechanisms of action and empirical evidence. Cognitive bias modification and neurophysiological interventions have promise for alcohol use and self-control as well and warrant further research. We offer several other suggestions for future research directions.

  1. Influence of control rod enhanced expansion devices on the course of unprotected transients in the EFR

    International Nuclear Information System (INIS)

    Kussmaul, G.

    1994-10-01

    In the safety analysis of fast reactors, unprotected accidents, such as ULOF and UTOP have to be considered, even when their frequency of occurrence lies far beyond the design basis accident. In the European Fast Reactor (EFR), the safety approach foresees further measures of risk minimization in the frame of the so-called Third Shutdown Level. One of the measures is a control rod enhanced expansion device, called ATHENa, which has been developed by KfK in collaboration with SIEMENS as a passive device to separate the absorbers from the drive lines in cases of accidental coolant temperature rises and to force the absorbers further into the core in case of failure to drop. The efficiency of the ATHENa devices to prevent soduim boiling and fuel melting in unprotected accidents in EFR has been investigated by calculations with the dynamics code DYANA2. In the case of ULOF accidents, sodium boiling can be prevented, if at least one out of 24 absorber rods equipped with ATHENa devices drops into the core after delatching from the drive lines. In the extremely remote case that all rods remain jammed after delatching, they are pushed by the ATHENa decices into the core with an enhanced expansion coefficient (∼ 10 times). Even then, sodium boiling could be prevented by extending of the pump coast down halving time from 10 to 12 s or by adjusting the delatching temperature to a value not higher than about 40 C above nominal coolant outlet. In UTOP accidents caused by the uncontrolled withdrawal of a control rod, the main concern is incipient fuel melting. The results of the calculations have shown that the power rise can be terminated by delatching the absorbers, before fuel melting occurs, if the ramp rate is mechanically limited to values of 1 /s or less. Again, even in the worst case that all rods remain jammed, fuel melting could be prevented by adjusting the delatching temperature to a similar value as in the ULOF case. (orig.) [de

  2. Comprehensive simulation-enhanced training curriculum for an advanced minimally invasive procedure: a randomized controlled trial.

    Science.gov (United States)

    Zevin, Boris; Dedy, Nicolas J; Bonrath, Esther M; Grantcharov, Teodor P

    2017-05-01

    There is no comprehensive simulation-enhanced training curriculum to address cognitive, psychomotor, and nontechnical skills for an advanced minimally invasive procedure. 1) To develop and provide evidence of validity for a comprehensive simulation-enhanced training (SET) curriculum for an advanced minimally invasive procedure; (2) to demonstrate transfer of acquired psychomotor skills from a simulation laboratory to live porcine model; and (3) to compare training outcomes of SET curriculum group and chief resident group. University. This prospective single-blinded, randomized, controlled trial allocated 20 intermediate-level surgery residents to receive either conventional training (control) or SET curriculum training (intervention). The SET curriculum consisted of cognitive, psychomotor, and nontechnical training modules. Psychomotor skills in a live anesthetized porcine model in the OR was the primary outcome. Knowledge of advanced minimally invasive and bariatric surgery and nontechnical skills in a simulated OR crisis scenario were the secondary outcomes. Residents in the SET curriculum group went on to perform a laparoscopic jejunojejunostomy in the OR. Cognitive, psychomotor, and nontechnical skills of SET curriculum group were also compared to a group of 12 chief surgery residents. SET curriculum group demonstrated superior psychomotor skills in a live porcine model (56 [47-62] versus 44 [38-53], Ppsychomotor skills in the live porcine model and in the OR in a human patient (56 [47-62] versus 63 [61-68]; P = .21). SET curriculum group demonstrated inferior knowledge (13 [11-15] versus 16 [14-16]; P<.05), equivalent psychomotor skill (63 [61-68] versus 68 [62-74]; P = .50), and superior nontechnical skills (41 [38-45] versus 34 [27-35], P<.01) compared with chief resident group. Completion of the SET curriculum resulted in superior training outcomes, compared with conventional surgery training. Implementation of the SET curriculum can standardize training

  3. Chelant-enhanced heavy metals uptake by Eucalyptus trees under controlled deficit irrigation

    Science.gov (United States)

    Fine, Pinchas; Rathod, Paresh; Beriozkin, Anna; Ein-Gal, Oz; Hass, Amir

    2014-05-01

    Enhancement of phytoremediation of heavy metal polluted soils employs organic ligands, aimed to solubilize, phytoextract and translocate metals into the canopy. The use of more persistent chelants (e.g. EDTA) is phasing out due to concerns over their role in the environment. We tested the hypothesis that controlled deficit irrigation (CDI) of the fast growing, salinity resistant Eucalyptus camaldulensis coupled with timely EDTA application enhances sediment phytoremediation while minimizing leaching of metal complexes below the root-zone. This was tested in 220-L lysimeters packed with sand mixed with metals polluted biosolids. One year old trees were brought under CDI with tap or RO water for two growing seasons. EDTA, EDDS and citric acid fertigation at 2 mM started in each May for 2.5-3.5 months, and prescribed soil leaching and sampling of tree leaves started thereafter. While all 3 chelants solubilized biosolids metal in batch extraction (EDDS often being the more efficient), EDTA was the only to increased metal concentrations both in the soil solution and in the Eucalyptus leaves. The average concentrations in the soil solution and in the leaves, in the EDTA vs. control (chelant-free) treatments, all respectively, were: Cd - 200 mg L-1 vs. 1.0, and 67 vs. 21 mg kg-1; Cu: 90 vs. 1.5 mg L-1, and 17 vs. 3.0 mg kg-1; Cr: 4.0 vs. 1.4 mg L-1, and 3.0 vs. 1.0 mg kg-1; Ni: 60 mg L-1 vs. 14, and 20 vs. 6.0 mg kg-1; Pb: >44 vs. 0.1 mg L-1, and 9.0 vs. 1.0 mg kg-1; and Zn: 650 vs. 4.0 mg L-1 and 200 vs. 70 mg kg-1. While EDDS was undetectable in all the leachates, EDTA concentrated to up to 100 mM. At 10 mM soil solution concentration, EDDS half-life in acclimated lysimeter media was 5-11 days and that of EDTA was ≥27-d. The study suggests that sustainable phytostabilization and phytoextraction of heavy metals are achievable under CDI with EDTA augmentation at low dose. This was yet futile with the biodegradable EDDS and citric acid. CDI with RO water further widened

  4. Influence of IL-1RN intron 2 variable number of tandem repeats (VNTR) polymorphism on bipolar disorder.

    Science.gov (United States)

    Rafiei, A; Hosseini, S H; Taheri, M; Hosseni-khah, Z; Hajilooi, M; Mazaheri, Z

    2013-01-01

    Several lines of evidence point to the role of neurobiological mechanisms and genetic background in bipolar disorder (BD). The interleukin-1 receptor antagonist (IL-1Ra) is the principal regulator of IL-1α and IL-1β bioactivities. This study aimed to investigate the potential role of the variable number of tandem repeats (VNTR) polymorphisms of the IL-1Ra gene (IL1RN) in conferring susceptibility to BD. In total, 217 patients meeting DSM-IV-TR criteria for BD and 212 controls were recruited for the study. Genotyping of IL1RN was determined by polymerase chain reaction amplification of VNTR of 86 base pairs in intron 2 of IL1RN. The genotype distribution of IL1RN polymorphism was significantly different between BD patients and controls. The IL1RN*1/2 genotype was more prevalent in BD patients than in controls (44.2 vs. 30.2%, p = 0.003). Multiple logistic regression analysis demonstrated that IL1RN*1/2 heterozygotes had a significantly higher risk for BD (OR 1.83 and 95% CI 1.22-2.74, p = 0.003). Further stratification of the BD patients into IL1RN*2 allele carrier and noncarrier subgroups revealed a strong association between IL1RN*2 carriage and prolongation of the disease (p = 0.02). These findings suggest a positive association between VNTR polymorphism in IL1RN and BD. Additional studies, particularly with a prospective approach, are necessary to clarify the precise role of the VNTR polymorphism on the disease in different ethnic populations. Copyright © 2013 S. Karger AG, Basel.

  5. Phylogenetic evidence for the acquisition of ribosomal RNA introns subsequent to the divergence of some of the major Tetrahymena groups

    DEFF Research Database (Denmark)

    Sogin, M L; Ingold, A; Karlok, M

    1986-01-01

    Previous work has demonstrated the presence of a self-splicing intron in the large subunit ribosomal RNA coding region in some strains of the ciliate protozoan Tetrahymena. Sequence comparisons of the intron regions from six Tetrahymena species showed these to fall into three homology groups....... This phylogeny was consistent with the groupings suggested by comparisons of other biochemical characters including cytoskeletal proteins, isozyme analyses, and restriction maps of complete rRNA transcription units. The homology groupings that were based upon the intron sequence data do not agree....... In an attempt to evaluate the evolutionary origins of the intervening sequences, we have now determined complete small subunit ribosomal RNA gene sequences from 13 species of Tetrahymena and the absolute number of nucleotide differences between the sequences was used to construct a phylogenetic tree...

  6. Phylogenetic inferences of Nepenthes species in Peninsular Malaysia revealed by chloroplast (trnL intron) and nuclear (ITS) DNA sequences.

    Science.gov (United States)

    Bunawan, Hamidun; Yen, Choong Chee; Yaakop, Salmah; Noor, Normah Mohd

    2017-01-26

    The chloroplastic trnL intron and the nuclear internal transcribed spacer (ITS) region were sequenced for 11 Nepenthes species recorded in Peninsular Malaysia to examine their phylogenetic relationship and to evaluate the usage of trnL intron and ITS sequences for phylogenetic reconstruction of this genus. Phylogeny reconstruction was carried out using neighbor-joining, maximum parsimony and Bayesian analyses. All the trees revealed two major clusters, a lowland group consisting of N. ampullaria, N. mirabilis, N. gracilis and N. rafflesiana, and another containing both intermediately distributed species (N. albomarginata and N. benstonei) and four highland species (N. sanguinea, N. macfarlanei, N. ramispina and N. alba). The trnL intron and ITS sequences proved to provide phylogenetic informative characters for deriving a phylogeny of Nepenthes species in Peninsular Malaysia. To our knowledge, this is the first molecular phylogenetic study of Nepenthes species occurring along an altitudinal gradient in Peninsular Malaysia.

  7. A Placebo-Controlled Trial of Riboflavin for Enhancement of Ultramarathon Recovery.

    Science.gov (United States)

    Hoffman, Martin D; Valentino, Taylor R; Stuempfle, Kristin J; Hassid, Brandon V

    2017-12-01

    Riboflavin is known to protect tissue from oxidative damage but, to our knowledge, has not been explored as a means to control exercise-related muscle soreness. This study investigated whether acute ingestion of riboflavin reduces muscle pain and soreness during and after completion of a 161-km ultramarathon and improves functional recovery after the event. In this double-blind, placebo-controlled trial, participants of the 2016 161-km Western States Endurance Run were assigned to receive a riboflavin or placebo capsule shortly before the race start and when reaching 90 km. Capsules contained either 100 mg of riboflavin or 95 mg of maltodextrin and 5 mg of 10% ß-carotene. Subjects provided muscle pain and soreness ratings before, during, and immediately after the race and for the 10 subsequent days. Subjects also completed 400-m runs at maximum speed on days 3, 5, and 10 after the race. For the 32 (18 in the riboflavin group, 14 in the placebo group) race finishers completing the study, muscle pain and soreness ratings during and immediately after the race were found to be significantly lower (p = .043) for the riboflavin group. Analysis of the 400-m run times also showed significantly faster (p soreness had returned to pre-race levels by 5 days after the race and that 400-m run times had returned to pre-race performance levels by 10 days after the race. This preliminary work suggests that riboflavin supplementation before and during prolonged running might reduce muscle pain and soreness during and at the completion of the exercise and may enhance early functional recovery after the exercise.

  8. Controlled Growth of Gold Nanostars: Effect of Spike Length on SERS Signal Enhancement.

    Science.gov (United States)

    Sheen Mers, S V; Umadevi, S; Ganesh, V

    2017-05-19

    Two different types of gold nanostars (Au NS), namely, short-spiked nanostars (SSNS) and long-spiked nanostars (LSNS), are prepared by using a hexagonal lyotropic liquid-crystalline (LLC) phase as a template. The formation, size and length of spikes or arms of the resultant Au NS are controlled by preparation in either a hexagonal LLC phase or an isotropic phase. These NS are anchored onto indium tin oxide (ITO) electrodes through a self-assembled monolayer of 3-mercaptopropyltrimethoxysilane, which acts as a linker molecule. Structural and morphological characterisations of SSNS- and LSNS-anchored ITO electrodes are performed by means of microscopic and spectroscopic analyses. Further electrochemical techniques, namely, cyclic voltammetry and electrochemical impedance spectroscopy, are also used to confirm the immobilisation of these Au NS on ITO electrodes and to study the electrochemical characteristics. These studies clearly reveal the formation of star-shaped, branched, anisotropic nanostructures of gold during the template preparation method and these Au NS are successfully anchored onto ITO electrodes through a covalent immobilisation strategy. Furthermore, the SERS activity of these Au NS is analysed by using glutathione and crystal violet as analytes and by employing glass and ITO as substrates. It is interesting to note that SSNS show a significant enhancement in SERS signals relative to those of LSNS. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Enhancing the control of force in putting by video game training.

    Science.gov (United States)

    Fery, Y A; Ponserre, S

    2001-10-10

    Even if golf video games provide no proprioceptive afferences on actual putting movement, they may give sufficient substitutive visual cues to enhance force control in this skill. It was hypothesized that this usefulness requires, however, two conditions: the video game must provide reliable demonstrations of actual putts, and the user must want to use the game to make progress in actual putting. Accordingly, a video game was selected on the basis of its fidelity to the real-world game. It allowed two different methods of adjusting the virtual player's putting force in order to hole a putt: an analogue method that consisted of focusing on the virtual player's movement and a symbolic method that consisted of focusing on the movement of a gauge on a scale representing the virtual player's putting force. The participants had to use one of these methods with either the intention of making progress in actual putting or in a second condition to simply enjoy the game. Results showed a positive transfer of video playing to actual putting skill for the learning group and also, to a lesser degree, for the enjoyment group; but only when they used the symbolic method. Results are discussed in the context of how vision may convey force cues in sports video games.

  10. Enhanced Control of Transient Raman Scattering Using Buffered Hydrogen in Hollow-Core Photonic Crystal Fibers

    Science.gov (United States)

    Hosseini, P.; Novoa, D.; Abdolvand, A.; Russell, P. St. J.

    2017-12-01

    Many reports on stimulated Raman scattering in mixtures of Raman-active and noble gases indicate that the addition of a dispersive buffer gas increases the phase mismatch to higher-order Stokes and anti-Stokes sidebands, resulting in a preferential conversion to the first few Stokes lines, accompanied by a significant reduction in the Raman gain due to collisions with gas molecules. Here we report that, provided the dispersion can be precisely controlled, the effective Raman gain in a gas-filled hollow-core photonic crystal fiber can actually be significantly enhanced when a buffer gas is added. This counterintuitive behavior occurs when the nonlinear coupling between the interacting fields is strong and can result in a performance similar to that of a pure Raman-active gas, but at a much lower total gas pressure, allowing competing effects such as Raman backscattering to be suppressed. We report high modal purity in all the emitted sidebands, along with anti-Stokes conversion efficiencies as high as 5% in the visible and 2% in the ultraviolet. This new class of gas-based waveguide device, which allows the nonlinear optical response to be beneficially pressure-tuned by the addition of buffer gases, may find important applications in laser science and spectroscopy.

  11. FY98 Final Report Initial Interfacial Chemical Control for Enhancement of Composite Material Strength; TOPICAL

    International Nuclear Information System (INIS)

    GE Fryxell; KL Alford; KL Simmons; RD Voise; WD Samuels

    1999-01-01

    The U.S. Army Armament Research Development and Engineering Center (ARDEC) sponsored this research project to support the development of new self-assembled monolayer fiber coatings. These coatings can greatly increase the bond strength between the fiber and the resin matrix of a composite material. Composite ammunition components molded from such materials will exhibit higher strength than current materials, and will provide a major improvement in the performance of composites in military applications. Use of composite materials in military applications is desirable because of the lighter weight of the materials and their high strengths. The FY97 project investigated initial interfacial chemical control for enhancement of composite material strength. The core of the project was to modify the covalent interface of glass fibers (or other reinforcing fibers) to induce strong, uniform, defect-free adhesion between the fibers' surfaces and the polymer matrix. Installing a self-assembled monolayer tailored to the specific matrix resin accomplished this. Simply, the self-assembled monolayer modifies the fiber to make it appear to have the same chemical composition as the resin matrix. The self-assembled monolayer creates a receptive, hydrophobic interface that the thermoset resin (or polymer precursors) would wet more effectively, leading to a higher contact surface area and more efficient adhesion. The FY97 work phase demonstrated that it is possible to increase the adhesive strength, as well as increase the heat deflection temperature through the use of self-assembled monolayer

  12. Enhanced control of Mycobacterium tuberculosis extrapulmonary dissemination in mice by an arabinomannan-protein conjugate vaccine.

    Directory of Open Access Journals (Sweden)

    Rafael Prados-Rosales

    2017-03-01

    Full Text Available Currently there are a dozen or so of new vaccine candidates in clinical trials for prevention of tuberculosis (TB and each formulation attempts to elicit protection by enhancement of cell-mediated immunity (CMI. In contrast, most approved vaccines against other bacterial pathogens are believed to mediate protection by eliciting antibody responses. However, it has been difficult to apply this formula to TB because of the difficulty in reliably eliciting protective antibodies. Here, we developed capsular polysaccharide conjugates by linking mycobacterial capsular arabinomannan (AM to either Mtb Ag85b or B. anthracis protective antigen (PA. Further, we studied their immunogenicity by ELISA and AM glycan microarrays and protection efficacy in mice. Immunization with either Abg85b-AM or PA-AM conjugates elicited an AM-specific antibody response in mice. AM binding antibodies stimulated transcriptional changes in Mtb. Sera from AM conjugate immunized mice reacted against a broad spectrum of AM structural variants and specifically recognized arabinan fragments. Conjugate vaccine immunized mice infected with Mtb had lower bacterial numbers in lungs and spleen, and lived longer than control mice. These findings provide additional evidence that humoral immunity can contribute to protection against Mtb.

  13. Electro—magnetic control of shear flow over a cylinder for drag reduction and lift enhancement

    International Nuclear Information System (INIS)

    Zhang Hui; Fan Bao-Chun; Chen Zhi-Hua; Chen Shuai; Li Hong-Zhi

    2013-01-01

    In this paper, the electro—magnetic control of a cylinder wake in shear flow is investigated numerically. The effects of the shear rate and Lorentz force on the cylinder wake, the distribution of hydrodynamic force, and the drag/lift phase diagram are discussed in detail. It is revealed that Lorentz force can be classified into the field Lorentz force and the wall Lorentz force and they affect the drag and lift forces independently. The drag/lift phase diagram with a shape of ''8'' consists of two closed curves, which correspond to the halves of the shedding cycle dominated by the upper and lower vortices respectively. The free stream shear (K > 0) induces the diagram to move downward and leftward, so that the average lift force directs toward the downside. With the upper Lorentz force, the diagram moves downwards and to the right by the field Lorentz force, thus resulting in the drag increase and the lift reduction, whereas it moves upward and to the left by the wall Lorentz force, leading to the drag reduction and the lift increase. Finally the diagram is dominated by the wall Lorentz force, thus moving upward and leftward. Therefore the upper Lorentz force, which enhances the lift force, can be used to overcome the lift loss due to the free stream shear, which is also obtained in the experiment. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  14. Haptic feedback enhances rhythmic motor control by reducing variability, not improving convergence rate.

    Science.gov (United States)

    Ankarali, M Mert; Tutkun Sen, H; De, Avik; Okamura, Allison M; Cowan, Noah J

    2014-03-01

    Stability and performance during rhythmic motor behaviors such as locomotion are critical for survival across taxa: falling down would bode well for neither cheetah nor gazelle. Little is known about how haptic feedback, particularly during discrete events such as the heel-strike event during walking, enhances rhythmic behavior. To determine the effect of haptic cues on rhythmic motor performance, we investigated a virtual paddle juggling behavior, analogous to bouncing a table tennis ball on a paddle. Here, we show that a force impulse to the hand at the moment of ball-paddle collision categorically improves performance over visual feedback alone, not by regulating the rate of convergence to steady state (e.g., via higher gain feedback or modifying the steady-state hand motion), but rather by reducing cycle-to-cycle variability. This suggests that the timing and state cues afforded by haptic feedback decrease the nervous system's uncertainty of the state of the ball to enable more accurate control but that the feedback gain itself is unaltered. This decrease in variability leads to a substantial increase in the mean first passage time, a measure of the long-term metastability of a stochastic dynamical system. Rhythmic tasks such as locomotion and juggling involve intermittent contact with the environment (i.e., hybrid transitions), and the timing of such transitions is generally easy to sense via haptic feedback. This timing information may improve metastability, equating to less frequent falls or other failures depending on the task.

  15. The use of interactive computer vision and robot hand controllers for enhancing manufacturing safety

    Science.gov (United States)

    Marzwell, Neville I.; Jacobus, Charles J.; Peurach, Thomas M.; Mitchell, Brian T.

    1994-01-01

    Current available robotic systems provide limited support for CAD-based model-driven visualization, sensing algorithm development and integration, and automated graphical planning systems. This paper describes ongoing work which provides the functionality necessary to apply advanced robotics to automated manufacturing and assembly operations. An interface has been built which incorporates 6-DOF tactile manipulation, displays for three dimensional graphical models, and automated tracking functions which depend on automated machine vision. A set of tools for single and multiple focal plane sensor image processing and understanding has been demonstrated which utilizes object recognition models. The resulting tool will enable sensing and planning from computationally simple graphical objects. A synergistic interplay between human and operator vision is created from programmable feedback received from the controller. This approach can be used as the basis for implementing enhanced safety in automated robotics manufacturing, assembly, repair and inspection tasks in both ground and space applications. Thus, an interactive capability has been developed to match the modeled environment to the real task environment for safe and predictable task execution.

  16. Application of pentacene thin-film transistors with controlled threshold voltages to enhancement/depletion inverters

    Science.gov (United States)

    Takahashi, Hajime; Hanafusa, Yuki; Kimura, Yoshinari; Kitamura, Masatoshi

    2018-03-01

    Oxygen plasma treatment has been carried out to control the threshold voltage in organic thin-film transistors (TFTs) having a SiO2 gate dielectric prepared by rf sputtering. The threshold voltage linearly changed in the range of ‑3.7 to 3.1 V with the increase in plasma treatment time. Although the amount of change is smaller than that for organic TFTs having thermally grown SiO2, the tendency of the change was similar to that for thermally grown SiO2. To realize different plasma treatment times on the same substrate, a certain region on the SiO2 surface was selected using a shadow mask, and was treated with oxygen plasma. Using the process, organic TFTs with negative threshold voltages and those with positive threshold voltages were fabricated on the same substrate. As a result, enhancement/depletion inverters consisting of the organic TFTs operated at supply voltages of 5 to 15 V.

  17. Modulation of splicing of the preceding intron by antisense oligonucleotide complementary to intra-exon sequence deleted in dystrophin Kobe

    Energy Technology Data Exchange (ETDEWEB)

    Takeshima, Y.; Matuso, M.; Sakamoto, H.; Nishio, H. [Kobe Univ. School of Medicine and Science (Japan)

    1994-09-01

    Molecular analysis of dystrophin Kobe showed that exon 19 of the dystrophin gene bearing a 52 bp deletion was skipped during splicing, although the known consensus sequences at the 5{prime} and 3{prime} splice site of exon 19 were maintained. These data suggest that the deleted sequence of exon 19 may function as a cis-acting factor for exact splicing for the upstream intron. To investigate this potential role, an in vitro splicing system using dystrophin precursors was established. A two-exon precursor containing exon 18, truncated intron 18, and exon 19 was accurately spliced. However, splicing of intron 18 was dramatically inhibited when wild exon 19 was replaced with mutated exon 19. Even though the length of exon 19 was restored to normal by replacing the deleted sequence with other sequence, splicing of intron 18 was not fully reactivated. Characteristically, splicing of intron 18 was inactivated more markedly when the replaced sequence contained less polypurine stretches. These data suggested that modification of the exon sequence would result in a splicing abnormality. Antisense 31 mer 2`-O-methyl ribonucleotide was targeted against 5{prime} end of deleted region of exon 19 to modulate splicing of the mRNA precursor. Splicing of intron 18 was inhibited in a dose- and time-dependent manner. This is the first in vitro evidence to show splicing of dystrophin pre-mRNA can be managed by antisense oligonucleotides. These experiments represent an approach in which antisense oligonucleotides are used to restore the function of a defective dystrophin gene in Duchenne muscular dystrophy by inducing skipping of certain exons during splicing.

  18. Dynamic Stability Enhancement and Power Flow Control of a Hybrid Wind and Marine-Current Farm Using SMES

    DEFF Research Database (Denmark)

    Wang, Li; Chen, Shiang-Shong; Lee, Wei-Jen

    2009-01-01

    This paper presents a control scheme based on a superconducting magnetic energy storage (SMES) unit to achieve both power flow control and damping enhancement of a novel hybrid wind and marine-current farm (MCF) connected to a large power grid. The performance of the studied wind farm (WF......) is simulated by an equivalent 80-MW induction generator (IG) while an equivalent 60-MW IG is employed to simulate the characteristics of theMCF. A damping controller for the SMES unit is designed by using modal control theory to contribute effective damping characteristics to the studied combined WF and MCF...

  19. Fox-2 Splicing Factor Binds to a Conserved Intron Motif to PromoteInclusion of Protein 4.1R Alternative Exon 16

    Energy Technology Data Exchange (ETDEWEB)

    Ponthier, Julie L.; Schluepen, Christina; Chen, Weiguo; Lersch,Robert A.; Gee, Sherry L.; Hou, Victor C.; Lo, Annie J.; Short, Sarah A.; Chasis, Joel A.; Winkelmann, John C.; Conboy, John G.

    2006-03-01

    Activation of protein 4.1R exon 16 (E16) inclusion during erythropoiesis represents a physiologically important splicing switch that increases 4.1R affinity for spectrin and actin. Previous studies showed that negative regulation of E16 splicing is mediated by the binding of hnRNP A/B proteins to silencer elements in the exon and that downregulation of hnRNP A/B proteins in erythroblasts leads to activation of E16 inclusion. This paper demonstrates that positive regulation of E16 splicing can be mediated by Fox-2 or Fox-1, two closely related splicing factors that possess identical RNA recognition motifs. SELEX experiments with human Fox-1 revealed highly selective binding to the hexamer UGCAUG. Both Fox-1 and Fox-2 were able to bind the conserved UGCAUG elements in the proximal intron downstream of E16, and both could activate E16 splicing in HeLa cell co-transfection assays in a UGCAUG-dependent manner. Conversely, knockdown of Fox-2 expression, achieved with two different siRNA sequences resulted in decreased E16 splicing. Moreover, immunoblot experiments demonstrate mouse erythroblasts express Fox-2, but not Fox-1. These findings suggest that Fox-2 is a physiological activator of E16 splicing in differentiating erythroid cells in vivo. Recent experiments show that UGCAUG is present in the proximal intron sequence of many tissue-specific alternative exons, and we propose that the Fox family of splicing enhancers plays an important role in alternative splicing switches during differentiation in metazoan organisms.

  20. Phylogenetic evidence for the acquisition of ribosomal RNA introns subsequent to the divergence of some of the major Tetrahymena groups

    DEFF Research Database (Denmark)

    Sogin, M L; Ingold, A; Karlok, M

    1986-01-01

    Previous work has demonstrated the presence of a self-splicing intron in the large subunit ribosomal RNA coding region in some strains of the ciliate protozoan Tetrahymena. Sequence comparisons of the intron regions from six Tetrahymena species showed these to fall into three homology groups....... In an attempt to evaluate the evolutionary origins of the intervening sequences, we have now determined complete small subunit ribosomal RNA gene sequences from 13 species of Tetrahymena and the absolute number of nucleotide differences between the sequences was used to construct a phylogenetic tree...

  1. The retrohoming of linear group II intron RNAs in Drosophila melanogaster occurs by both DNA ligase 4-dependent and -independent mechanisms.

    Directory of Open Access Journals (Sweden)

    Travis B White

    Full Text Available Mobile group II introns are bacterial retrotransposons that are thought to have invaded early eukaryotes and evolved into introns and retroelements in higher organisms. In bacteria, group II introns typically retrohome via full reverse splicing of an excised intron lariat RNA into a DNA site, where it is reverse transcribed by the intron-encoded protein. Recently, we showed that linear group II intron RNAs, which can result from hydrolytic splicing or debranching of lariat RNAs, can retrohome in eukaryotes by performing only the first step of reverse splicing, ligating their 3' end to the downstream DNA exon. Reverse transcription then yields an intron cDNA, whose free end is linked to the upstream DNA exon by an error-prone process that yields junctions similar to those formed by non-homologous end joining (NHEJ. Here, by using Drosophila melanogaster NHEJ mutants, we show that linear intron RNA retrohoming occurs by major Lig4-dependent and minor Lig4-independent mechanisms, which appear to be related to classical and alternate NHEJ, respectively. The DNA repair polymerase θ plays a crucial role in both pathways. Surprisingly, however, mutations in Ku70, which functions in capping chromosome ends during NHEJ, have only moderate, possibly indirect effects, suggesting that both Lig4 and the alternate end-joining ligase act in some retrohoming events independently of Ku. Another potential Lig4-independent mechanism, reverse transcriptase template switching from the intron RNA to the upstream exon DNA, occurs in vitro, but gives junctions differing from the majority in vivo. Our results show that group II introns can utilize cellular NHEJ enzymes for retromobility in higher organisms, possibly exploiting mechanisms that contribute to retrotransposition and mitigate DNA damage by resident retrotransposons. Additionally, our results reveal novel activities of group II intron reverse transcriptases, with implications for retrohoming mechanisms and

  2. A Randomized Control Trial: Supplementing Hearing Aid Use with Listening and Communication Enhancement (LACE) Auditory Training.

    Science.gov (United States)

    Saunders, Gabrielle H; Smith, Sherri L; Chisolm, Theresa H; Frederick, Melissa T; McArdle, Rachel A; Wilson, Richard H

    2016-01-01

    To examine the effectiveness of the Listening and Communication Enhancement (LACE) program as a supplement to standard-of-care hearing aid intervention in a Veteran population. A multisite randomized controlled trial was conducted to compare outcomes following standard-of-care hearing aid intervention supplemented with (1) LACE training using the 10-session DVD format, (2) LACE training using the 20-session computer-based format, (3) placebo auditory training (AT) consisting of actively listening to 10 hr of digitized books on a computer, and (4) educational counseling-the control group. The study involved 3 VA sites and enrolled 279 veterans. Both new and experienced hearing aid users participated to determine if outcomes differed as a function of hearing aid user status. Data for five behavioral and two self-report measures were collected during three research visits: baseline, immediately following the intervention period, and at 6 months postintervention. The five behavioral measures were selected to determine whether the perceptual and cognitive skills targeted in LACE training generalized to untrained tasks that required similar underlying skills. The two self-report measures were completed to determine whether the training resulted in a lessening of activity limitations and participation restrictions. Outcomes were obtained from 263 participants immediately following the intervention period and from 243 participants 6 months postintervention. Analyses of covariance comparing performance on each outcome measure separately were conducted using intervention and hearing aid user status as between-subject factors, visit as a within-subject factor, and baseline performance as a covariate. No statistically significant main effects or interactions were found for the use of LACE on any outcome measure. Findings from this randomized controlled trial show that LACE training does not result in improved outcomes over standard-of-care hearing aid intervention alone

  3. Enhanced understanding of non-axisymmetric intrinsic and controlled field impacts in tokamaks

    Science.gov (United States)

    In, Y.; Park, J.-K.; Jeon, Y. M.; Kim, J.; Park, G. Y.; Ahn, J.-W.; Loarte, A.; Ko, W. H.; Lee, H. H.; Yoo, J. W.; Juhn, J. W.; Yoon, S. W.; Park, H.; Physics Task Force in KSTAR, 3D

    2017-11-01

    An extensive study of intrinsic and controlled non-axisymmetric field (δB) impacts in KSTAR has enhanced the understanding about non-axisymmetric field physics and its implications, in particular, on resonant magnetic perturbation (RMP) physics and power threshold (P th) for L-H transition. The n  =  1 intrinsic non-axisymmetric field in KSTAR was measured to remain as low as δB/B 0 ~ 4  ×  10-5 even at high-beta plasmas (β N ~ 2), which corresponds to approximately 20% below the targeted ITER tolerance level. As for the RMP edge-localized-modes (ELM) control, robust n  =  1 RMP ELM-crash-suppression has been not only sustained for more than ~90 τ E, but also confirmed to be compatible with rotating RMP. An optimal window of radial position of lower X-point (i.e. R x   =  1.44+/- 0.02 m) proved to be quite critical to reach full n  =  1 RMP-driven ELM-crash-suppression, while a constraint of the safety factor could be relaxed (q 95  =  5 +/- 0.25). A more encouraging finding was that even when R x cannot be positioned in the optimal window, another systematic scan in the vicinity of the previously optimal R x allows for a new optimal window with relatively small variations of plasma parameters. Also, we have addressed the importance of optimal phasing (i.e. toroidal phase difference between adjacent rows) for n  =  1 RMP-driven ELM control, consistent with an ideal plasma response modeling which could predict phasing-dependent ELM suppression windows. In support of ITER RMP study, intentionally misaligned RMPs have been found to be quite effective during ELM-mitigation stage in lowering the peaks of divertor heat flux, as well as in broadening the ‘wet’ areas. Besides, a systematic survey of P th dependence on non-axisymmetric field has revealed the potential limit of the merit of low intrinsic non-axisymmetry. Considering that the ITER RMP coils are composed of 3-rows, just like in KSTAR, further 3D

  4. Enhanced Stability and Controllability of an Ionic Diode Based on Funnel-Shaped Nanochannels with an Extended Critical Region.

    Science.gov (United States)

    Xiao, Kai; Xie, Ganhua; Zhang, Zhen; Kong, Xiang-Yu; Liu, Qian; Li, Pei; Wen, Liping; Jiang, Lei

    2016-05-01

    The enhanced stability and controllability of an ionic diode system based on funnel-shaped nanochannels with a much longer critical region is reported. The polarity of ion transport switching from anion/cation-selective to ambipolar can be controlled by tuning the length and charge of the critical region. This nanofluidic structure anticipates potential applications in single-molecule biosensing, water resource monitoring, and healthcare. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Fault ride-through enhancement using an enhanced field oriented control technique for converters of grid connected DFIG and STATCOM for different types of faults.

    Science.gov (United States)

    Ananth, D V N; Nagesh Kumar, G V

    2016-05-01

    With increase in electric power demand, transmission lines were forced to operate close to its full load and due to the drastic change in weather conditions, thermal limit is increasing and the system is operating with less security margin. To meet the increased power demand, a doubly fed induction generator (DFIG) based wind generation system is a better alternative. For improving power flow capability and increasing security STATCOM can be adopted. As per modern grid rules, DFIG needs to operate without losing synchronism called low voltage ride through (LVRT) during severe grid faults. Hence, an enhanced field oriented control technique (EFOC) was adopted in Rotor Side Converter of DFIG converter to improve power flow transfer and to improve dynamic and transient stability. A STATCOM is coordinated to the system for obtaining much better stability and enhanced operation during grid fault. For the EFOC technique, rotor flux reference changes its value from synchronous speed to zero during fault for injecting current at the rotor slip frequency. In this process DC-Offset component of flux is controlled, decomposition during symmetric and asymmetric faults. The offset decomposition of flux will be oscillatory in a conventional field oriented control, whereas in EFOC it was aimed to damp quickly. This paper mitigates voltage and limits surge currents to enhance the operation of DFIG during symmetrical and asymmetrical faults. The system performance with different types of faults like single line to ground, double line to ground and triple line to ground was applied and compared without and with a STATCOM occurring at the point of common coupling with fault resistance of a very small value at 0.001Ω. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

  6. Molecular evolution of Adh and LEAFY and the phylogenetic utility of their introns in Pyrus (Rosaceae

    Directory of Open Access Journals (Sweden)

    Cao Jiashu

    2011-09-01

    Full Text Available Abstract Background The genus Pyrus belongs to the tribe Pyreae (the former subfamily Maloideae of the family Rosaceae, and includes one of the most important commercial fruit crops, pear. The phylogeny of Pyrus has not been definitively reconstructed. In our previous efforts, the internal transcribed spacer region (ITS revealed a poorly resolved phylogeny due to non-concerted evolution of nrDNA arrays. Therefore, introns of low copy nuclear genes (LCNG are explored here for improved resolution. However, paralogs and lineage sorting are still two challenges for applying LCNGs in phylogenetic studies, and at least two independent nuclear loci should be compared. In this work the second intron of LEAFY and the alcohol dehydrogenase gene (Adh were selected to investigate their molecular evolution and phylogenetic utility. Results DNA sequence analyses revealed a complex ortholog and paralog structure of Adh genes in Pyrus and Malus, the pears and apples. Comparisons between sequences from RT-PCR and genomic PCR indicate that some Adh homologs are putatively nonfunctional. A partial region of Adh1 was sequenced for 18 Pyrus species and three subparalogs representing Adh1-1 were identified. These led to poorly resolved phylogenies due to low sequence divergence and the inclusion of putative recombinants. For the second intron of LEAFY, multiple inparalogs were discovered for both LFY1int2 and LFY2int2. LFY1int2 is inadequate for phylogenetic analysis due to lineage sorting of two inparalogs. LFY2int2-N, however, showed a relatively high sequence divergence and led to the best-resolved phylogeny. This study documents the coexistence of outparalogs and inparalogs, and lineage sorting of these paralogs and orthologous copies. It reveals putative recombinants that can lead to incorrect phylogenetic inferences, and presents an improved phylogenetic resolution of Pyrus using LFY2int2-N. Conclusions Our study represents the first phylogenetic analyses based

  7. ENHANCING THE STABILITY OF UNMANNED GROUND SPORT UTILITY VEHICLES THROUGH COORDINATED CONTROL UNDER MU-SPLIT AND GUST OF WIND

    Directory of Open Access Journals (Sweden)

    FITRI YAKUB

    2016-10-01

    Full Text Available This study describes a comparative study of steering and yaw moment control manoeuvres in model predictive control (MPC and linear quadratic control approaches for path following unmanned vehicles for different control manoeuvres: two-wheel steering, four-wheel steering, and direct yaw moment control. We then propose MPC with a proportional-integral (PI controller for the coordination of active front steering (AFS and active braking system, which particularly highlights direct yaw moment control (DYC manoeuvres. Based on the known trajectory, we tested a vehicle at middle forward speed with the disturbance consideration of the road surface adhesion and the wind for a double lane change scenario in order to follow the desired trajectory as close as possible, minimizing tracking errors, and enhancing vehicle stability and drivability. We compared two different controllers; i MPC with PI of an AFS and, ii MPC with PI for coordination of AFS and DYC. The operation of the proposed integrated control is demonstrated in a Matlab simulation environment by manoeuvring the vehicle along the desired trajectory. Simulation results showed that the proposed method had yielded better tracking performances, and were able to enhance the vehicle’s stability at a given speed even under road surface coefficient and wind.