Science.gov

Sample records for intergenic spacers repetitive

  1. Phylogeny of Porphyromonas gingivalis by Ribosomal Intergenic Spacer Region Analysis

    PubMed Central

    Rumpf, Robert W.; Griffen, Ann L.; Leys, Eugene J.

    2000-01-01

    Periodontitis has been associated with the presence of Porphyromonas gingivalis, and previous studies have shown phenotypic differences in the pathogenicities of strains of P. gingivalis. An accurate and comprehensive phylogeny of strains of P. gingivalis would be useful in determining if there is an evolutionary basis to pathogenicity in this species. Previous phylogenies of P. gingivalis strains based on random amplified polymorphic DNA (RAPD) analysis and multilocus enzyme electrophoresis (MLEE) show little agreement. While the 16S ribosomal gene is the standard for phylogenetic reconstruction among bacterial species, it is insufficiently variable for this purpose. In the present study, the phylogeny of P. gingivalis was constructed on the basis of the sequence of the most variable region of the ribosomal operon, the intergenic spacer region (ISR). Heteroduplex analysis of the ISR has been used to study the variability of P. gingivalis strains in periodontitis. In the present study, typing by heteroduplex analysis was compared to ISR sequence-based phylogeny and close agreement was observed. The two strains of P. gingivalis whose heteroduplex types are strongly associated with periodontitis were found to be closely related and were well separated from strains whose heteroduplex types are less strongly associated with disease, suggesting a relationship between pathogenicity and phylogeny. PMID:10790104

  2. Cladistic biogeography of Juglans (Juglandaceae) based on chloroplast DNA intergenic spacer sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phylogenetic utility of sequence variation from five chloroplast DNA intergenic spacer (IGS) regions: trnT-trnF, psbA-trnH, atpB-rbcL, trnV-16S rRNA, and trnS-trnfM was examined in the genus Juglans. A total of seventeen taxa representing the four sections within Juglans and an outgroup taxon, ...

  3. Extensive length variation in the ribosomal DNA intergenic spacer of yellow perch (Perca flavescens).

    PubMed

    Kakou, Bidénam; Angers, Bernard; Glémet, Hélène

    2016-03-01

    The intergenic spacer (IGS) is located between ribosomal RNA (rRNA) gene copies. Within the IGS, regulatory elements for rRNA gene transcription are found, as well as a varying number of other repetitive elements that are at the root of IGS length heterogeneity. This heterogeneity has been shown to have a functional significance through its effect on growth rate. Here, we present the structural organization of yellow perch (Perca flavescens) IGS based on its entire sequence, as well as the IGS length variation within a natural population. Yellow perch IGS structure has four discrete regions containing tandem repeat elements. For three of these regions, no specific length class was detected as allele size was seemingly normally distributed. However, for one repeat region, PCR amplification uncovered the presence of two distinctive IGS variants representing a length difference of 1116 bp. This repeat region was also devoid of any CpG sites despite a high GC content. Balanced selection may be holding the alleles in the population and would account for the high diversity of length variants observed for adjacent regions. Our study is an important precursor for further work aiming to assess the role of IGS length variation in influencing growth rate in fish. PMID:26841134

  4. Genotypic Characterization of Bradyrhizobium Strains Nodulating Endemic Woody Legumes of the Canary Islands by PCR-Restriction Fragment Length Polymorphism Analysis of Genes Encoding 16S rRNA (16S rDNA) and 16S-23S rDNA Intergenic Spacers, Repetitive Extragenic Palindromic PCR Genomic Fingerprinting, and Partial 16S rDNA Sequencing

    PubMed Central

    Vinuesa, Pablo; Rademaker, Jan L. W.; de Bruijn, Frans J.; Werner, Dietrich

    1998-01-01

    We present a phylogenetic analysis of nine strains of symbiotic nitrogen-fixing bacteria isolated from nodules of tagasaste (Chamaecytisus proliferus) and other endemic woody legumes of the Canary Islands, Spain. These and several reference strains were characterized genotypically at different levels of taxonomic resolution by computer-assisted analysis of 16S ribosomal DNA (rDNA) PCR-restriction fragment length polymorphisms (PCR-RFLPs), 16S-23S rDNA intergenic spacer (IGS) RFLPs, and repetitive extragenic palindromic PCR (rep-PCR) genomic fingerprints with BOX, ERIC, and REP primers. Cluster analysis of 16S rDNA restriction patterns with four tetrameric endonucleases grouped the Canarian isolates with the two reference strains, Bradyrhizobium japonicum USDA 110spc4 and Bradyrhizobium sp. strain (Centrosema) CIAT 3101, resolving three genotypes within these bradyrhizobia. In the analysis of IGS RFLPs with three enzymes, six groups were found, whereas rep-PCR fingerprinting revealed an even greater genotypic diversity, with only two of the Canarian strains having similar fingerprints. Furthermore, we show that IGS RFLPs and even very dissimilar rep-PCR fingerprints can be clustered into phylogenetically sound groupings by combining them with 16S rDNA RFLPs in computer-assisted cluster analysis of electrophoretic patterns. The DNA sequence analysis of a highly variable 264-bp segment of the 16S rRNA genes of these strains was found to be consistent with the fingerprint-based classification. Three different DNA sequences were obtained, one of which was not previously described, and all belonged to the B. japonicum/Rhodopseudomonas rDNA cluster. Nodulation assays revealed that none of the Canarian isolates nodulated Glycine max or Leucaena leucocephala, but all nodulated Acacia pendula, C. proliferus, Macroptilium atropurpureum, and Vigna unguiculata. PMID:9603820

  5. Molecular analysis of a NOR site polymorphism in brown trout (Salmo trutta): organization of rDNA intergenic spacers.

    PubMed

    Castro, J; Sánchez, L; Martínez, P; Lucchini, S D; Nardi, I

    1997-12-01

    Using restriction endonuclease mapping, we have analyzed the organization of rDNA (DNA coding for ribosomal RNA (rRNA)) units in the salmonid fish Salmo trutta, as an initial step toward understand the molecular basis of a nucleolar organizer region (NOR) site polymorphism detected in this species. The size of the rDNA units ranged between 15 and 23 kb, with remarkable variation both within individuals and between populations. Three regions of internal tandem repetitiveness responsible for this length polymorphism were located to the intergenic spacers. NOR site polymorphic individuals showed a higher number of length classes, in some cases forming a complete 1 kb fragment ladder. The amount of rRNA genes was as much as 8-fold higher in polymorphic individuals compared with standard individuals. All individuals from the most polymorphic population showed a 14-kb insertion of unknown nature in a small proportion (below 25%) of the 28S rRNA genes. PMID:18464877

  6. Molecular Identification of Closely Related Candida Species Using Two Ribosomal Intergenic Spacer Fingerprinting Methods

    PubMed Central

    Cornet, Muriel; Sendid, Boualem; Fradin, Chantal; Gaillardin, Claude; Poulain, Daniel; Nguyen, Huu-Vang

    2011-01-01

    Recent changes in the epidemiology of candidiasis highlighted an increase in non- Candida albicans species emphasizing the need for reliable identification methods. Molecular diagnostics in fungal infections may improve species characterization, particularly in cases of the closely related species in the Candida complexes. We developed two PCR/restriction fragment length polymorphism assays, targeting either a part of the intergenic spacer 2 or the entire intergenic spacer (IGS) of ribosomal DNA using a panel of 270 isolates. A part of the intergenic spacer was used for discrimination between C. albicans and C. dubliniensis and between species of the C. glabrata complex (C. glabrata/C. bracarensis/C. nivariensis). The whole IGS was applied to C. parapsilosis, C. metapsilosis, and C. orthopsilosis, and to separate C. famata (Debaryomyces hansenii) from C. guilliermondii (Pichia guilliermondii) and from the other species within this complex (ie, C. carpophila, C. fermentati and C. xestobii). Sharing similar biochemical patterns, Pichia norvegensis and C. inconspicua exhibited specific IGS profiles. Our study confirmed that isolates of C. guilliermondii were frequently mis-identified as C. famata. As much as 67% of the clinical isolates phenotypically determined as C. famata were recognized mostly as true P. guilliermondii. Conversely, 44% of the isolates initially identified as C. guilliermondii were corrected by the IGS fingerprints as C. parapsilosis, C. fermentati, or C. zeylanoides. These two PCR/restriction fragment length polymorphism methods may be used as reference tools [either alternatively or adjunctively to the existing ribosomal DNA (26S or ITS) sequence comparisons] for unambiguous determination of the Candida species for which phenotypic characterization remains problematic. PMID:21227390

  7. Sequencing of the Ribosomal Intergenic Spacer Region for Strain Identification of Porphyromonas gingivalis

    PubMed Central

    Rumpf, Robert W.; Griffen, Ann L.; Wen, Bo-Gui; Leys, Eugene J.

    1999-01-01

    The ribosomal intergenic spacer regions (ISRs) of 19 laboratory strains and 30 clinical samples of Porphyromonas gingivalis were amplified by PCR and sequenced to provide a strain identifier. The ISR is a variable region of DNA located between the conserved 16S and 23S rRNA genes. This makes it an ideal locus for differentiation of strains within a species: primers specific for the conserved flanking genes were used to amplify the ISR, which was then sequenced to identify the strain. We have constructed a P. gingivalis ISR sequence database to facilitate strain identification. ISR sequence analysis provides a strain identifier that can be easily reproduced among laboratories and catalogued for unambiguous comparison. PMID:10405432

  8. Sequence conservation and functional constraint on intergenic spacers in reduced genomes of the obligate symbiont Buchnera.

    PubMed

    Degnan, Patrick H; Ochman, Howard; Moran, Nancy A

    2011-09-01

    Analyses of genome reduction in obligate bacterial symbionts typically focus on the removal and retention of protein-coding regions, which are subject to ongoing inactivation and deletion. However, these same forces operate on intergenic spacers (IGSs) and affect their contents, maintenance, and rates of evolution. IGSs comprise both non-coding, non-functional regions, including decaying pseudogenes at varying stages of recognizability, as well as functional elements, such as genes for sRNAs and regulatory control elements. The genomes of Buchnera and other small genome symbionts display biased nucleotide compositions and high rates of sequence evolution and contain few recognizable regulatory elements. However, IGS lengths are highly correlated across divergent Buchnera genomes, suggesting the presence of functional elements. To identify functional regions within the IGSs, we sequenced two Buchnera genomes (from aphid species Uroleucon ambrosiae and Acyrthosiphon kondoi) and applied a phylogenetic footprinting approach to alignments of orthologous IGSs from a total of eight Buchnera genomes corresponding to six aphid species. Inclusion of these new genomes allowed comparative analyses at intermediate levels of divergence, enabling the detection of both conserved elements and previously unrecognized pseudogenes. Analyses of these genomes revealed that 232 of 336 IGS alignments over 50 nucleotides in length displayed substantial sequence conservation. Conserved alignment blocks within these IGSs encompassed 88 Shine-Dalgarno sequences, 55 transcriptional terminators, 5 Sigma-32 binding sites, and 12 novel small RNAs. Although pseudogene formation, and thus IGS formation, are ongoing processes in these genomes, a large proportion of intergenic spacers contain functional sequences. PMID:21912528

  9. Structure of rrn operons in pathogenic non-cultivable treponemes: sequence but not genomic position of intergenic spacers correlates with classification of Treponema pallidum and Treponema paraluiscuniculi strains

    PubMed Central

    Čejková, Darina; Zobaníková, Marie; Pospíšilová, Petra; Strouhal, Michal; Mikalová, Lenka; Weinstock, George M.

    2013-01-01

    This study examined the sequences of the two rRNA (rrn) operons of pathogenic non-cultivable treponemes, comprising 11 strains of T. pallidum ssp. pallidum (TPA), five strains of T. pallidum ssp. pertenue (TPE), two strains of T. pallidum ssp. endemicum (TEN), a simian Fribourg-Blanc strain and a rabbit T. paraluiscuniculi (TPc) strain. PCR was used to determine the type of 16S–23S ribosomal intergenic spacers in the rrn operons from 30 clinical samples belonging to five different genotypes. When compared with the TPA strains, TPc Cuniculi A strain had a 17 bp deletion, and the TPE, TEN and Fribourg-Blanc isolates had a deletion of 33 bp. Other than these deletions, only 17 heterogeneous sites were found within the entire region (excluding the 16S–23S intergenic spacer region encoding tRNA-Ile or tRNA-Ala). The pattern of nucleotide changes in the rrn operons corresponded to the classification of treponemal strains, whilst two different rrn spacer patterns (Ile/Ala and Ala/Ile) appeared to be distributed randomly across species/subspecies classification, time and geographical source of the treponemal strains. It is suggested that the random distribution of tRNA genes is caused by reciprocal translocation between repetitive sequences mediated by a recBCD-like system. PMID:23082031

  10. Structure of Intergenic Spacer IGS1 of Ribosomal Operon from Schistidium Mosses.

    PubMed

    Milyutina, I A; Ignatova, E A; Ignatov, M S; Goryunov, D V; Troitsky, A V

    2015-11-01

    The structure of the intergenic spacer 1 (IGS1) of the ribosomal operon from 12 species of Schistidium mosses was studied. In the IGS1 sequences of these species, three conserved regions and two areas of GC- and A-enriched repeats were identified. All of the studied mosses have a conserved pyrimidine-enriched motif at the 5'-end of IGS1. Species-specific nucleotide substitutions and insertions were found in the conserved areas. The repeated units contain single nucleotide substitutions that make unique the majority of repeated units. The positions of such repeats in IGS1 are species-specific, but their number can vary within the species and among operons of the same specimen. The comparison of IGS1 sequences from the Schistidium species and from representatives of ten other moss genera revealed the presence of common conserved motifs with similar localization. Presumably, these motifs are elements of termination of the pre-rRNA transcription and processing of rRNA. PMID:26615440

  11. PCR amplification and characterization of the intergenic spacer region of the ribosomal DNA in Pyrenophora graminea.

    PubMed

    Pecchia, S; Mercatelli, E; Vannacci, G

    1998-09-01

    Successful amplification of the whole intergenic spacer region of the nuclear ribosomal repeat (IGS) in Pyrenophora graminea was obtained with a PCR-based assay. Single amplification products showed length differences. Depending on the length of the IGS-PCR product, ca. 3.8 or 4.4 kb, two groups of isolates could be identified. The RFLP patterns of isolates obtained with the 6-base cutting enzymes Apal, BglII, DraI, EcoRV, HindIII and SacI were similar within each group and different between the two groups. Restriction patterns of IGS-PCR products digested with the 4-base cutting enzyme AluI were polymorphic among isolates in spite of their IGS-PCR product length. In order to characterize the long and short IGS-PCR products the restriction map is shown. The long product shows an additional HindIII site and a BglII site that is lacking in the short product. However, the latter shows a SacI site that is not present in the long IGS-PCR product. Therefore, the described PCR-RFLP analysis of the IGS appears to be a useful tool to resolve genetic variation between P. graminea isolates. PMID:9741081

  12. Diversity and Inheritance of Intergenic Spacer Sequences of 45S Ribosomal DNA among Accessions of Brassica oleracea L. var. capitata

    PubMed Central

    Yang, Kiwoung; Robin, Arif Hasan Khan; Yi, Go-Eun; Lee, Jonghoon; Chung, Mi-Young; Yang, Tae-Jin; Nou, Ill-Sup

    2015-01-01

    Ribosomal DNA (rDNA) of plants is present in high copy number and shows variation between and within species in the length of the intergenic spacer (IGS). The 45S rDNA of flowering plants includes the 5.8S, 18S and 25S rDNA genes, the internal transcribed spacer (ITS1 and ITS2), and the intergenic spacer 45S-IGS (25S-18S). This study identified six different types of 45S-IGS, A to F, which at 363 bp, 1121 bp, 1717 bp, 1969 bp, 2036 bp and 2111 bp in length, respectively, were much shorter than the reported reference IGS sequences in B. oleracea var. alboglabra. The shortest two IGS types, A and B, lacked the transcription initiation site, non-transcribed spacer, and external transcribed spacer. Functional behavior of those two IGS types in relation to rRNA synthesis is a subject of further investigation. The other four IGSs had subtle variations in the transcription termination site, guanine-cytosine (GC) content, and number of tandem repeats, but the external transcribed spacers of these four IGSs were quite similar in length. The 45S IGSs were found to follow Mendelian inheritance in a population of 15 F1s and their 30 inbred parental lines, which suggests that these sequences could be useful for development of new breeding tools. In addition, this study represents the first report of intra-specific (within subspecies) variation of the 45S IGS in B. oleracea. PMID:26633391

  13. An improved PCR method for direct identification of Porphyra (Bangiales, Rhodophyta) using conchocelis based on a RUBISCO intergenic spacer

    NASA Astrophysics Data System (ADS)

    Wang, Chao; Dong, Dong; Wang, Guangce; Zhang, Baoyu; Peng, Guang; Xu, Pu; Tang, Xiaorong

    2009-09-01

    An improved method of PCR in which the small segment of conchocelis is amplified directly without DNA extraction was used to amplify a RUBISCO intergenic spacer DNA fragment from nine species of red algal genus Porphyra (Bangiales, Rhodophyta), including Porphyra yezoensis (Jiangsu, China), P. haitanensis (Fujian, China), P. oligospermatangia (Qingdao, China), P. katadai (Qingdao, China), P. tenera (Qingdao, China), P. suborboculata (Fujian, China), P. pseudolinearis (Kogendo, Korea), P. linearis (Devon, England), and P. fallax (Seattle, USA). Standard PCR and the method developed here were both conducted using primers specific for the RUBISCO spacer region, after which the two PCR products were sequenced. The sequencing data of the amplicons obtained using both methods were identical, suggesting that the improved PCR method was functional. These findings indicate that the method developed here may be useful for the rapid identification of species of Porphyra in a germplasm bank. In addition, a phylogenetic tree was constructed using the RUBISCO spacer and partial rbcS sequence, and the results were in concordant with possible alternative phylogenies based on traditional morphological taxonomic characteristics, indicating that the RUBISCO spacer is a useful region for phylogenetic studies.

  14. PCR amplification of rRNA intergenic spacer regions as a method for epidemiologic typing of Clostridium difficile.

    PubMed Central

    Cartwright, C P; Stock, F; Beekmann, S E; Williams, E C; Gill, V J

    1995-01-01

    From January to March 1993, a suspected outbreak of antibiotic-associated diarrhea occurred on a pediatric oncology ward of the Clinical Center Hospital at the National Institutes of Health. Isolates of Clostridium difficile obtained from six patients implicated in this outbreak were typed by both PCR amplification of rRNA intergenic spacer regions (PCR ribotyping) and restriction endonuclease analysis of genomic DNA. Comparable results were obtained with both methods; five of the six patients were infected with the same strain of C. difficile. Subsequent analysis of 102 C. difficile isolates obtained from symptomatic patients throughout the Clinical Center revealed the existence of 41 distinct and reproducible PCR ribotypes. These data suggest that PCR ribotyping provides a discriminatory, reproducible, and simple alternative to conventional molecular approaches for typing strains of C. difficile. PMID:7699038

  15. A phylogenetic analysis of the genus Carica L. (Caricaceae) based on restriction fragment length variation in a cpDNA intergenic spacer region

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The phylogenetic relationships among twelve wild and cultivated species of Carica (Caricaceae) were analyzed using restriction fragment length variation in a 3.2-kb PCR amplified intergenic spacer region of the chloroplast DNA. A total of 138 fragments representing 137 restriction sites accounting f...

  16. The Mitochondrial Genome of the Leaf-Cutter Ant Atta laevigata: A Mitogenome with a Large Number of Intergenic Spacers

    PubMed Central

    Rodovalho, Cynara de Melo; Lyra, Mariana Lúcio; Ferro, Milene; Bacci, Maurício

    2014-01-01

    In this paper we describe the nearly complete mitochondrial genome of the leaf-cutter ant Atta laevigata, assembled using transcriptomic libraries from Sanger and Illumina next generation sequencing (NGS), and PCR products. This mitogenome was found to be very large (18,729 bp), given the presence of 30 non-coding intergenic spacers (IGS) spanning 3,808 bp. A portion of the putative control region remained unsequenced. The gene content and organization correspond to that inferred for the ancestral pancrustacea, except for two tRNA gene rearrangements that have been described previously in other ants. The IGS were highly variable in length and dispersed through the mitogenome. This pattern was also found for the other hymenopterans in particular for the monophyletic Apocrita. These spacers with unknown function may be valuable for characterizing genome evolution and distinguishing closely related species and individuals. NGS provided better coverage than Sanger sequencing, especially for tRNA and ribosomal subunit genes, thus facilitating efforts to fill in sequence gaps. The results obtained showed that data from transcriptomic libraries contain valuable information for assembling mitogenomes. The present data also provide a source of molecular markers that will be very important for improving our understanding of genomic evolutionary processes and phylogenetic relationships among hymenopterans. PMID:24828084

  17. PCR amplification of the 3' external transcribed and intergenic spacers of the ribosomal DNA repeat unit in three species of Saccharomyces.

    PubMed

    Molina, F I; Jong, S C; Huffman, J L

    1993-04-15

    Two spacer regions outside the ribosomal DNA (rDNA) transcriptional unit in three species of Saccharomyces, S. cerevisiae, S. carlsbergensis and S. pastorianus, were amplified using the polymerase chain reaction. These regions were composed of the 3' external transcribed spacer (ETS) and the intergenic spacer (IGS). Primers were developed from sequence alignments and by taking the reverse complement of a previously described sequence. The region amplified spanned base position 3110 on the 26S rRNA to base position 27 on the 5S rRNA of S. cerevisiae. Nine of the twelve strains used in this study exhibited different restriction profiles, showing that the spacers are highly variable between species. The results suggest that PCR fingerprinting of the non-coding spacer regions can be used to distinguish between closely related Saccharomyces species and may have potential in DNA profiling of other yeasts. PMID:8099889

  18. Correlation of maple sap composition with bacterial and fungal communities determined by multiplex automated ribosomal intergenic spacer analysis (MARISA).

    PubMed

    Filteau, Marie; Lagacé, Luc; LaPointe, Gisèle; Roy, Denis

    2011-08-01

    During collection, maple sap is contaminated by bacteria and fungi that subsequently colonize the tubing system. The bacterial microbiota has been more characterized than the fungal microbiota, but the impact of both components on maple sap quality remains unclear. This study focused on identifying bacterial and fungal members of maple sap and correlating microbiota composition with maple sap properties. A multiplex automated ribosomal intergenic spacer analysis (MARISA) method was developed to presumptively identify bacterial and fungal members of maple sap samples collected from 19 production sites during the tapping period. Results indicate that the fungal community of maple sap is mainly composed of yeast related to Mrakia sp., Mrakiella sp., Guehomyces pullulans, Cryptococcus victoriae and Williopsis saturnus. Mrakia, Mrakiella and Guehomyces peaks were identified in samples of all production sites and can be considered dominant and stable members of the fungal microbiota of maple sap. A multivariate analysis based on MARISA profiles and maple sap chemical composition data showed correlations between Candida sake, Janthinobacterium lividum, Williopsis sp., Leuconostoc mesenteroides, Mrakia sp., Rhodococcus sp., Pseudomonas tolaasii, G. pullulans and maple sap composition at different flow periods. This study provides new insights on the relationship between microbial community and maple sap quality. PMID:21569942

  19. Species-specific repeat units in the intergenic spacer of the ribosomal RNA cistron of Anopheles aquasalis Curry.

    PubMed

    Perera, O P; Cockburn, A F; Mitchell, S E; Conn, J; Seawright, J A

    1998-11-01

    A genomic DNA library of Anopheles aquasalis Curry was screened for clones that hybridized more intensely to DNA from A. aquasalis than to DNA from A. benarrochi Gabaldon, Cova Garcia, and Lopez, A. konderi Galvao and Damasceno, A. nuneztovari Gabaldon cytotypes A, B, and C, A. oswaldoi (Peryassu), A. rangeli Gabaldon, Cova Garcia, and Lopez, or A. trinkae Faran. Two specific clones (2.5 kilobasepairs [kbp] and 3.0 kbp) from A. aquasalis were isolated. Both A. aquasalis-specific clones were from the intergenic spacer region of the ribosomal RNA (rRNA) cistron. Upon digestion with Rsa I, a 900-bp fragment from the clone AA-1 hybridized specifically to A. aquasalis DNA. Analysis of the DNA sequence of this fragment revealed four tandemly repeated 36-bp units. Three of these repeat units were identical, and the fourth was 94% identical to the others. The DNA sequence of a highly conserved region of these repeats was used to synthesize an oligonucleotide probe specific to A. aquasalis. PMID:9840580

  20. Detection of spatial and temporal influences on bacterial communities in an urban stream by automated ribosomal intergenic ribosomal spacer analysis.

    PubMed

    Or, Amitai; Gophna, Uri

    2011-01-01

    The Yarqon is the largest urban river in Israel, and is a slow-flowing stream whose water originates mostly from wastewater treatment plants. Thus, its microbial community is expected to be heavily impacted both by anthropogenic factors and by seasonal temporal variation. In order to identify the main factors that influence the bacterial community, and their spatial-temporal variation, 50 samples were collected representing five different time points and eleven locations. Samples were analyzed for biotic and a-biotic parameters and the bacterial populations were analyzed by Automated Ribosomal Intergenic Spacer Analysis (ARISA). Bacterial richness and diversity were calculated and compared across samples. Canonical Correspondence Analysis (CCA) showed that ARISA clustered the samples according to temporal variation. Molecular fingerprinting analysis provided a snapshot of the microbial community and showed good correlation with geochemical parameters, despite the rapid changes of the Mediterranean environment and the anthropogenic impact. Molecular fingerprinting methods based on natural fragment length polymorphisms may therefore represent a supplementary approach for stream monitoring, alongside physico-chemical measurements. PMID:21869567

  1. Evaluation of automated ribosomal intergenic spacer analysis for bacterial fingerprinting of rumen microbiome compared to pyrosequencing technology.

    PubMed

    Jami, Elie; Shterzer, Naama; Mizrahi, Itzhak

    2014-01-01

    The mammalian gut houses a complex microbial community which is believed to play a significant role in host physiology. In recent years, several microbial community analysis methods have been implemented to study the whole gut microbial environment, in contrast to classical microbiological methods focusing on bacteria which can be cultivated. One of these is automated ribosomal intergenic spacer analysis (ARISA), an inexpensive and popular way of analyzing bacterial diversity and community fingerprinting in ecological samples. ARISA uses the natural variability in length of the DNA fragment found between the 16S and 23S genes in different bacterial lineages to infer diversity. This method is now being supplanted by affordable next-generation sequencing technologies that can also simultaneously annotate operational taxonomic units for taxonomic identification. We compared ARISA and pyrosequencing of samples from the rumen microbiome of cows, previously sampled at different stages of development and varying in microbial complexity using several ecological parameters. We revealed close agreement between ARISA and pyrosequencing outputs, especially in their ability to discriminate samples from different ecological niches. In contrast, the ARISA method seemed to underestimate sample richness. The good performance of the relatively inexpensive ARISA makes it relevant for straightforward use in bacterial fingerprinting analysis as well as for quick cross-validation of pyrosequencing data. PMID:25437610

  2. Evaluation of Automated Ribosomal Intergenic Spacer Analysis for Bacterial Fingerprinting of Rumen Microbiome Compared to Pyrosequencing Technology

    PubMed Central

    Jami, Elie; Shterzer, Naama; Mizrahi, Itzhak

    2014-01-01

    The mammalian gut houses a complex microbial community which is believed to play a significant role in host physiology. In recent years, several microbial community analysis methods have been implemented to study the whole gut microbial environment, in contrast to classical microbiological methods focusing on bacteria which can be cultivated. One of these is automated ribosomal intergenic spacer analysis (ARISA), an inexpensive and popular way of analyzing bacterial diversity and community fingerprinting in ecological samples. ARISA uses the natural variability in length of the DNA fragment found between the 16S and 23S genes in different bacterial lineages to infer diversity. This method is now being supplanted by affordable next-generation sequencing technologies that can also simultaneously annotate operational taxonomic units for taxonomic identification. We compared ARISA and pyrosequencing of samples from the rumen microbiome of cows, previously sampled at different stages of development and varying in microbial complexity using several ecological parameters. We revealed close agreement between ARISA and pyrosequencing outputs, especially in their ability to discriminate samples from different ecological niches. In contrast, the ARISA method seemed to underestimate sample richness. The good performance of the relatively inexpensive ARISA makes it relevant for straightforward use in bacterial fingerprinting analysis as well as for quick cross-validation of pyrosequencing data. PMID:25437610

  3. Comparison of the bacterial community structure within the equine hindgut and faeces using Automated Ribosomal Intergenic Spacer Analysis (ARISA).

    PubMed

    Sadet-Bourgeteau, S; Philippeau, C; Dequiedt, S; Julliand, V

    2014-12-01

    The horse's hindgut bacterial ecosystem has often been studied using faecal samples. However few studies compared both bacterial ecosystems and the validity of using faecal samples may be questionable. Hence, the present study aimed to compare the structure of the equine bacterial community in the hindgut (caecum, right ventral colon) and faeces using a fingerprint technique known as Automated Ribosomal Intergenic Spacer Analysis (ARISA). Two DNA extraction methods were also assessed. Intestinal contents and faeces were sampled 3 h after the morning meal on four adult fistulated horses fed meadow hay and pelleted concentrate. Irrespective of the intestinal segment, Principal Component Analysis of ARISA profiles showed a strong individual effect (P<0.0001). However, across the study, faecal bacterial community structure significantly (P<0.001) differed from those of the caecum and colon, while there was no difference between the two hindgut communities. The use of a QIAamp(®) DNA Stool Mini kit increased the quality of DNA extracted irrespective of sample type. The differences observed between faecal and hindgut bacterial communities challenge the use of faeces as a representative for hindgut activity. Further investigations are necessary to compare bacterial activity between the hindgut and faeces in order to understand the validity of using faecal samples. PMID:25075719

  4. Length polymorphisms in tRNA intergenic spacers detected by using the polymerase chain reaction can distinguish streptococcal strains and species.

    PubMed Central

    McClelland, M; Petersen, C; Welsh, J

    1992-01-01

    Intergenic tRNA spacers from strains of streptococcal groups A, B, and G were amplified by using the polymerase chain reaction (PCR) at low stringency with consensus tRNA gene primers. Cloning and sequencing showed that many of the homologous intergenic spacers differed in length between species. The sequences of the tRNA genes that flank these polymorphic spacers were determined and used to synthesize fully complementary primers. With these primers at high stringency, PCR products which varied in lengths from 53 to 71 bp, depending on the species or strain, were obtained from streptococcal DNAs, even in the presence of a 1,000-fold mass excess of human DNA. PCR products, the lengths of which could also be used for classification, were obtained at high stringency from a few genera closely related to Streptococcus. No products were obtained from genomic DNAs from more distantly related genera. Production of species- or strain-specific tRNA intergenic length polymorphisms with primers that generate characteristic products from a variety of species within the same genus should be applicable to many organisms, including those that would otherwise be difficult to culture or identify. Images PMID:1378058

  5. Influence of commonly used primer systems on automated ribosomal intergenic spacer analysis of bacterial communities in environmental samples.

    PubMed

    Purahong, Witoon; Stempfhuber, Barbara; Lentendu, Guillaume; Francioli, Davide; Reitz, Thomas; Buscot, François; Schloter, Michael; Krüger, Dirk

    2015-01-01

    Due to the high diversity of bacteria in many ecosystems, their slow generation times, specific but mostly unknown nutrient requirements and syntrophic interactions, isolation based approaches in microbial ecology mostly fail to describe microbial community structure. Thus, cultivation independent techniques, which rely on directly extracted nucleic acids from the environment, are a well-used alternative. For example, bacterial automated ribosomal intergenic spacer analysis (B-ARISA) is one of the widely used methods for fingerprinting bacterial communities after PCR-based amplification of selected regions of the operon coding for rRNA genes using community DNA. However, B-ARISA alone does not provide any taxonomic information and the results may be severely biased in relation to the primer set selection. Furthermore, amplified DNA stemming from mitochondrial or chloroplast templates might strongly bias the obtained fingerprints. In this study, we determined the applicability of three different B-ARISA primer sets to the study of bacterial communities. The results from in silico analysis harnessing publicly available sequence databases showed that all three primer sets tested are specific to bacteria but only two primers sets assure high bacterial taxa coverage (1406f/23Sr and ITSF/ITSReub). Considering the study of bacteria in a plant interface, the primer set ITSF/ITSReub was found to amplify (in silico) sequences of some important crop species such as Sorghum bicolor and Zea mays. Bacterial genera and plant species potentially amplified by different primer sets are given. These data were confirmed when DNA extracted from soil and plant samples were analyzed. The presented information could be useful when interpreting existing B-ARISA results and planning B-ARISA experiments, especially when plant DNA can be expected. PMID:25749323

  6. 16S–23S rRNA Gene Intergenic Spacer Region Variability Helps Resolve Closely Related Sphingomonads

    PubMed Central

    Tokajian, Sima; Issa, Nahla; Salloum, Tamara; Ibrahim, Joe; Farah, Maya

    2016-01-01

    Sphingomonads comprise a physiologically versatile group many of which appear to be adapted to oligotrophic environments, but several also had features in their genomes indicative of host associations. In this study, the extent variability of the 16S–23S rDNA intergenic spacer (ITS) sequences of 14 ATCC reference sphingomonad strains and 23 isolates recovered from drinking water was investigated through PCR amplification and sequencing. Sequencing analysis of the 16S–23S rRNA gene ITS region revealed that the ITS sizes for all studied isolates varied between 415 and 849 bp, while their G+C content was 42.2–57.9 mol%. Five distinct ITS types were identified: ITSnone (without tRNA genes), ITSAla(TGC), ITSAla(TGC)+Ile(GAT), ITSIle(GAT)+Ala(TGC), and ITS Ile(GAT)+Pseudo. All of the identified tRNAAla(TGC) molecules consisted of 73 bases, and all of the tRNAIle(GAT) molecules consisted of 74 bases. We also detected striking variability in the size of the ITS region among the various examined isolates. Highest variability was detected within the ITS-2. The importance of this study is that this is the first comparison of the 16S–23S rDNA ITS sequence similarities and tRNA genes from sphingomonads. Collectively the data obtained in this study revealed the heterogeneity and extent of variability within the ITS region compared to the 16S rRNA gene within closely related isolates. Sequence and length polymorphisms within the ITS region along with the ITS types (tRNA-containing or lacking and the type of tRNA) and ITS-2 size and sequence similarities allowed us to overcome the limitation we previously encountered in resolving closely related isolates based on the 16S rRNA gene sequence. PMID:26904019

  7. Detection of Clostridium tyrobutyricum in milk to prevent late blowing in cheese by automated ribosomal intergenic spacer analysis.

    PubMed

    Panelli, Simona; Brambati, Eva; Bonacina, Cesare; Feligini, Maria

    2013-10-01

    Clostridium tyrobutyricum has been identified as the main causal agent of the late blowing defect in cheese, with major effects on quality and commercial value. In this work, for the first time, we applied automated ribosomal intergenic spacer analysis (ARISA) approach to diagnose the presence of C. tyrobutyricum in raw milk before cheesemaking. A species-specific primer set was designed and used for this original application of the ARISA. Sensitivity of detection, reproducibility of the fluorescent PCR assay, and repeatability of the capillary electrophoretic analysis of amplicons were evaluated using DNA extracted from milk added with known amounts of C. tyrobutyricum genome copies, ranging from 3 × 10(6) to 3. Results indicated that the sensitivity of the technique permits to detect the bacterium in all the samples. The reproducibility, evaluated by analyzing 3 sets of serial dilutions, resulted satisfactory, with little deviation within PCR reactions amplifying the same starting amount of template (standard deviations ≤ 0.1, coefficients of variation ≤ 3%). The peaks' fluorescence displayed an evident correspondence with the number of genome copies contained in each dilution. The capillary electrophoretic analysis, tested by running a single PCR product per dilution point in 10 repeats, resulted efficient and highly repeatable, with excellent coefficients of variation ≤ 2% and standard deviations ≤ 0.1 in all the sample sets. This application of ARISA gives good estimates of the total C. tyrobutyricum DNA content allowing a specific, fine-scale resolution of this pollutant species in a complex system as milk. A further advantage linked to the automatization of the process. PMID:24106762

  8. Differentiation of Closely Related Carnobacterium Food Isolates Based on 16S-23S Ribosomal DNA Intergenic Spacer Region Polymorphism

    PubMed Central

    Kabadjova, Petia; Dousset, Xavier; Le Cam, Virginie; Prevost, Hervé

    2002-01-01

    A novel strategy for identification of Carnobacterium food isolates based on restriction fragment length polymorphism (RFLP) of PCR-amplified 16S-23S ribosomal intergenic spacer regions (ISRs) was developed. PCR amplification from all Carnobacterium strains studied always yielded three ISR amplicons, which were designated the small ISR (S-ISR), the medium ISR (M-ISR), and the large ISR (L-ISR). The lengths of these ISRs varied from one species to another. Carnobacterium divergens NCDO 2763T and C. mobile DSM 4849T generated one major S-ISR band (ca. 400 bp) and minor M-ISR and L-ISR bands (ca. 500 and ca. 600 bp, respectively). The ISRs amplified from C. gallinarum NCFB 2766T and C. piscicola NCDO 2762T were larger (S-ISR, ca. 600 bp; M-ISR, ca. 700 bp; and L-ISR, ca. 800 bp). The L-ISR contained two tDNAs coding for tRNAIle and tRNAAla genes. The M-ISR included one tRNAAla gene, and the S-ISR did not contain a tDNA gene. The RFLP scheme devised involves estimation of variable PCR product sizes together with HinfI, TaqI, and HindIII restriction analysis. Forty-two isolates yielded four unique band patterns that correctly resolved these isolates into four Carnobacterium species. This method is very suitable for rapid, low-cost identification of a wide variety of Carnobacterium species without sequencing. PMID:12406725

  9. Paenibacillus larvae 16S-23S rDNA intergenic transcribed spacer (ITS) regions: DNA fingerprinting and characterization.

    PubMed

    Dingman, Douglas W

    2012-07-01

    Paenibacillus larvae is the causative agent of American foulbrood in honey bee (Apis mellifera) larvae. PCR amplification of the 16S-23S ribosomal DNA (rDNA) intergenic transcribed spacer (ITS) regions, and agarose gel electrophoresis of the amplified DNA, was performed using genomic DNA collected from 134 P. larvae strains isolated in Connecticut, six Northern Regional Research Laboratory stock strains, four strains isolated in Argentina, and one strain isolated in Chile. Following electrophoresis of amplified DNA, all isolates exhibited a common migratory profile (i.e., ITS-PCR fingerprint pattern) of six DNA bands. This profile represented a unique ITS-PCR DNA fingerprint that was useful as a fast, simple, and accurate procedure for identification of P. larvae. Digestion of ITS-PCR amplified DNA, using mung bean nuclease prior to electrophoresis, characterized only three of the six electrophoresis bands as homoduplex DNA and indicating three true ITS regions. These three ITS regions, DNA migratory band sizes of 915, 1010, and 1474 bp, signify a minimum of three types of rrn operons within P. larvae. DNA sequence analysis of ITS region DNA, using P. larvae NRRL B-3553, identified the 3' terminal nucleotides of the 16S rRNA gene, 5' terminal nucleotides of the 23S rRNA gene, and the complete DNA sequences of the 5S rRNA, tRNA(ala), and tRNA(ile) genes. Gene organization within the three rrn operon types was 16S-23S, 16S-tRNA(ala)-23S, and l6S-5S-tRNA(ile)-tRNA(ala)-23S and these operons were named rrnA, rrnF, and rrnG, respectively. The 23S rRNA gene was shown by I-CeuI digestion and pulsed-field gel electrophoresis of genomic DNA to be present as seven copies. This was suggestive of seven rrn operon copies within the P. larvae genome. Investigation of the 16S-23S rDNA regions of this bacterium has aided the development of a diagnostic procedure and has helped genomic mapping investigations via characterization of the ITS regions. PMID:22510214

  10. Phylogenetic relationships of Carpha and its relatives (Schoeneae, Cyperaceae) inferred from chloroplast trnL intron and trnL-trnF intergenic spacer sequences.

    PubMed

    Zhang, Xiufu; Marchant, Adam; Wilson, Karen L; Bruhl, Jeremy J

    2004-05-01

    Within the tribe Schoeneae (Cyperaceae), the relationships between Carpha and its relatives have not been certain, and the limits and definition of Carpha have been controversial. Further, the relationships of species within Carpha have been unclear. In this study, cladistic analyses based on chloroplast trnL intron and trnL-trnF intergenic spacer sequence data were undertaken to estimate phylogenetic relationships in and around Carpha. This study found that Trianoptiles is sister to Carpha; Ptilothrix is sister to Cyathochaeta rather than to Carpha as suggested by some former authors; and Gymnoschoenus is distant from Carpha and its close relatives. The merging of Schoenoides back into Oreobolus is supported. The findings also revealed the non-monophyletic status of Costularia and of Schoenus, and indicated the phylogenetic relationships of species within Carpha. PMID:15062800

  11. Chloroplast genome differences between Asian and American Equisetum arvense (Equisetaceae) and the origin of the hypervariable trnY-trnE intergenic spacer.

    PubMed

    Kim, Hyoung Tae; Kim, Ki-Joong

    2014-01-01

    Comparative analyses of complete chloroplast (cp) DNA sequences within a species may provide clues to understand the population dynamics and colonization histories of plant species. Equisetum arvense (Equisetaceae) is a widely distributed fern species in northeastern Asia, Europe, and North America. The complete cp DNA sequences from Asian and American E. arvense individuals were compared in this study. The Asian E. arvense cp genome was 583 bp shorter than that of the American E. arvense. In total, 159 indels were observed between two individuals, most of which were concentrated on the hypervariable trnY-trnE intergenic spacer (IGS) in the large single-copy (LSC) region of the cp genome. This IGS region held a series of 19 bp repeating units. The numbers of the 19 bp repeat unit were responsible for 78% of the total length difference between the two cp genomes. Furthermore, only other closely related species of Equisetum also show the hypervariable nature of the trnY-trnE IGS. By contrast, only a single indel was observed in the gene coding regions: the ycf1 gene showed 24 bp differences between the two continental individuals due to a single tandem-repeat indel. A total of 165 single-nucleotide polymorphisms (SNPs) were recorded between the two cp genomes. Of these, 52 SNPs (31.5%) were distributed in coding regions, 13 SNPs (7.9%) were in introns, and 100 SNPs (60.6%) were in intergenic spacers (IGS). The overall difference between the Asian and American E. arvense cp genomes was 0.12%. Despite the relatively high genetic diversity between Asian and American E. arvense, the two populations are recognized as a single species based on their high morphological similarity. This indicated that the two regional populations have been in morphological stasis. PMID:25157804

  12. Chloroplast Genome Differences between Asian and American Equisetum arvense (Equisetaceae) and the Origin of the Hypervariable trnY-trnE Intergenic Spacer

    PubMed Central

    Kim, Hyoung Tae; Kim, Ki-Joong

    2014-01-01

    Comparative analyses of complete chloroplast (cp) DNA sequences within a species may provide clues to understand the population dynamics and colonization histories of plant species. Equisetum arvense (Equisetaceae) is a widely distributed fern species in northeastern Asia, Europe, and North America. The complete cp DNA sequences from Asian and American E. arvense individuals were compared in this study. The Asian E. arvense cp genome was 583 bp shorter than that of the American E. arvense. In total, 159 indels were observed between two individuals, most of which were concentrated on the hypervariable trnY-trnE intergenic spacer (IGS) in the large single-copy (LSC) region of the cp genome. This IGS region held a series of 19 bp repeating units. The numbers of the 19 bp repeat unit were responsible for 78% of the total length difference between the two cp genomes. Furthermore, only other closely related species of Equisetum also show the hypervariable nature of the trnY-trnE IGS. By contrast, only a single indel was observed in the gene coding regions: the ycf1 gene showed 24 bp differences between the two continental individuals due to a single tandem-repeat indel. A total of 165 single-nucleotide polymorphisms (SNPs) were recorded between the two cp genomes. Of these, 52 SNPs (31.5%) were distributed in coding regions, 13 SNPs (7.9%) were in introns, and 100 SNPs (60.6%) were in intergenic spacers (IGS). The overall difference between the Asian and American E. arvense cp genomes was 0.12%. Despite the relatively high genetic diversity between Asian and American E. arvense, the two populations are recognized as a single species based on their high morphological similarity. This indicated that the two regional populations have been in morphological stasis. PMID:25157804

  13. Effectiveness of enterobacterial repetitive intergenic consensus PCR and random amplified polymorphic DNA fingerprinting for Helicobacter pylori strain differentiation.

    PubMed

    Finger, S Alison; Velapatiño, Billie; Kosek, Margaret; Santivañez, Livia; Dailidiene, Daiva; Quino, Willi; Balqui, Jacqueline; Herrera, Phabiola; Berg, Douglas E; Gilman, Robert H

    2006-07-01

    We compared the robustness and discriminatory power of the enterobacterial repetitive intergenic consensus (ERIC) and random amplified polymorphic DNA (RAPD) fingerprinting methods for detecting cases of mixed Helicobacter pylori infection in Peruvian shantytown residents. H. pylori isolates from 63 participants were cultured, and five single colonies and a pool of additional colonies from each participant were analyzed by ERIC-PCR and by RAPD tests with four 10-nucleotide primers (one primer per reaction). There was 94% agreement between the ERIC and RAPD profiles in classifying sets of isolates as uniform versus closely related but not identical versus probably unrelated, indicating a high kappa statistic of 0.8942. Subtle differences in related ERIC or RAPD patterns likely reflect gene transfer between strains, recombination, and/or mutation, whereas markedly different patterns reflect infection by unrelated strains. At least half of infected shantytown residents seemed to carry more than one H. pylori strain, although in 19 of 31 persons, the strains were closely related. Three RAPD tests, each with a different primer, were needed to achieve the sensitivity of one ERIC test. ERIC-PCR constitutes a resource- and time-efficient method for H. pylori strain differentiation. PMID:16820463

  14. Molecular typing among beef isolates of Escherichia coli using consensus repetitive intergenic enterobacteria-polymerase chain reaction (ERIC-PCR)

    NASA Astrophysics Data System (ADS)

    Zoolkifli, Nurliyana Wan; Mutalib, Sahilah Abd

    2013-11-01

    Genomic DNA of Escherichia coli were characterized by enterobacterial repetitive intergenic consensus-Polymerase chain reaction (ERIC-PCR) and the presence of Shiga toxin gene-I (Stx1) and Shiga toxin gene-2 (Stx2). These isolates were originated from imported raw beef which are come from two countries namely Australia and India. The isolation of E. coli was conducted by using Eosin Methylene Blue Agar (EMBA). A total of 94 strains had been isolated from 30 samples of imported raw beefand 42 strains had been detected positively E. coli by doing biochemical tests. All strains had been tested and the results of biochemical tests showed that 3 strains were from Australia samples while the other 39 strains were from India samples. The biochemical tests used are Indole test, Methyl Red test, Voges-Proskauer test and Citrate test. All the 42 strains were examined for Shiga toxin (stx1 and stx2) gene detection by two pair primers which are stx2F (5'-TTCTTCGGTATCCTATTCCC-3'), stx2R (5'-ATGCATCTCTGGTCATTGTA-3'), stx1F (5'-CAGTTAATGTGGTGGCGAAG-3'), and stx1R (5'-CTGTCACAGTAACAACCGT-3'). The results showed that none of the strains are positive for Shiga toxin gene. Application of ERIC-PCR method towards E. coli had successfully shown the high diversity polymorphism in 21 different genome types of DNA with primers ERIC1R (5'- CACTTAGGGGTCCTCGAATGTA- 3') and ERIC2R (5'- AAGTAAGTGACTGGGGTGACGC- 3').

  15. Comparative analysis of the genes encoding 23S-5S rRNA intergenic spacer regions of Lactobacillus casei-related strains.

    PubMed

    Chen, H; Lim, C K; Lee, Y K; Chan, Y N

    2000-03-01

    In this study, investigations into the 23S-5S rRNA intergenic spacer regions (ISRs) of the Lactobacillus casei group were performed. A 1.6 kb fragment, from Lactobacillus paracasei strain ATCC 27092, containing part of the 5S rRNA gene (60 bp), the 5S-23S spacer region (198 bp) and part of the 23S rRNA gene (1295 bp) was cloned and sequenced (GenBank no. AF098107). This fragment was used as a probe to determine the rRNA restriction fragment length polymorphism (RFLP) patterns of nine strains belonging to the Lactobacillus casei group, along with four other non-Lactobacillus casei lactobacilli species. A pair of PCR primers, 23-Fl and 5-Ru, was designed and used for PCR amplification of the 23S-5S rRNA ISRs of these strains. The ISR length and sequence polymorphisms provided additional information for the taxonomic study of the Lactobacillus casei group. The spacer-length polymorphism of Lactobacillus rhamnosus was distinct from those of the other strains and this observation is consistent with the classification of Lactobacillus rhamnosus proposed by Mori et al. For all Lactobacillus casei and Lactobacillus paracasei strains, two major bands (approx. 250 and 170 bp in size) were obtained except in the case of Lactobacillus paracasei subsp. tolerans strain NCIMB 9709T, which yielded only one amplified product (250 bp). The sequencing data of the PCR products of seven well-characterized Lactobacillus casei and Lactobacillus paracasei strains revealed the presence of a 76/80 bp insertion/deletion with some random, single-base substitutions between the longer and shorter spacers for each respective strain. A few base variations were also detected within different strains in this group although the overall sequence similarity was very high (95.9-99.5%). The rRNA RFLP and the spacer sequence of Lactobacillus casei type strain ATCC 393T exhibited unique identities in this cluster. On the other hand, Lactobacillus casei strain ATCC 334 showed a high level of similarity

  16. Identification of Mushroom Species by Automated rRNA Intergenic Spacer Analysis (ARISA) and Its Application to a Suspected Case of Food Poisoning with Tricholoma ustale.

    PubMed

    Sugawara, Ryota; Yamada, Sayumi; Tu, Zhihao; Sugawara, Akiko; Hoshiba, Toshihiro; Eisaka, Sadao; Yamaguchi, Akihiro

    2016-01-01

    Automated rRNA intergenic spacer analysis (ARISA), a method of microbiome analysis, was evaluated for species identification of mushrooms based on the specific fragment sizes. We used 51 wild mushroom-fruiting bodies collected in the centre of Hokkaido and two cultivated mushrooms. Samples were hot-air-dried and DNA were extracted by a beads beating procedure. Sequencing analysis of portions of the rRNA gene (rDNA) provided 33 identifications of mushrooms by genus or species. The results of ARISA identification based on the combination of the fragment sizes corresponding to two inter spacer regions (ITS2 and ITS1) of rDNA within±0.1% accuracy showed that 27 out of the 33 species had specific fragment sizes differentiated from other species. The remaining 6 species formed 3 pairs that showed overlapping fragment sizes. In addition, within-species polymorphisms were observed as 1 bp differences among 32 samples of 13 species. ARISA was applied to investigate a case of suspected food poisoning in which the mushroom was thought to be a toxic Kakishimeji. The morphological identification of the mushroom was ambiguous since the remaining sample lacked a part of the fruiting body. Further, yeast colonies had grown on the surface of the fruiting body during storage. The ARISA fragment size of the mushroom showed 7 bp difference from that of the candidate toxic mushroom. Although ARISA could be a useful tools for estimation of mushroom species, especially in case where the fruiting bodies have deteriorated or been processed, further studies are necessary for reliable identification. For example, it may be necessary to adopt more informative genes which could provide clearer species-specific polymorphisms than the ITS regions. PMID:27211917

  17. Bat white-nose syndrome: a real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructanstructans.

    USGS Publications Warehouse

    Muller, Laura K.; Lorch, Jeffrey M.; Lindner, Daniel L.; O'Connor, Michael; Gargas, Andrea; Blehert, David S.

    2013-01-01

    The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The test is highly sensitive, consistently detecting as little as 3.3 fg of genomic DNA from G. destructans. The real-time PCR test specifically amplified genomic DNA from G. destructans but did not amplify target sequence from 54 closely related fungal isolates (including 43 Geomyces spp. isolates) associated with bats. The test was further qualified by analyzing DNA extracted from 91 bat wing skin samples, and PCR results matched histopathology findings. These data indicate the real-time TaqMan PCR method described herein is a sensitive, specific, and rapid test to detect DNA from G. destructans and provides a valuable tool for WNS diagnostics and research.

  18. Bat white-nose syndrome: a real-time TaqMan polymerase chain reaction test targeting the intergenic spacer region of Geomyces destructans.

    PubMed

    Muller, Laura K; Lorch, Jeffrey M; Lindner, Daniel L; O'Connor, Michael; Gargas, Andrea; Blehert, David S

    2013-01-01

    The fungus Geomyces destructans is the causative agent of white-nose syndrome (WNS), a disease that has killed millions of North American hibernating bats. We describe a real-time TaqMan PCR test that detects DNA from G. destructans by targeting a portion of the multicopy intergenic spacer region of the rRNA gene complex. The test is highly sensitive, consistently detecting as little as 3.3 fg genomic DNA from G. destructans. The real-time PCR test specifically amplified genomic DNA from G. destructans but did not amplify target sequence from 54 closely related fungal isolates (including 43 Geomyces spp. isolates) associated with bats. The test was qualified further by analyzing DNA extracted from 91 bat wing skin samples, and PCR results matched histopathology findings. These data indicate the real-time TaqMan PCR method described herein is a sensitive, specific and rapid test to detect DNA from G. destructans and provides a valuable tool for WNS diagnostics and research. PMID:22962349

  19. Detection and quantification of schistosome DNA in freshwater snails using either fluorescent probes in real-time PCR or oligochromatographic dipstick assays targeting the ribosomal intergenic spacer.

    PubMed

    Kane, Richard A; Stothard, J Russell; Rollinson, David; Leclipteux, Thierry; Evraerts, Jonathan; Standley, Claire J; Allan, Fiona; Betson, Martha; Kaba, Rehana; Mertens, Pascal; Laurent, Thierry

    2013-11-01

    Several DNA probes were designed for use in real-time polymerase chain reaction (PCR) assays to target sequence variation within the ribosomal intergenic spacer (IGS) of schistosomes. A sub-section of the IGS (∼300bp) was amplified, with cross-specific primers, after which group-specific fluorescent, locked nucleic acid probes were assessed for their ability to differentiate and quantify DNA from Schistosoma haematobium and Schistosoma mansoni group parasites. A number of fluorescent probe candidates were screened and validated against genomic DNA from adult schistosome worms and laboratory infected freshwater snails. Two fluorescent, locked nucleic acid probes ShaemLNA5 and SmanLNA2, of 20-26bp in length, were identified and found to be effective in providing evidence of infection in field-collected snails. To adapt these real-time PCR assays for more resource-poor laboratory settings, a PCR-restriction fragment length polymorphism (RFLP) assay was developed and primer/probe combinations were modified for use in oligochromatography, a DNA 'dipstick' technology. An appropriate dipstick was developed, inclusive of internal amplification and amplicon migration controls that could be of particular importance for assessing schistosome transmission dynamics. These assays and tools also have future potential for use in detection of schistosome infections in humans and livestock. PMID:22100540

  20. Nature of polymorphisms in 16S-23S rRNA gene intergenic transcribed spacer fingerprinting of Bacillus and related genera.

    PubMed

    Daffonchio, Daniele; Cherif, Ameur; Brusetti, Lorenzo; Rizzi, Aurora; Mora, Diego; Boudabous, Abdellatif; Borin, Sara

    2003-09-01

    The intergenic transcribed spacers (ITS) between the 16S and 23S rRNA genetic loci are frequently used in PCR fingerprinting to discriminate bacterial strains at the species and intraspecies levels. We investigated the molecular nature of polymorphisms in ITS-PCR fingerprinting of low-G+C-content spore-forming bacteria belonging to the genera Bacillus, Brevibacillus, Geobacillus, and Paenibacillus: We found that besides the polymorphisms in the homoduplex fragments amplified by PCR, heteroduplex products formed during PCR between amplicons from different ribosomal operons, with or without tRNA genes in the ITS, contribute to the interstrain variability in ITS-PCR fingerprinting patterns obtained in polyacrylamide-based gel matrices. The heteroduplex nature of the discriminating bands was demonstrated by fragment separation in denaturing polyacrylamide gels, by capillary electrophoresis, and by cloning, sequencing, and recombination of purified short and tRNA gene-containing long ITS. We also found that heteroduplex product formation is enhanced by increasing the number of PCR cycles. Homoduplex-heteroduplex polymorphisms (HHP) in a conserved region, such as the 16S and 23S rRNA gene ITS, allowed discrimination of closely related strains and species undistinguishable by other methods, indicating that ITS-HHP analysis is an easy and reproducible additional tool for strain typing. PMID:12957895

  1. Technical note: Comparison of automated ribosomal intergenic spacer analysis and denaturing gradient gel electrophoresis to assess bacterial diversity in the rumen of sheep.

    PubMed

    Saro, C; Ranilla, M J; Cifuentes, A; Rosselló-Mora, R; Carro, M D

    2014-03-01

    The aim of this study was to compare automated ribosomal intergenic spacer analysis (ARISA) and denaturing gradient gel electrophoresis (DGGE) techniques to assess bacterial diversity in the rumen of sheep. Sheep were fed 2 diets with 70% of either alfalfa hay or grass hay, and the solid (SOL) and liquid (LIQ) phases of the rumen were sampled immediately before feeding (0 h) and at 4 and 8 h postfeeding. Both techniques detected similar differences between forages, with alfalfa hay promoting greater (P < 0.05) bacterial diversity than grass hay. In contrast, whereas ARISA analysis showed a decrease (P < 0.05) of bacterial diversity in SOL at 4 h postfeeding compared with 0 and 8 h samplings, no variations (P > 0.05) over the postfeeding period were detected by DGGE. The ARISA technique showed lower (P < 0.05) bacterial diversity in SOL than in LIQ samples at 4 h postfeeding, but no differences (P > 0.05) in bacterial diversity between both rumen phases were detected by DGGE. Under the conditions of this study, the DGGE was not sensitive enough to detect some changes in ruminal bacterial communities, and therefore ARISA was considered more accurate for assessing bacterial diversity of ruminal samples. The results highlight the influence of the fingerprinting technique used to draw conclusions on factors affecting ruminal bacterial diversity. PMID:24492564

  2. PCR-based analysis of the intergenic spacers of the Nor loci on the A genomes of Triticum diploids and polyploids.

    PubMed

    Sallares, R; Brown, T A

    1999-02-01

    We present DNA sequence data showing population variation in the intergenic spacer (IGS) regions of the ribosomal DNAs (rDNAs) on the A genomes of 27 diploid and polyploid wheats. PCRs (polymerase chain reactions) specific for the A(m) genome gave products with five populations of Triticum monococcum but did not give products with AABB or AABBDD wheats. PCRs specific to the A(u) genome of T. urartu gave products with all the AABB and AABBDD polyploids that were tested, but not with T. monococcum. AAGG tetraploids gave products only with the A(u)-specific primers, but the AAAAGG hexaploid T. zhukovskyi gave products with both the A(u) and A(m) primers. Phylogenetic analysis showed a substantial degree of IGS divergence for both the A(m) and A(u) genomes in diploids and polyploids compared with other genomes of Triticum and Aegilops. The rate of evolution of the IGS is much greater than previously reported for the internal transcribed region of the rDNAs but the view that the IGS only gives random noise is rejected, the IGS sequences presented here reflecting the general evolutionary trends affecting the wheat genome as a whole. PMID:10208005

  3. The Mycoplasma gallisepticum 16S-23S rRNA intergenic spacer region sequence as a novel tool for epizootiological studies.

    PubMed

    Raviv, Ziv; Callison, S; Ferguson-Noel, N; Laibinis, V; Wooten, R; Kleven, S H

    2007-06-01

    Mycoplasma gallisepticum (MG) contains two sets of rRNA genes (5S, 16S and 23S) in its genome, but only one of the two is organized in an operon cluster and contains a unique 660-nucleotide intergenic spacer region (IGSR) between the 16S and the 23S rRNA genes. We designed a polymerase chain reaction (PCR) for the specific amplification of the complete MG IGSR segment. The MG IGSR PCR was tested on 18 avian mollicute species and was confirmed as MG specific. The reaction sensitivity was demonstrated by comparing it to the well-established MG mgc2 PCR. The MG IGSR sequence was found to be highly variable (discrimination [D] index of 0.950) among a variety of MG laboratory strains, vaccine strains, and field isolates. The sequencing of the MG IGSR appears to be a valuable single-locus sequence typing (SLST) tool for MG isolate differentiation in diagnostic cases and epizootiological studies. PMID:17626483

  4. Dynamic changes in the distribution of a satellite homologous to intergenic 26-18S rDNA spacer in the evolution of Nicotiana.

    PubMed Central

    Lim, K Y; Skalicka, K; Koukalova, B; Volkov, R A; Matyasek, R; Hemleben, V; Leitch, A R; Kovarik, A

    2004-01-01

    An approximately 135-bp sequence called the A1/A2 repeat was isolated from the transcribed region of the 26-18S rDNA intergenic spacer (IGS) of Nicotiana tomentosiformis. Fluorescence in situ hybridization (FISH) and Southern blot analysis revealed its occurrence as an independent satellite (termed an A1/A2 satellite) outside of rDNA loci in species of Nicotiana section Tomentosae. The chromosomal location, patterns of genomic dispersion, and copy numbers of its tandemly arranged units varied between the species. In more distantly related Nicotiana species the A1/A2 repeats were found only at the nucleolar organizer regions (NOR). There was a trend toward the elimination of the A1/A2 satellite in N. tabacum (tobacco), an allotetraploid with parents closely related to the diploids N. sylvestris and N. tomentosiformis. This process may have already commenced in an S(3) generation of synthetic tobacco. Cytosine residues in the IGS were significantly hypomethylated compared with the A1/A2 satellite. There was no clear separation between the IGS and satellite fractions in sequence analysis of individual clones and we found no evidence for CG suppression. Taken together the data indicate a dynamic nature of the A1/A2 repeats in Nicotiana genomes, with evidence for recurrent integration, copy number expansions, and contractions. PMID:15126410

  5. The nuclear ribosomal DNA intergenic spacer as a target sequence to study intraspecific diversity of the ectomycorrhizal basidiomycete Hebeloma cylindrosporum directly on pinus root systems.

    PubMed

    Guidot, A; Lumini, E; Debaud, J C; Marmeisse, R

    1999-03-01

    Polymorphism of the nuclear ribosomal DNA intergenic spacer (IGS) of the ectomycorrhizal basidiomycete Hebeloma cylindrosporum was studied to evaluate whether this sequence could be used in field studies to estimate the diversity of strains forming mycorrhizas on individual Pinus pinaster root systems. This sequence was amplified by PCR from 125 haploid homokaryotic strains collected in 14 P. pinaster stands along the Atlantic coast of France by using conserved oligonucleotide primers. Restriction enzyme digestion of the amplified 3.4-kbp-long IGS allowed us to characterize 24 alleles whose frequencies differed. Nine of these alleles were found only once, whereas about 60% of the strains contained four of the alleles. Local populations could be almost as diverse as the entire population along a 150-km stretch of coastline that was examined; for example, 13 alleles were found in a single forest stand. The IGS from one strain was partially sequenced, and the sequence data were used to design oligonucleotides which allowed separate PCR amplification of three different segments of the IGS. Most polymorphisms observed among the full-length IGS regions resulted from polymorphisms in an internal ca. 1,500-bp-long sequence characterized by length variations that may have resulted from variable numbers of a T2AG3 motif. This internal polymorphic sequence could not be amplified from the genomes of nine other Hebeloma species. Analysis of this internal sequence amplified from the haploid progenies of 10 fruiting bodies collected in a 70-m2 area resulted in identification of six allelic forms and seven distinct diplotypes out of the 21 possible different combinations. Moreover, optimization of the PCR conditions resulted in amplification of this sequence from more than 80% of the DNA samples extracted from individual H. cylindrosporum infected P. pinaster mycorrhizal root tips, thus demonstrating the usefulness of this sequence for studying the below-ground diversity of

  6. The Nuclear Ribosomal DNA Intergenic Spacer as a Target Sequence To Study Intraspecific Diversity of the Ectomycorrhizal Basidiomycete Hebeloma cylindrosporum Directly on Pinus Root Systems

    PubMed Central

    Guidot, Alice; Lumini, Erica; Debaud, Jean-Claude; Marmeisse, Roland

    1999-01-01

    Polymorphism of the nuclear ribosomal DNA intergenic spacer (IGS) of the ectomycorrhizal basidiomycete Hebeloma cylindrosporum was studied to evaluate whether this sequence could be used in field studies to estimate the diversity of strains forming mycorrhizas on individual Pinus pinaster root systems. This sequence was amplified by PCR from 125 haploid homokaryotic strains collected in 14 P. pinaster stands along the Atlantic coast of France by using conserved oligonucleotide primers. Restriction enzyme digestion of the amplified 3.4-kbp-long IGS allowed us to characterize 24 alleles whose frequencies differed. Nine of these alleles were found only once, whereas about 60% of the strains contained four of the alleles. Local populations could be almost as diverse as the entire population along a 150-km stretch of coastline that was examined; for example, 13 alleles were found in a single forest stand. The IGS from one strain was partially sequenced, and the sequence data were used to design oligonucleotides which allowed separate PCR amplification of three different segments of the IGS. Most polymorphisms observed among the full-length IGS regions resulted from polymorphisms in an internal ca. 1,500-bp-long sequence characterized by length variations that may have resulted from variable numbers of a T2AG3 motif. This internal polymorphic sequence could not be amplified from the genomes of nine other Hebeloma species. Analysis of this internal sequence amplified from the haploid progenies of 10 fruiting bodies collected in a 70-m2 area resulted in identification of six allelic forms and seven distinct diplotypes out of the 21 possible different combinations. Moreover, optimization of the PCR conditions resulted in amplification of this sequence from more than 80% of the DNA samples extracted from individual H. cylindrosporum infected P. pinaster mycorrhizal root tips, thus demonstrating the usefulness of this sequence for studying the below-ground diversity of

  7. Specific Detection of Bradyrhizobium and Rhizobium Strains Colonizing Rice (Oryza sativa) Roots by 16S-23S Ribosomal DNA Intergenic Spacer-Targeted PCR

    PubMed Central

    Tan, Zhiyuan; Hurek, Thomas; Vinuesa, Pablo; Müller, Peter; Ladha, Jagdish K.; Reinhold-Hurek, Barbara

    2001-01-01

    In addition to forming symbiotic nodules on legumes, rhizobial strains are members of soil or rhizosphere communities or occur as endophytes, e.g., in rice. Two rhizobial strains which have been isolated from root nodules of the aquatic legumes Aeschynomene fluminensis (IRBG271) and Sesbania aculeata (IRBG74) were previously found to promote rice growth. In addition to analyzing their phylogenetic positions, we assessed the suitability of the 16S-23S ribosomal DNA (rDNA) intergenic spacer (IGS) sequences for the differentiation of closely related rhizobial taxa and for the development of PCR protocols allowing the specific detection of strains in the environment. 16S rDNA sequence analysis (sequence identity, 99%) and phylogenetic analysis of IGS sequences showed that strain IRBG271 was related to but distinct from Bradyrhizobium elkanii. Rhizobium sp. (Sesbania) strain IRBG74 was located in the Rhizobium-Agrobacterium cluster as a novel lineage according to phylogenetic 16S rDNA analysis (96.8 to 98.9% sequence identity with Agrobacterium tumefaciens; emended name, Rhizobium radiobacter). Strain IRBG74 harbored four copies of rRNA operons whose IGS sequences varied only slightly (2 to 9 nucleotides). The IGS sequence analyses allowed intraspecies differentiation, especially in the genus Bradyrhizobium, as illustrated here for strains of Bradyrhizobium japonicum, B. elkanii, Bradyrhizobium liaoningense, and Bradyrhizobium sp. (Chamaecytisus) strain BTA-1. It also clearly differentiated fast-growing rhizobial species and strains, albeit with lower statistical significance. Moreover, the high sequence variability allowed the development of highly specific IGS-targeted nested-PCR assays. Strains IRBG74 and IRBG271 were specifically detected in complex DNA mixtures of numerous related bacteria and in the DNA of roots of gnotobiotically cultured or even of soil-grown rice plants after inoculation. Thus, IGS sequence analysis is an attractive technique for both microbial

  8. Evolution of the rpoB-psbZ region in fern plastid genomes: notable structural rearrangements and highly variable intergenic spacers

    PubMed Central

    2011-01-01

    Background The rpoB-psbZ (BZ) region of some fern plastid genomes (plastomes) has been noted to go through considerable genomic changes. Unraveling its evolutionary dynamics across all fern lineages will lead to clarify the fundamental process shaping fern plastome structure and organization. Results A total of 24 fern BZ sequences were investigated with taxon sampling covering all the extant fern orders. We found that: (i) a tree fern Plagiogyria japonica contained a novel gene order that can be generated from either the ancestral Angiopteris type or the derived Adiantum type via a single inversion; (ii) the trnY-trnE intergenic spacer (IGS) of the filmy fern Vandenboschia radicans was expanded 3-fold due to the tandem 27-bp repeats which showed strong sequence similarity with the anticodon domain of trnY; (iii) the trnY-trnE IGSs of two horsetail ferns Equisetum ramosissimum and E. arvense underwent an unprecedented 5-kb long expansion, more than a quarter of which was consisted of a single type of direct repeats also relevant to the trnY anticodon domain; and (iv) ycf66 has independently lost at least four times in ferns. Conclusions Our results provided fresh insights into the evolutionary process of fern BZ regions. The intermediate BZ gene order was not detected, supporting that the Adiantum type was generated by two inversions occurring in pairs. The occurrence of Vandenboschia 27-bp repeats represents the first evidence of partial tRNA gene duplication in fern plastomes. Repeats potentially forming a stem-loop structure play major roles in the expansion of the trnY-trnE IGS. PMID:21486489

  9. Bacterial Diversity and Community Structure in an Aerated Lagoon Revealed by Ribosomal Intergenic Spacer Analyses and 16S Ribosomal DNA Sequencing

    PubMed Central

    Yu, Zhongtang; Mohn, William W.

    2001-01-01

    We investigated the bacterial community structure in an aerated plug-flow lagoon treating pulp and paper mill effluent. For this investigation, we developed a composite method based on analyses of PCR amplicons containing the ribosomal intergenic spacer (RIS) and its flanking partial 16S rRNA gene. Community percent similarity was determined on the basis of RIS length polymorphism. A community succession was evident in the lagoon, indicated by a progressive community transition through seven sample locations. The most abrupt changes in community structure were associated with a temperature change from 39 to 35°C and with increases in dissolved oxygen. The temporal differences in community structure, based on summer and winter samplings, were greater than the spatial differences during either season. Clone libraries of rDNA-RIS amplicons were constructed from each of three summer samples. Among 90 clones analyzed (30 clones from each sample), 56 phylotypes were distinguished by restriction fragment length polymorphism. Indices of phylotype richness, evenness, and diversity all increased in clone libraries from the beginning to the end of the lagoon. A representative clone of each phylotype was phylogenetically analyzed on the basis of its partial 16S rRNA gene sequence (ca. 450 bp). Phylogenetic analysis confirmed the increase in diversity and further indicated increasing richness of bacterial divisions. Pioneers in the community spatial succession appeared to include thermotolerant, microaerophilic methanol-oxidizing bacteria related to the genus Methylobacillus, as well as thermotolerant, microaerophilic nitrogen-fixing bacteria related to the genus Azospirillum. PMID:11282606

  10. [Unusual motifs of the nucleotide sequence adjacent to the putative transcription initiation site in the rDNA intergenic spacer of diploid wheat Triticum urartu Thum. ex Gandil, T. boeoticum Boiss, and T. monococcum L].

    PubMed

    Akhunov, E D; Chemeris, A V; Vakhitov, V A

    1997-11-01

    In the intergenic spacer (IGS) of rDNA of diploid wheats Triticum urartu, T. boeoticum, and T. monococcum, the uncommon motives adjacent to the site of transcription initiation (TIS) are revealed. They are located in the region from -6 to +1 relative to the putative TIS and are not encountered in cereals studied earlier. In T. urartu and T. boeoticum, the motif TACTATG has been revealed, in T. monococcum--TATTATG, while diploid Aegilops speltoides has the motif TATAGTA, typical of the remaining cereal species. The TIS-surrounding rDNA IGS region of diploid wheats was compared to the correspondent known rDNA IGS regions of different plant and animal species. PMID:9480224

  11. Trypanosoma cruzi I genotypes in different geographic regions and transmission cycles based on a microsatellite motif of the intergenic spacer of spliced leader genes✯

    PubMed Central

    Cura, Carolina I.; Mejía-Jaramillo, Ana M.; Duffy, Tomás; Burgos, Juan M.; Rodriguero, Marcela; Cardinal, Marta V.; Kjos, Sonia; Gurgel-Gonçalves, Rodrigo; Blanchet, Denis; De Pablos, Luis M.; Tomasini, Nicolás; Silva, Alex Da; Russomando, Graciela; Cuba Cuba, Cesar A.; Aznar, Christine; Abate, Teresa; Levin, Mariano J.; Osuna, Antonio; Gürtler, Ricardo E.; Diosque, Patricio; Solari, Aldo; Triana-Chávez, Omar; Schijman, Alejandro G.

    2011-01-01

    The intergenic region of spliced-leader (SL-IR) genes from 105 Trypanosoma cruzi I (Tc I) infected biological samples, culture isolates and stocks from 11 endemic countries, from Argentina to the USA were characterised, allowing identification of 76 genotypes with 54 polymorphic sites from 123 aligned sequences. On the basis of the microsatellite motif proposed by Herrera et al. (2007) to define four haplotypes in Colombia, we could classify these genotypes into four distinct Tc I SL-IR groups, three corresponding to the former haplotypes Ia (11 genotypes), Ib (11 genotypes) and Id (35 genotypes); and one novel group, Ie (19 genotypes). Genotypes harboring the Tc Ic motif were not detected in our study. Tc Ia was associated with domestic cycles in southern and northern South America and sylvatic cycles in Central and North America. Tc Ib was found in all transmission cycles from Colombia. Tc Id was identified in all transmission cycles from Argentina and Colombia, including Chagas cardiomyopathy patients, sylvatic Brazilian samples and human cases from French Guiana, Panama and Venezuela. Tc Ie gathered five samples from domestic Triatoma infestans from northern Argentina, nine samples from wild Mepraia spinolai and Mepraia gajardoi and two chagasic patients from Chile and one from a Bolivian patient with chagasic reactivation. Mixed infections by Tc Ia + Tc Id, Tc Ia + Tc Ie and Tc Id + Tc Ie were detected in vector faeces and isolates from human and vector samples. In addition, Tc Ia and Tc Id were identified in different tissues from a heart transplanted Chagas cardiomyopathy patient with reactivation, denoting histotropism. Trypanosoma cruzi I SL-IR genotypes from parasites infecting Triatoma gerstaeckeri and Didelphis virginiana from USA, T. infestans from Paraguay, Rhodnius nasutus and Rhodnius neglectus from Brazil and M. spinolai and M. gajardoi from Chile are to our knowledge described for the first time. PMID:20670628

  12. Molecular organization of 5S rDNAs in Rajidae (Chondrichthyes): Structural features and evolution of piscine 5S rRNA genes and nontranscribed intergenic spacers.

    PubMed

    Pasolini, Paola; Costagliola, Domenico; Rocco, Lucia; Tinti, Fausto

    2006-05-01

    The genomic and gene organisation of 5S rDNA clusters have been extensively characterized in bony fish and eukaryotes, providing general issues for understanding the molecular evolution of this multigene DNA family. By contrast, the 5S rDNA features have been rarely investigated in cartilaginous fish (only three species). Here, we provide evidence for a dual 5S rDNA gene system in the Rajidae by sequence analysis of the coding region (5S) and adjacent nontranscribed spacer (NTS) in five Mediterranean species of rays (Rajidae), and in a large number of piscine taxa including lampreys and bony fish. As documented in several bony fish, two functional 5S rDNA types were found here also in the rajid genome: a short one (I) and a long one (II), distinguished by distinct 5S and NTS sequences. That the ancestral piscine genome had these two 5S rDNA loci might be argued from the occurrence of homologous dual gene systems that exist in several fish taxa and from 5S phylogenetic relationships. An extensive analysis of NTS-II sequences of Rajidae and Dasyatidae revealed the occurrence of large simple sequence repeat (SSR) regions that are formed by microsatellite arrays. The localization and organization of SSR within the NTS-II are conserved in Rajiformes since the Upper Cretaceous. The direct correlation between the SSRs extension and the NTS length indicated that they might play a role in the maintenance of the larger 5S rDNA clusters in rays. The phylogenetic analysis indicated that NTS-II is a valuable systematic tool limited to distantly related taxa of Rajiformes. PMID:16612546

  13. Development and Validation of an Improved PCR Method Using the 23S-5S Intergenic Spacer for Detection of Rickettsiae in Dermacentor variabilis Ticks and Tissue Samples from Humans and Laboratory Animals.

    PubMed

    Kakumanu, Madhavi L; Ponnusamy, Loganathan; Sutton, Haley T; Meshnick, Steven R; Nicholson, William L; Apperson, Charles S

    2016-04-01

    A novel nested PCR assay was developed to detectRickettsiaspp. in ticks and tissue samples from humans and laboratory animals. Primers were designed for the nested run to amplify a variable region of the 23S-5S intergenic spacer (IGS) ofRickettsiaspp. The newly designed primers were evaluated using genomic DNA from 11Rickettsiaspecies belonging to the spotted fever, typhus, and ancestral groups and, in parallel, compared to otherRickettsia-specific PCR targets (ompA,gltA, and the 17-kDa protein gene). The new 23S-5S IGS nested PCR assay amplified all 11Rickettsiaspp., but the assays employing other PCR targets did not. The novel nested assay was sensitive enough to detect one copy of a cloned 23S-5S IGS fragment from "CandidatusRickettsia amblyommii." Subsequently, the detection efficiency of the 23S-5S IGS nested assay was compared to those of the other three assays using genomic DNA extracted from 40 adultDermacentor variabilisticks. The nested 23S-5S IGS assay detectedRickettsiaDNA in 45% of the ticks, while the amplification rates of the other three assays ranged between 5 and 20%. The novel PCR assay was validated using clinical samples from humans and laboratory animals that were known to be infected with pathogenic species ofRickettsia The nested 23S-5S IGS PCR assay was coupled with reverse line blot hybridization with species-specific probes for high-throughput detection and simultaneous identification of the species ofRickettsiain the ticks. "CandidatusRickettsia amblyommii,"R. montanensis,R. felis, andR. belliiwere frequently identified species, along with some potentially novelRickettsiastrains that were closely related toR. belliiandR. conorii. PMID:26818674

  14. Development and Validation of an Improved PCR Method Using the 23S-5S Intergenic Spacer for Detection of Rickettsiae in Dermacentor variabilis Ticks and Tissue Samples from Humans and Laboratory Animals

    PubMed Central

    Kakumanu, Madhavi L.; Ponnusamy, Loganathan; Sutton, Haley T.; Meshnick, Steven R.; Nicholson, William L.

    2016-01-01

    A novel nested PCR assay was developed to detect Rickettsia spp. in ticks and tissue samples from humans and laboratory animals. Primers were designed for the nested run to amplify a variable region of the 23S-5S intergenic spacer (IGS) of Rickettsia spp. The newly designed primers were evaluated using genomic DNA from 11 Rickettsia species belonging to the spotted fever, typhus, and ancestral groups and, in parallel, compared to other Rickettsia-specific PCR targets (ompA, gltA, and the 17-kDa protein gene). The new 23S-5S IGS nested PCR assay amplified all 11 Rickettsia spp., but the assays employing other PCR targets did not. The novel nested assay was sensitive enough to detect one copy of a cloned 23S-5S IGS fragment from “Candidatus Rickettsia amblyommii.” Subsequently, the detection efficiency of the 23S-5S IGS nested assay was compared to those of the other three assays using genomic DNA extracted from 40 adult Dermacentor variabilis ticks. The nested 23S-5S IGS assay detected Rickettsia DNA in 45% of the ticks, while the amplification rates of the other three assays ranged between 5 and 20%. The novel PCR assay was validated using clinical samples from humans and laboratory animals that were known to be infected with pathogenic species of Rickettsia. The nested 23S-5S IGS PCR assay was coupled with reverse line blot hybridization with species-specific probes for high-throughput detection and simultaneous identification of the species of Rickettsia in the ticks. “Candidatus Rickettsia amblyommii,” R. montanensis, R. felis, and R. bellii were frequently identified species, along with some potentially novel Rickettsia strains that were closely related to R. bellii and R. conorii. PMID:26818674

  15. Differentiation of Debaryomyces hansenii and Candida famata by rRNA gene intergenic spacer fingerprinting and reassessment of phylogenetic relationships among D. hansenii, C. famata, D. fabryi, C. flareri (=D. subglobosus) and D. prosopidis: description of D. vietnamensis sp. nov. closely related to D. nepalensis.

    PubMed

    Nguyen, Huu-Vang; Gaillardin, Claude; Neuvéglise, Cécile

    2009-06-01

    The intergenic spacer rDNA amplification and AluI fingerprinting (IGSAF) method detected four distinct groups among 170 Debaryomyces hansenii strains: D. hansenii var. hansenii; Candida famata var. famata; D. hansenii var. fabryi and C. famata var. flareri. IGS sequence comparison of representative strains showed that D. hansenii var. hansenii and C. famata var. famata belonged to one species, whereas D. hansenii var. fabryi and C. famata var. flareri belonged to two different ones. This confirmed the following three species recently reinstated: D. hansenii (=C. famata), Debaryomyces fabryi and Debaryomyces subglobosus (=Candida flareri). Accordingly, growth at 37 degrees C may no longer be used to differentiate D. hansenii from D. fabryi. Riboflavin production is more specific for D. fabryi and D. subglobosus strains. IGSAF identified all the other 17 species of the genus Debaryomyces, six of them sharing with D. hansenii an rRNA gene unit harbouring two 5S rRNA genes. The phylogenetic tree established with IGS sequences was congruent with the one based on ACT1, GPD1 and COX2 sequences depicting a distinct D. hansenii clade close to the D. subglobosus, Debaryomyces prosopidis and D. fabryi clade. Description of Debaryomyces vietnamensis sp. nov. (type strain CBS 10535(T), MUCL 51648(T)), closely related to Debaryomyces nepalensis is given. PMID:19385997

  16. IntergenicDB: a database for intergenic sequences

    PubMed Central

    Notari, Daniel Luis; Molin, Aurione; Davanzo, Vanessa; Picolotto, Douglas; Ribeiro, Helena Graziottin; Silva, Scheila de Avila e

    2014-01-01

    A whole genome contains not only coding regions, but also non-coding regions. These are located between the end of a given coding region and the beginning of the following coding region. For this reason, the information about gene regulation process underlies in intergenic regions. There is no easy way to obtain intergenic regions from current available databases. IntergenicDB was developed to integrate data of intergenic regions and their gene related information from NCBI databases. The main goal of INTERGENICDB is to offer friendly database for intergenic sequences of bacterial genomes. Availability http://intergenicdb.bioinfoucs.com/ PMID:25097383

  17. Spacer fluids

    SciTech Connect

    Wilson, W.N.; Bradshaw, R.D.; Wilton, B.S.; Carpenter, R.B.

    1992-05-19

    This patent describes a method for cementing a wellbore penetrating an earth formation into which a conduit extends, the wellbore having a space occupied by a drilling fluid. It comprises displacing the drilling fluid from the space with a spacer fluid comprising: sulfonated styrene-maleic anhydride copolymer, bentonite, welan gum, surfactant and a weighting agent; and displacing the spacer composition and filling the wellbore space with a settable cement composition.

  18. Repetitive Sequences

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Repetitive sequences, or repeats, account for a substantial portion of the eukaryotic genomes. These sequences include very different types of DNA with respect to mode of origin, function, structure, and genomic distribution. Two large families of repetitive sequences can be readily recognized, ta...

  19. Intraspecific diversity within Diaporthe helianthi: evidence from rDNA intergenic spacer (IGS) sequence analysis.

    PubMed

    Pecchia, Susanna; Mercatelli, Elisabetta; Vannacci, Giovanni

    2004-04-01

    Diaporthe helianthi is the causal agent of sunflower stem canker, a serious pathogen of sunflower in Europe but recorded sporadically in Italy. The genetic diversity of D. helianthi isolates from different geographic origins (Argentina, France, Italy, Yugoslavia, Romania) was investigated using IGS sequences. A 400 bp fragment of the portion of the IGS region flanking the 5' end of the 18S gene was amplified from each isolate. The aligned nucleotide sequences showed intraspecific sequence homology from 99-100% among French/Yugoslavian isolates to 95-100% among Italian isolates. French/Yugoslavian isolates shared 90-92% sequence homology with Italian isolates. The phylogenetic tree obtained from the aligned data revealed three separate groups. Group 1 included all isolates from France and former Yugoslavia and one isolate from Argentina; Group 2 included all Italian isolates and one isolate from Argentina. The most distantly related isolate was that from Romania (Group 3). The average genetic distances among isolates within Group 1 and within Group 2 were 0.22 and 3.29 respectively. The analysis showed that all isolates originating from countries where severe outbreaks of the disease are reported annually (France and former Yugoslavia) form a well defined taxon characterized by relatively low variability. This group is distinct from the group formed by isolates originating from Italy, whose variability is relatively much higher. Results obtained revealed a marked differentiation among pathogen isolates, and members of Group 1 seem not yet to have spread into Italian sunflower-growing areas. PMID:15180160

  20. Intergenic Locations of Rice Centromeric Chromatin

    PubMed Central

    Yan, Huihuang; Talbert, Paul B; Lee, Hye-Ran; Jett, Jamie; Henikoff, Steven; Chen, Feng; Jiang, Jiming

    2008-01-01

    Centromeres are sites for assembly of the chromosomal structures that mediate faithful segregation at mitosis and meiosis. Plant and animal centromeres are typically located in megabase-sized arrays of tandem satellite repeats, making their precise mapping difficult. However, some rice centromeres are largely embedded in nonsatellite DNA, providing an excellent model to study centromere structure and evolution. We used chromatin immunoprecipitation and 454 sequencing to define the boundaries of nine of the 12 centromeres of rice. Centromere regions from chromosomes 8 and 9 were found to share synteny, most likely reflecting an ancient genome duplication. For four centromeres, we mapped discrete subdomains of binding by the centromeric histone variant CENH3. These subdomains were depleted in both intact and nonfunctional genes relative to interspersed subdomains lacking CENH3. The intergenic location of rice centromeric chromatin resembles the situation for human neocentromeres and supports a model of the evolution of centromeres from gene-poor regions. PMID:19067486

  1. Phylogeny of Panax using chloroplast trnC-trnD intergenic region and the utility of trnC-trnD in interspecific studies of plants.

    PubMed

    Lee, Chunghee; Wen, Jun

    2004-06-01

    Sequences of the chloroplast trnC-trnD region and the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA were obtained for all species of Panax L. (the ginseng plant genus, Araliaceae) to reconstruct phylogenetic relationships. The trnC-trnD phylogeny is congruent with the ITS phylogeny for the diploid taxa of Panax. This study is the first use of the trnC-trnD sequence data for phylogenetic analysis at the interspecific level. We evaluated this DNA region for its phylogenetic utility at the lower taxonomic level for flowering plants. The trnC-trnD region includes the trnC-petN intergenic spacer, the petN gene, the petN-psbM intergenic spacer, the psbM gene, and the psbM-trnD intergenic spacer. The petN and psbM genes are small, 90 and 104-114 bp across angiosperms, respectively, and have conserved sequences. We have designed universal amplification and sequencing primers within these two genes. Using these primers, we have successfully amplified the entire trnC-trnD region for a diversity of flowering plant groups, including Aralia L. (Araliaceae), Calycanthus L. (Calycanthaceae), Corylus L. (Betulaceae), Hamamelis L. (Hamamelidaceae), Hydrocotyle L. (Apiaceae), Illigera Blume (Hernandiaceae), Nelumbo Adans. (Nelumbonaceae), Nolana L. ex L.f. (Solanaceae), Prunus L. (Rosaceae), and Staphylea L. (Staphyleaceae). In Panax, the trnC-trnD region provides a similar number of informative phylogenetic characters as the ITS regions and a slightly higher number of informative characters than the chloroplast ndhF gene. We thus demonstrate the utility of the trnC-trnD region for lower-level phylogenetic studies in flowering plants. PMID:15120387

  2. Phylogenetic analysis of encapsulated and non-encapsulated Trichinella species by studying the 5S rDNA tandemly repeated intergenic region.

    PubMed

    van der Giessen, J W B; Fonville, M; Briels, I; Pozio, E

    2005-09-01

    The identification of sequence regions in the genomes of pathogens which can be useful to distinguish among species and genotypes, is of great importance for epidemiological, molecular, and phylogenetic studies. The 5S ribosomal DNA intergenic spacer region has been identified as a good target to distinguish among eight Trichinella species and genotypes. The recent discovery of two non-encapsulated species in this genus, Trichinella papuae and Trichinella zimbabwensis, which can infect both mammals and reptiles, has suggested analyzing their 5S rDNA. Amplification of the tandem repeats of the 5S rDNA intergenic region of encapsulated species of Trichinella shows a 751bp fragment, whereas the three non-encapsulated species show a fragment of 800bp with T. pseudospiralis showing an additional fragment of 522bp. Although the size of the 800bp PCR fragments of T. papuae and T. zimbabwensis are similar to that of T. pseudospiralis, there are differences in the 5S rDNA intergenic regions among the three non-encapsulated species. Phylogenetic analysis of the 5S rDNA intergenic regions shows a clustering together of the three non-encapsulated Trichinella species that is well separated from the encapsulated ones. In addition, a single PCR-based method allows distinguishing non-encapsulated and encapsulated species. PMID:16076532

  3. Complete Sequence Construction of the Highly Repetitive Ribosomal RNA Gene Repeats in Eukaryotes Using Whole Genome Sequence Data.

    PubMed

    Agrawal, Saumya; Ganley, Austen R D

    2016-01-01

    The ribosomal RNA genes (rDNA) encode the major rRNA species of the ribosome, and thus are essential across life. These genes are highly repetitive in most eukaryotes, forming blocks of tandem repeats that form the core of nucleoli. The primary role of the rDNA in encoding rRNA has been long understood, but more recently the rDNA has been implicated in a number of other important biological phenomena, including genome stability, cell cycle, and epigenetic silencing. Noncoding elements, primarily located in the intergenic spacer region, appear to mediate many of these phenomena. Although sequence information is available for the genomes of many organisms, in almost all cases rDNA repeat sequences are lacking, primarily due to problems in assembling these intriguing regions during whole genome assemblies. Here, we present a method to obtain complete rDNA repeat unit sequences from whole genome assemblies. Limitations of next generation sequencing (NGS) data make them unsuitable for assembling complete rDNA unit sequences; therefore, the method we present relies on the use of Sanger whole genome sequence data. Our method makes use of the Arachne assembler, which can assemble highly repetitive regions such as the rDNA in a memory-efficient way. We provide a detailed step-by-step protocol for generating rDNA sequences from whole genome Sanger sequence data using Arachne, for refining complete rDNA unit sequences, and for validating the sequences obtained. In principle, our method will work for any species where the rDNA is organized into tandem repeats. This will help researchers working on species without a complete rDNA sequence, those working on evolutionary aspects of the rDNA, and those interested in conducting phylogenetic footprinting studies with the rDNA. PMID:27576718

  4. Repetition Reduction: Lexical Repetition in the Absence of Referent Repetition

    ERIC Educational Resources Information Center

    Lam, Tuan Q.; Watson, Duane G.

    2014-01-01

    Compared to words that are new to a discourse, repeated words are produced with reduced acoustic prominence. Although these effects are often attributed to priming in the production system, the locus of the effect within the production system remains unresolved because, in natural speech, repetition often involves repetition of referents and…

  5. Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis.

    PubMed

    Moghe, Gaurav D; Lehti-Shiu, Melissa D; Seddon, Alex E; Yin, Shan; Chen, Yani; Juntawong, Piyada; Brandizzi, Federica; Bailey-Serres, Julia; Shiu, Shin-Han

    2013-01-01

    The Arabidopsis (Arabidopsis thaliana) genome is the most well-annotated plant genome. However, transcriptome sequencing in Arabidopsis continues to suggest the presence of polyadenylated (polyA) transcripts originating from presumed intergenic regions. It is not clear whether these transcripts represent novel noncoding or protein-coding genes. To understand the nature of intergenic polyA transcription, we first assessed its abundance using multiple messenger RNA sequencing data sets. We found 6,545 intergenic transcribed fragments (ITFs) occupying 3.6% of Arabidopsis intergenic space. In contrast to transcribed fragments that map to protein-coding and RNA genes, most ITFs are significantly shorter, are expressed at significantly lower levels, and tend to be more data set specific. A surprisingly large number of ITFs (32.1%) may be protein coding based on evidence of translation. However, our results indicate that these "translated" ITFs tend to be close to and are likely associated with known genes. To investigate if ITFs are under selection and are functional, we assessed ITF conservation through cross-species as well as within-species comparisons. Our analysis reveals that 237 ITFs, including 49 with translation evidence, are under strong selective constraint and relatively distant from annotated features. These ITFs are likely parts of novel genes. However, the selective pressure imposed on most ITFs is similar to that of randomly selected, untranscribed intergenic sequences. Our findings indicate that despite the prevalence of ITFs, apart from the possibility of genomic contamination, many may be background or noisy transcripts derived from "junk" DNA, whose production may be inherent to the process of transcription and which, on rare occasions, may act as catalysts for the creation of novel genes. PMID:23132786

  6. Anti-spacer double patterning

    NASA Astrophysics Data System (ADS)

    Hyatt, Michael; Huang, Karen; DeVilliers, Anton; Slezak, Mark; Liu, Zhi

    2014-03-01

    With extreme UV not ready for HVM for the 20nm and 14nm nodes, double patterning options that extend the use of 193nm immersion lithography beyond the optical resolution limits, such as LELE (Litho-Etch-Litho-Etch) and SADP (Self Aligned Double Patterning), are being used for critical layers for these nodes. LELE requires very stringent overlay capability of the optical exposure tool. The spacer scheme of SADP starts with a conformal film of material around the mandrels and etched along the mandrel sidewalls to form patterns with doubled frequency. SADP, while having the advantage of being a self-aligned process, adds a number of process steps and strict control of the mandrel profile is required. In this paper, we will demonstrate a novel technique - ASDP (Anti-Spacer Double Patterning), which uses only spin-on materials to achieve self-aligned double patterning. After initial resist patterning, an Anti-Spacer Generator (ASG) material is coated on the resist pattern to create the developable spacer region. Another layer of material is then coated and processed to generate the second pattern in between the first resist pattern. We were able to define 37.5nm half pitch pattern features using this technique as well as sub-resolution features for an asymmetric pattern. In this paper we will review the capability of the process in terms of CD control and LWR (line width roughness) and discuss the limitations of the process.

  7. Strain typing of Zygosaccharomyces yeast species using a single molecular method based on polymorphism of the intergenic spacer region (IGS).

    PubMed

    Wrent, Petra; Rivas, Eva-María; Peinado, José M; de Silóniz, María-Isabel

    2010-08-15

    Unlike previously reported methods that need a combination of several typing techniques, we have developed a single method for strain typing of the Zygosaccharomyces bailii, Z. mellis and Z. rouxii spoilage species. Strains belonging to other species have also been included for comparison. We have demonstrated that the IGS-PCR RFLP method has a high discriminative power. Considering the three endonucleases used in this work, we have obtained a variability of 100% for Z. mellis and Z. rouxii strains and up to 70% for Z. bailii. We have also detected two misidentified Z. mellis strains (CBS 711 and CBS 7412) which have RFLP patterns with a set of bands characteristic of Z. rouxii strains. Sequencing of 26S rDNA D1/D2 domains and the 5.8-ITS rDNA region confirmed these strains as Z. rouxii. The method also groups three certified hybrid strains of Zygosaccharomyces in a separate cluster. PMID:20619910

  8. Spacer grid assembly and locking mechanism

    DOEpatents

    Snyder, Jr., Harold J.; Veca, Anthony R.; Donck, Harry A.

    1982-01-01

    A spacer grid assembly is disclosed for retaining a plurality of fuel rods in substantially parallel spaced relation, the spacer grids being formed with rhombic openings defining contact means for engaging from one to four fuel rods arranged in each opening, the spacer grids being of symmetric configuration with their rhombic openings being asymmetrically offset to permit inversion and relative rotation of the similar spacer grids for improved support of the fuel rods. An improved locking mechanism includes tie bars having chordal surfaces to facilitate their installation in slotted circular openings of the spacer grids, the tie rods being rotatable into locking engagement with the slotted openings.

  9. Generator stator core vent duct spacer posts

    DOEpatents

    Griffith, John Wesley; Tong, Wei

    2003-06-24

    Generator stator cores are constructed by stacking many layers of magnetic laminations. Ventilation ducts may be inserted between these layers by inserting spacers into the core stack. The ventilation ducts allow for the passage of cooling gas through the core during operation. The spacers or spacer posts are positioned between groups of the magnetic laminations to define the ventilation ducts. The spacer posts are secured with longitudinal axes thereof substantially parallel to the core axis. With this structure, core tightness can be assured while maximizing ventilation duct cross section for gas flow and minimizing magnetic loss in the spacers.

  10. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes.

    PubMed Central

    Versalovic, J; Koeuth, T; Lupski, J R

    1991-01-01

    Dispersed repetitive DNA sequences have been described recently in eubacteria. To assess the distribution and evolutionary conservation of two distinct prokaryotic repetitive elements, consensus oligonucleotides were used in polymerase chain reaction [PCR] amplification and slot blot hybridization experiments with genomic DNA from diverse eubacterial species. Oligonucleotides matching Repetitive Extragenic Palindromic [REP] elements and Enterobacterial Repetitive Intergenic Consensus [ERIC] sequences were synthesized and tested as opposing PCR primers in the amplification of eubacterial genomic DNA. REP and ERIC consensus oligonucleotides produced clearly resolvable bands by agarose gel electrophoresis following PCR amplification. These band patterns provided unambiguous DNA fingerprints of different eubacterial species and strains. Both REP and ERIC probes hybridized preferentially to genomic DNA from Gram-negative enteric bacteria and related species. Widespread distribution of these repetitive DNA elements in the genomes of various microorganisms should enable rapid identification of bacterial species and strains, and be useful for the analysis of prokaryotic genomes. Images PMID:1762913

  11. Mechanical evaluation of unipolar hip spacer constructs.

    PubMed

    Kummer, Frederick J; Strauss, Eric; Wright, Kevin; Kubiak, Erik N; Di Cesare, Paul E

    2008-10-01

    The strengths of 3 hip spacer constructs--Steinmann pins, a short intramedullary nail (both cement-incorporated), and a Charnley prosthesis--were determined and compared with the strength of a commercially available hip spacer. The hip prosthesis construct was more than twice as strong as the other 2 constructs and was equivalent in strength to the commercial spacer. For spacer applications in which limited weight-bearing is anticipated, the hip prosthesis construct appears more efficacious, but its pros and cons should be compared with those of the commercial product. PMID:19081880

  12. Variation in the Spacer Regions Separating tRNA Genes in Renibacterium salmoninarum Distinguishes Recent Clinical Isolates from the Same Location

    PubMed Central

    Alexander, Sarah M.; Grayson, T. Hilton; Chambers, Edel M.; Cooper, Lynne F.; Barker, Gavin A.; Gilpin, Martyn L.

    2001-01-01

    A means for distinguishing between clinical isolates of Renibacterium salmoninarum that is based on the PCR amplification of length polymorphisms in the tRNA intergenic spacer regions (tDNA-ILPs) was investigated. The method used primers specific to nucleotide sequences of R. salmoninarum tRNA genes and tRNA intergenic spacer regions that had been generated by using consensus tRNA gene primers. Twenty-one PCR products were sequenced from five isolates of R. salmoninarum from the United States, England, and Scotland, and four complete tRNA genes and spacer regions were identified. Sixteen specific PCR primers were designed and tested singly and in all possible pairwise combinations for their potential to discriminate between isolates from recent clinical outbreaks of bacterial kidney disease (BKD) in the United Kingdom. Fourteen of the isolates were cultured from kidney samples taken from fish displaying clinical signs of BKD on five farms, and some of the isolates came from the same farm and at the same time. The tDNA-ILP profiles separated 22 clinical isolates into nine groups and highlighted that some farms may have had more than one source of infection. The grouping of isolates improved on the discriminatory power of previously reported typing methods based on randomly amplified polymorphic DNA analysis and restriction fragment length profiles developed using insertion sequence IS994. Our method enabled us to make divisions between closely related clinical isolates of R. salmoninarum that have identical exact tandem repeat (ETR-A) loci, rRNA intergenic spacer sequences, and IS994 profiles. PMID:11136759

  13. Variation in the spacer regions separating tRNA genes in Renibacterium salmoninarum distinguishes recent clinical isolates from the same location.

    PubMed

    Alexander, S M; Grayson, T H; Chambers, E M; Cooper, L F; Barker, G A; Gilpin, M L

    2001-01-01

    A means for distinguishing between clinical isolates of Renibacterium salmoninarum that is based on the PCR amplification of length polymorphisms in the tRNA intergenic spacer regions (tDNA-ILPs) was investigated. The method used primers specific to nucleotide sequences of R. salmoninarum tRNA genes and tRNA intergenic spacer regions that had been generated by using consensus tRNA gene primers. Twenty-one PCR products were sequenced from five isolates of R. salmoninarum from the United States, England, and Scotland, and four complete tRNA genes and spacer regions were identified. Sixteen specific PCR primers were designed and tested singly and in all possible pairwise combinations for their potential to discriminate between isolates from recent clinical outbreaks of bacterial kidney disease (BKD) in the United Kingdom. Fourteen of the isolates were cultured from kidney samples taken from fish displaying clinical signs of BKD on five farms, and some of the isolates came from the same farm and at the same time. The tDNA-ILP profiles separated 22 clinical isolates into nine groups and highlighted that some farms may have had more than one source of infection. The grouping of isolates improved on the discriminatory power of previously reported typing methods based on randomly amplified polymorphic DNA analysis and restriction fragment length profiles developed using insertion sequence IS994. Our method enabled us to make divisions between closely related clinical isolates of R. salmoninarum that have identical exact tandem repeat (ETR-A) loci, rRNA intergenic spacer sequences, and IS994 profiles. PMID:11136759

  14. Repetitive Stress Injuries

    MedlinePlus

    ... any problems since. What Are Repetitive Stress Injuries? Repetitive stress injuries (RSIs) are injuries that happen when too much stress is placed on a part of the body, resulting in inflammation (pain and swelling), muscle strain, or tissue damage. This stress generally occurs from ...

  15. The Negative Repetition Effect

    ERIC Educational Resources Information Center

    Mulligan, Neil W.; Peterson, Daniel J.

    2013-01-01

    A fundamental property of human memory is that repetition enhances memory. Peterson and Mulligan (2012) recently documented a surprising "negative repetition effect," in which participants who studied a list of cue-target pairs twice recalled fewer targets than a group who studied the pairs only once. Words within a pair rhymed, and…

  16. Replicating repetitive DNA.

    PubMed

    Tognetti, Silvia; Speck, Christian

    2016-05-27

    The function and regulation of repetitive DNA, the 'dark matter' of the genome, is still only rudimentarily understood. Now a study investigating DNA replication of repetitive centromeric chromosome segments has started to expose a fascinating replication program that involves suppression of ATR signalling, in particular during replication stress. PMID:27230530

  17. Roles of repetitive sequences

    SciTech Connect

    Bell, G.I.

    1991-12-31

    The DNA of higher eukaryotes contains many repetitive sequences. The study of repetitive sequences is important, not only because many have important biological function, but also because they provide information on genome organization, evolution and dynamics. In this paper, I will first discuss some generic effects that repetitive sequences will have upon genome dynamics and evolution. In particular, it will be shown that repetitive sequences foster recombination among, and turnover of, the elements of a genome. I will then consider some examples of repetitive sequences, notably minisatellite sequences and telomere sequences as examples of tandem repeats, without and with respectively known function, and Alu sequences as an example of interspersed repeats. Some other examples will also be considered in less detail.

  18. Polymorphism at the ribosomal DNA spacers and its relation to breeding structure of the widespread mushroom Schizophyllum commune.

    PubMed Central

    James, T Y; Moncalvo, J M; Li, S; Vilgalys, R

    2001-01-01

    The common split-gilled mushroom Schizophyllum commune is found throughout the world on woody substrates. This study addresses the dispersal and population structure of this fungal species by studying the phylogeny and evolutionary dynamics of ribosomal DNA (rDNA) spacer regions. Extensive sampling (n = 195) of sequences of the intergenic spacer region (IGS1) revealed a large number of unique haplotypes (n = 143). The phylogeny of these IGS1 sequences revealed strong geographic patterns and supported three evolutionarily distinct lineages within the global population. The same three geographic lineages were found in phylogenetic analysis of both other rDNA spacer regions (IGS2 and ITS). However, nested clade analysis of the IGS1 phylogeny suggested the population structure of S. commune has undergone recent changes, such as a long distance colonization of western North America from Europe as well as a recent range expansion in the Caribbean. Among all spacer regions, variation in length and nucleotide sequence was observed between but not within the tandem rDNA repeats (arrays). This pattern is consistent with strong within-array and weak among-array homogenizing forces. We present evidence for the suppression of recombination between rDNA arrays on homologous chromosomes that may account for this pattern of concerted evolution. PMID:11139499

  19. Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

    PubMed Central

    McManus, Michael T.

    2013-01-01

    Known protein coding gene exons compose less than 3% of the human genome. The remaining 97% is largely uncharted territory, with only a small fraction characterized. The recent observation of transcription in this intergenic territory has stimulated debate about the extent of intergenic transcription and whether these intergenic RNAs are functional. Here we directly observed with a large set of RNA-seq data covering a wide array of human tissue types that the majority of the genome is indeed transcribed, corroborating recent observations by the ENCODE project. Furthermore, using de novo transcriptome assembly of this RNA-seq data, we found that intergenic regions encode far more long intergenic noncoding RNAs (lincRNAs) than previously described, helping to resolve the discrepancy between the vast amount of observed intergenic transcription and the limited number of previously known lincRNAs. In total, we identified tens of thousands of putative lincRNAs expressed at a minimum of one copy per cell, significantly expanding upon prior lincRNA annotation sets. These lincRNAs are specifically regulated and conserved rather than being the product of transcriptional noise. In addition, lincRNAs are strongly enriched for trait-associated SNPs suggesting a new mechanism by which intergenic trait-associated regions may function. These findings will enable the discovery and interrogation of novel intergenic functional elements. PMID:23818866

  20. A report of cat scratch disease in Korea confirmed by PCR amplification of the 16S-23S rRNA intergenic region of Bartonella henselae.

    PubMed

    Suh, Borum; Chun, Jin-Kyoung; Yong, Dongeun; Lee, Yang Soon; Jeong, Seok Hoon; Yang, Woo Ick; Kim, Dong Soo

    2010-02-01

    We report a case of cat scratch disease in an 8-yr-old girl who presented with fever and enlargement of both axillary lymph nodes. Both aerobic and anaerobic cultures of the lymph node aspirate were negative for microbial growth. Gram staining and Warthin-Starry silver staining did not reveal any organism. Purified DNA from the PCR-amplicon of the 16S-23S rRNA intergenic region was sequenced and showed 99.7% identity with the corresponding sequence of Bartonella henselae strain Houston-1. Our findings suggest that the internal transcribed spacer is a reliable region for PCR identification of Bartonella species. In patients with lymphadenitis, a history of contact with cats or dogs necessitates the use of diagnostic approaches that employ not only the conventional staining and culture but also molecular methods to detect B. henselae. PMID:20197720

  1. LISA telescope spacer design investigations

    NASA Astrophysics Data System (ADS)

    Sanjuan, Josep; Mueller, Guido; Livas, Jeffrey; Preston, Alix; Arsenovic, Petar; Castellucci, Kevin; Generie, Joseph; Howard, Joseph; Stebbins, Robin

    ) and materials such as Silicon Carbide (SiC) and Carbon Fiber Reinforced Plastic (CFRP) are considered to be used in the telescope spacer structure. We will describe our experimental efforts to understand and quantify the behavior of different materials and also discuss a first investigation of a specific on-axis SiC telescope spacer for LISA. This work is supported by NASA contract 00069955.

  2. Repetition priming in music.

    PubMed

    Hutchins, Sean; Palmer, Caroline

    2008-06-01

    The authors explore priming effects of pitch repetition in music in 3 experiments. Musically untrained participants heard a short melody and sang the last pitch of the melody as quickly as possible. Each experiment manipulated (a) whether or not the tone to be sung (target) was heard earlier in the melody (primed) and (b) the prime-target distance (measured in events). Experiment 1 used variable-length melodies, whereas Experiments 2 and 3 used fixed-length melodies. Experiment 3 changed the timbre of the target tone. In all experiments, fast-responding participants produced repeated tones faster than nonrepeated tones, and this repetition benefit decreased as prime-target distances increased. All participants produced expected tonic endings faster than less expected nontonic endings. Repetition and tonal priming effects are compared with harmonic priming effects in music and with repetition priming effects in language. PMID:18505332

  3. Indirect decentralized repetitive control

    NASA Technical Reports Server (NTRS)

    Lee, Soo Cheol; Longman, Richard W.

    1993-01-01

    Learning control refers to controllers that learn to improve their performance at executing a given task, based on experience performing this specific task. In a previous work, the authors presented a theory of indirect decentralized learning control based on use of indirect adaptive control concepts employing simultaneous identification and control. This paper extends these results to apply to the indirect repetitive control problem in which a periodic (i.e., repetitive) command is given to a control system. Decentralized indirect repetitive control algorithms are presented that have guaranteed convergence to zero tracking error under very general conditions. The original motivation of the repetitive control and learning control fields was learning in robots doing repetitive tasks such as on an assembly line. This paper starts with decentralized discrete time systems, and progresses to the robot application, modeling the robot as a time varying linear system in the neighborhood of the desired trajectory. Decentralized repetitive control is natural for this application because the feedback control for link rotations is normally implemented in a decentralized manner, treating each link as if it is independent of the other links.

  4. Characterizing temporal repetition

    SciTech Connect

    Cukierman, D.; Delgrande, J.

    1996-12-31

    We are investigating the representation and reasoning about schedulable, repeated activities, specified using calendars. Examples of such activities include meeting every Tuesday and Thursday during a semester and attending a seminar every first day of a month. This research provides for a valuable framework for scheduling systems, financial systems and, in general, date-based systems. Very recently work has been done related to reasoning about repetition in the Artificial Intelligence community and others. A partial reference list is provided here. However, to our knowledge no extensive taxonomy of repetition has been proposed in the literature. We believe that reasoning about repeated activities calls for a study and precise definition of the topological characteristics in a repetitive series. In this abstract we summarize a proposal to classify types of repetition according to parameters. The combination of all possible values of these parameters provides a complete taxonomy of repetitive classes with respect to the proposed parameters. Several notions of repetition are considered, some are extremely general, some are very specific.

  5. Identification of Cistanche species (Orobanchaceae) based on sequences of the plastid psbA-trnH intergenic region.

    PubMed

    Han, Jian-Ping; Song, Jing-Yuan; Liu, Chang; Chen, Jun; Qian, Jun; Zhu, Ying-Jie; Shi, Lin-Chun; Yao, Hui; Chen, Shi-Lin

    2010-01-01

    The dried succulent stems of Cistanche (Cistanche deserticola Y. C. Ma and Cistanche tubulosa Wight.) are one of the most widely used components of traditional Chinese medicines. However, it is often confused and substituted with the roots of Orobanche pycnostachya, Boschniakia rossica (Cham. & Schltdl.) Standl., Cistanche sinensis Beck, and Cistanche salsa (C. A. Mey.) Beck. In this study, we identified psbA-trnH regions from species and tested their suitable for the identification of the above mentioned taxa. The psbA-trnH sequences showed considerable variations between species and thus were revealed as a promising candidate for barcoding of Cistanche species. Additionally, the average genetic distance of psbA-trnH ranging from 0.077% to 0.743%. In contrast, the intra-specific variation among Cistanche species was found to be significantly different from those of other species, with percentages of variation studied ranged from 0% to 0.007%. The sequence difference between the psbA-trnH sequences of Cistanche species and Orobanche pycnostachya ranged from 0.979% to 1.149%. The distance between the Cistanche species and Boschniakia rossica ranged from 1.066% to 1.224%. Our results suggest that the psbA-trnH intergenic spacer region represent a barcode that can be used to identify Cistanche species and other morphologically undistinguishable species. PMID:21348418

  6. The negative repetition effect.

    PubMed

    Mulligan, Neil W; Peterson, Daniel J

    2013-09-01

    A fundamental property of human memory is that repetition enhances memory. Peterson and Mulligan (2012) recently documented a surprising negative repetition effect, in which participants who studied a list of cue-target pairs twice recalled fewer targets than a group who studied the pairs only once. Words within a pair rhymed, and across pairs, the target words were drawn from a small set of categories. In the repetition condition, the pairs were initially presented in a random order and then presented a 2nd time blocked by the category of the target words. In the single presentation condition, the pairs were presented only in the blocked order. Participants in the former condition recalled fewer target words on a free recall test despite having seen the word pairs twice (the negative repetition effect). This phenomenon is explored in a series of 5 experiments assessing 3 theoretical accounts of the effect. The experiments demonstrate that the negative repetition effect generalizes over multiple encoding conditions (reading and generative encoding), over different memory tests (free and cued recall), and over delay (5 min and 2 days). The results argue against a retrieval account and a levels-of-processing account but are consistent with the item-specific-relational account, the account upon which the effect was initially predicated. PMID:23421508

  7. Modular domains of the Dicistroviridae intergenic internal ribosome entry site

    PubMed Central

    Jang, Christopher J.; Jan, Eric

    2010-01-01

    The intergenic region internal ribosome entry site (IGR IRES) of the Dicistroviridae viral family can directly assemble 80S ribosomes and initiate translation at a non-AUG codon from the ribosomal A-site. These functions are directed by two independently folded domains of the IGR IRES. One domain, composed of overlapping pseudoknots II and III (PKII/III), mediates ribosome recruitment. The second domain, composed of PKI, mimics a tRNA anticodon–codon interaction to position the ribosome at the ribosomal A-site. Although adopting a common secondary structure, the dicistrovirus IGR IRESs can be grouped into two classes based on distinct features within each domain. In this study, we report on the modularity of the IGR IRESs and show that the ribosome-binding domain and the tRNA anticodon mimicry domain are functionally interchangeable between the Type I and the Type II IGR IRESs. Using structural probing, ribosome-binding assays, and ribosome positioning analysis by toeprinting assays, we show that the chimeric IRESs fold properly, assemble 80S ribosomes, and can mediate IRES translation in rabbit reticulocyte lysates. We also demonstrate that the chimeric IRESs can stimulate the ribosome-dependent GTPase activity of eEF2, which suggests that the ribosome is primed for a step downstream from IRES binding. Overall, the results demonstrate that the dicistrovirus IGR IRESs are composed of two modular domains that work in concert to manipulate the ribosome and direct translation initiation. PMID:20423979

  8. Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends.

    PubMed

    Tajnik, Mojca; Vigilante, Alessandra; Braun, Simon; Hänel, Heike; Luscombe, Nicholas M; Ule, Jernej; Zarnack, Kathi; König, Julian

    2015-12-01

    The 3' untranslated regions (3' UTRs) of transcripts serve as important hubs for posttranscriptional gene expression regulation. Here, we find that the exonisation of intergenic Alu elements introduced new terminal exons and polyadenylation sites during human genome evolution. While Alu exonisation from introns has been described previously, we shed light on a novel mechanism to create alternative 3' UTRs, thereby opening opportunities for differential posttranscriptional regulation. On the mechanistic level, we show that intergenic Alu exonisation can compete both with alternative splicing and polyadenylation in the upstream gene. Notably, the Alu-derived isoforms are often expressed in a tissue-specific manner, and the Alu-derived 3' UTRs can alter mRNA stability. In summary, we demonstrate that intergenic elements can affect processing of preceding genes, and elucidate how intergenic Alu exonisation can contribute to tissue-specific posttranscriptional regulation by expanding the repertoire of 3' UTRs. PMID:26400176

  9. The ribosomal gene spacer region in archaebacteria

    NASA Technical Reports Server (NTRS)

    Achenbach-Richter, L.; Woese, C. R.

    1988-01-01

    Sequences for the spacer regions that separate the 16S and 23S ribosomal RNA genes have been determined for four more (strategically placed) archaebacteria. These confirm the general rule that methanogens and extreme halophiles have spacers that contain a single tRNAala gene, while tRNA genes are not found in the spacer region of the true extreme thermophiles. The present study also shows that the spacer regions from the sulfate reducing Archaeglobus and the extreme thermophile Thermococcus (both of which cluster phylogenetically with the methanogens and extreme halophiles) contain each a tRNAala gene. Thus, not only all methanogens and extreme halophiles show this characteristic, but all organisms on the "methanogen branch" of the archaebacterial tree appear to do so. The finding of a tRNA gene in the spacer region of the extreme thermophile Thermococcus celer is the first known phenotypic property that links this organism with its phylogenetic counterparts, the methanogens, rather than with its phenotypic counterparts, the sulfur-dependent extreme thermophiles.

  10. Repetition through Successive Approximations.

    ERIC Educational Resources Information Center

    Littell, Katherine M.

    This study was conducted in an attempt to provide an alternative to the long-established method of tape listening and repetition drills, a method that has had disappointing results. It is suggested that the rate of speed of phonic presentation is not commensurate with the rate of comprehension. The proposed method seeks to prevent cognitive…

  11. Novel porcine repetitive elements

    Technology Transfer Automated Retrieval System (TEKTRAN)

    An analysis of 220 fully sequenced porcine BACs generated by the Comparative Vertebrate Sequencing Initiative (http://www.nisc.nih.gov/) revealed 27 distinct, novel porcine repetitive elements ranging in length from 55 to 1059 nucleotides. This set of fully sequenced BACs covers approximately 1% of...

  12. Repetition Priming in Music

    ERIC Educational Resources Information Center

    Hutchins, Sean; Palmer, Caroline

    2008-01-01

    The authors explore priming effects of pitch repetition in music in 3 experiments. Musically untrained participants heard a short melody and sang the last pitch of the melody as quickly as possible. Each experiment manipulated (a) whether or not the tone to be sung (target) was heard earlier in the melody (primed) and (b) the prime-target distance…

  13. The Mitochondrial Genome of Conus textile, coxI-coxII Intergenic Sequences and Conoidean Evolution

    PubMed Central

    Bandyopadhyay, Pradip K; Stevenson, Bradford J.; Ownby, John-Paul; Cady, Matthew T.; Watkins, Maren; Olivera, Baldomero M.

    2009-01-01

    The cone snails belong to the superfamily Conoidea, comprising ∼10,000 venomous marine gastropods. We determined the complete mitochondrial DNA sequence of Conus textile. The gene order is identical in Conus textile, Lophiotoma cerithiformis (another Conoidean gastropod), and the neogastropod Ilyanassa obsoleta, (not in the superfamily Conoidea). However, the intergenic interval between the coxI/coxII genes, was much longer in C. textile (165 bp) than in any other previously analyzed gastropod. We used the intergenic region to evaluate evolutionary patterns. In most neogastropods and three conidean families the intergenic interval is small (<30 nucleotides). Within Conus, the variation is from 130-170 bp, and each different clade within Conus has a narrower size distribution. In Conasprella, a subgenus traditionally assigned to Conus, the intergenic regions vary between 200-500 bp, suggesting that the species in Conasprella are not congeneric with Conus. The intergenic region was used for phylogenetic analysis of a group of fish-hunting Conus, despite the short length resolution was better than using standard markers. Thus, the coxI/coxII intergenic region can be used both to define evolutionary relationships between species in a clade, and to understand broad evolutionary patterns across the large superfamily Conoidea. PMID:17936021

  14. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

    PubMed Central

    2011-01-01

    Background DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have developed/refined methods for enrichment of methylated genomic fragments using the methyl-binding domain of the human MBD2 protein (MBD2-MBD) followed by analysis with high-density tiling microarrays. This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells. Results Examining this data using computational methods that were designed specifically for DNA methylation tiling array data revealed widespread methylation of both gene promoter and non-promoter regions in cancer and normal cells. In addition to identifying several novel cancer hypermethylated 5' gene upstream regions that mediated epigenetic gene silencing, we also found several hypermethylated 3' gene downstream, intragenic and intergenic regions. The hypermethylated intragenic regions were highly enriched for overlap with intron-exon boundaries, suggesting a possible role in regulation of alternative transcriptional start sites, exon usage and/or splicing. The hypermethylated intergenic regions showed significant enrichment for conservation across vertebrate species. A sampling of these newly identified promoter (ADAMTS1 and SCARF2 genes) and non-promoter (downstream or within DSCR9, C21orf57 and HLCS genes) hypermethylated regions were effective in distinguishing malignant from normal prostate tissues and/or cell lines. Conclusions Comparison of chromosome-wide DNA methylation patterns in normal and malignant prostate cells revealed significant methylation of gene-proximal and conserved intergenic sequences. Such analyses can be easily extended for genome-wide methylation analysis in health and disease. PMID:21669002

  15. Separator-spacer for electrochemical systems

    DOEpatents

    Grimes, Patrick G.; Einstein, Harry; Newby, Kenneth R.; Bellows, Richard J.

    1983-08-02

    An electrochemical cell construction features a novel co-extruded plastic electrode in an interleaved construction with a novel integral separator-spacer. Also featured is a leak and impact resistant construction for preventing the spill of corrosive materials in the event of rupture.

  16. Allele-specific germ cell epimutation in the spacer promoter of the 45S ribosomal RNA gene after Cr(III) exposure

    SciTech Connect

    Shiao, Y.-H. . E-mail: shiao@mail.ncifrcf.gov; Crawford, Erik B.; Anderson, Lucy M.; Patel, Pritesh; Ko, Kinarm

    2005-06-15

    Paternal exposure of mice to Cr(III) causes increased tumor risk in offspring; an epigenetic mechanism has been hypothesized. Representational difference analysis of gene methylation in sperm revealed hypomethylation in the 45S ribosomal RNA (rRNA) gene after Cr(III) exposure, compared with controls. The most striking effects were seen in the rRNA spacer promoter, a region in the intergenic region of rRNA gene clusters that can influence transcription. Methylation of the rRNA spacer promoter has not been studied heretofore. Sperm DNAs from Cr(III)-treated and control mice were modified by the bisulfite method followed by PCR amplification of the spacer promoter, including 27 CpG sites. Cloning and dideoxy sequencing identified sequence variants (T or G at base -2214) in the spacer promoter. The T allele had less DNA methylation than the G allele in control mice (17 of 17 clones vs. 42 of 72 clones, P = 0.0004). In spite of diversity of sperm DNA methylation patterns, the DNA clones from Cr(III)-exposed mice had fewer methylated CpG sites, by an average of 19% (P < 0.0001). This difference was limited to the G allele. The pyrosequencing technique was applied to quantify the percentage of methylation directly from amplified PCR products. Strikingly, for nine CpG sites including the spacer promoter core region, hypomethylation was highly significant in the Cr(III)-treated group (paired T test, P < 0.0001). Thus, one allele of the 45S rRNA spacer promoter is hypomethylated in sperm germ cells after Cr(III) exposure. This epimutation may lead to increase of tumor risk in the offspring.

  17. Molecular profiling of microbial communities from contaminated sources: Use of subtractive cloning methods and rDNA spacer sequences. 1998 annual progress report

    SciTech Connect

    Robb, F.T.

    1998-06-01

    'The major objective of the research is to provide appropriate sequences and to assemble a high-density DNA array of oligonucleotides that can be used for rapid profiling of microbial populations from polluted areas. The sequences to be assigned to the DNA array are chosen from from cloned genomic DNA sequences (the ribosomal operon, described below) from groundwater at DOE sites containing organic solvents. The sites, Hanford Nuclear Plant and Lawrence Livermore Site 300, have well characterized pollutant histories, which have been provided by the collaborators. At this mid-point of the project, over 60 unique sequence classes of intergenic spacer region have been idedntified from the first sample site. The use of these sequences as hybridization probes, and their frequency of occurrence, allow a clear distinction between bacterial communities before and after remediation by acetate/nitrate pumping. The authors have developed the hybridization conditions for identifying PCR products in a 96 well format, a versatile alignment and visualization program (acronym: MALIGN) developed by Dr. Dennis Maeder, has been used to align the ISRs, which are variable in length and sometimes in position of the tRNAs. Finally, in collaboration with Dr. W. Chen and Dr. J. Zhou at ORNL, they have significant evidence that mass spectrometer analysis can be used to determine the lengths of PCR amplified intergenic spacer DNA.'

  18. Role of the intergenic dinucleotide in vesicular stomatitis virus RNA transcription.

    PubMed Central

    Barr, J N; Whelan, S P; Wertz, G W

    1997-01-01

    To investigate the role played by the intergenic dinucleotide sequence of the conserved vesicular stomatitis virus (VSV) gene junction in modulation of polymerase activity, we analyzed the RNA synthesis activities of bicistrionic genomic analogs that contained either the authentic N/P gene junction or gene junctions that had been altered to contain either the 16 possible dinucleotide combinations, single nucleotide intergenic sequences, or no intergenic sequence at all. Quantitative measurements of the amounts of upstream, downstream, and readthrough mRNAs that were transcribed by these mutant templates showed that the behavior of the viral polymerase was profoundly affected by the nucleotide sequence that it encountered as it traversed the gene junction, although the polymerase was able to accommodate a remarkable degree of sequence variation without altogether losing the ability to terminate and reinitiate transcription. Alteration or removal of the intergenic sequence such that the U tract responsible for synthesis of the upstream mRNA poly(A) tail was effectively positioned adjacent to the consensus downstream gene start signal resulted in almost complete abrogation of downstream mRNA synthesis, thus defining the intergenic sequence as an essential sequence element of the gene junction. Many genome analogs with altered intergenic sequences directed abundant synthesis of a readthrough transcript without correspondingly high levels of downstream mRNA, an observation inconsistent with the shunting model of VSV transcription, which suggests that polymerase molecules are prepositioned at gene junctions, awaiting a push from upstream. Instead, the findings of this study support a model of sequential transcription in which initiation of downstream mRNA can occur only following termination of the preceding transcript. PMID:9032308

  19. Tube support grid and spacer therefor

    DOEpatents

    Ringsmuth, Richard J.; Kaufman, Jay S.

    1986-01-01

    A tube support grid and spacers therefor provide radially inward preloading of heat exchange tubes to minimize stress upon base welds due to differential thermal expansion. The grid comprises a concentric series of rings and spacers with opposing concave sides for conforming to the tubes and V-shaped ends to provide resilient flexibility. The flexibility aids in assembly and in transmitting seismic vibrations from the tubes to a shroud. The tube support grid may be assembled in place to achieve the desired inwardly radial preloading of the heat exchange tubes. Tab and slot assembly further minimizes stresses in the system. The radii of the grid rings may be preselected to effect the desired radially inward preloading.

  20. Honeycomb spacer crush stength test results

    SciTech Connect

    Leader, D.R.

    1993-09-15

    This report discusses aluminum honeycomb spacers, which are used as an energy absorbent material in shipping packages for off site shipment of radioactive materials and which were ordered in two crush strengths, 1,000 psi and 2,000 psi for use in drop tests requested by the Packaging and Transportation group as part of the shipping container rectification process. Both the group as part of the shipping container rectification process. Both the vendor and the SRTC Materials Laboratory performed crush strength measurements on test samples made from the material used to fabricate the actual spacers. The measurements of crush strength made in the SRTC Materials Laboratory are within 100 psi of the measurements made by the manufacturer for all samples tested and all test measurements are within 10% of the specified crush strength, which is acceptable to the P&T group for the planned tests.

  1. Organization of spacer DNA in chromatin.

    PubMed Central

    Lohr, D; Van Holde, K E

    1979-01-01

    Detailed analysis of the DNA fragment patterns produced by DNase I digestion of yeast, HeLa, and chicken erythrocyte nuclei reveals surprising features of nucleosome phasing. First, the spacer regions in phased yeast chromatin must be of lengths (10m + 5) base pairs, where m = 0, 1, 2,....This feature is not seen in parallel studies of chicken erythrocyte chromatin. The 5-base pair increment in the yeast spacer imposes interesting restraints on the higher order structure of yeast chromatin. Second, we have been able to simulate the DNase I cutting patterns and get good agreement with the observed yeast patterns. Third, three different chromatins show a long range periodicity in the DNase I digest pattern, with a period half that of the staphylococcal nuclease repeat. These results suggest that the amount of chromatin observed in discrete extended-ladder bands is a minimum estimate of phasing and in fact phasing may be a more general feature. Images PMID:392519

  2. Heterogeneous diversity of spacers within CRISPR

    NASA Astrophysics Data System (ADS)

    Deem, Michael; He, Jiankui

    2011-03-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of anti-viral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face. 1) J. He and M. W. Deem, Phys. Rev. Lett. 105 (2010) 128102

  3. Improved nuclear fuel assembly grid spacer

    DOEpatents

    Marshall, John; Kaplan, Samuel

    1977-01-01

    An improved fuel assembly grid spacer and method of retaining the basic fuel rod support elements in position within the fuel assembly containment channel. The improvement involves attachment of the grids to the hexagonal channel and of forming the basic fuel rod support element into a grid structure, which provides a design which is insensitive to potential channel distortion (ballooning) at high fluence levels. In addition the improved method eliminates problems associated with component fabrication and assembly.

  4. Radiological evaluation of acetabular erosion after antibiotic-impregnated polymethylmethacrylate spacer (Spacer-G).

    PubMed

    García-Oltra, Ester; Bori, Guillem; Tomas, Xavier; Gallart, Xavier; Garcia, Sebastian; Soriano, Alex

    2013-06-01

    Different types of hip spacers have been described (hand-made, custom-molded or prefabricated) for treatment of a chronic hip infection. A potential disadvantage of monoblock prefabricated spacer is that it may cause acetabular bone loss. This study assesses the radiological acetabular erosion using an antibiotic-impregnated pre-fabricated polymethylmethacrylate Spacer-G. We retrospectively reviewed the radiographs of thirty five patients who were managed with Spacer-G to treat chronic hip infection. No acetabular erosion were observed in thirty two patients with a mean time from the first to second stage and from the first to the last radiograph of 5.09 and 3.77 months respectively. In three patients the time between the radiographs was more than one year and the second stage was not performed; two developed a protrusion acetabuli whereas the other one a destruction of the acetabular roof. Using a Spacer-G in chronic hip infection treatment for less than one year is not associated with radiological acetabular erosion if the patient is maintained at partial weight bearing. PMID:23142448

  5. Ribosomal operon intergenic sequence (IGS) heterogeneity in Campylobacter coli and Campylobacter jejuni

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Campylobacter jejuni and Campylobacter coli are closely related species that can not be distinguished by their 16S or 23S rRNA genes. However, the intergenic sequence (IGS) fragment that is between the 16S and 23S genes is markedly different and characteristic for each species. A peculiarity of th...

  6. Use of the CP and CPm Intergene Sequences to Discriminate CTV Strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There is a need to develop a rapid assay to distinguish potentially mild vs severe strains of Citrus tristeza virus. Multiple alignment performed on the coat protein (CP) and the minor coat protein (CPm) intergene sequences (~80-100 bp) from different CTV isolates revealed that severe strains (VT, ...

  7. Identification of Lactobacillus strains of goose origin using MALDI-TOF mass spectrometry and 16S-23S rDNA intergenic spacer PCR analysis.

    PubMed

    Dec, Marta; Urban-Chmiel, Renata; Gnat, Sebastian; Puchalski, Andrzej; Wernicki, Andrzej

    2014-04-01

    The objective of our study was to identify Lactobacillus sp. strains of goose origin using MALDI-TOF mass spectrometry, ITS-PCR and ITS-PCR/RFLP. All three techniques proved to be valuable tools for identification of avian lactobacilli and produced comparable classification results. Lactobacillus strains were isolated from 100% of geese aged 3 weeks to 4 years, but from only 25% of chicks aged 1-10 days. Among the 104 strains isolated, we distinguished 14 Lactobacillus species. The dominant species was Lactobacillus salivarius (35.6%), followed by Lactobacillus johnsonii (18.3%), Lactobacillus ingluviei (11.5%) and Lactobacillus agilis (7.7%). The intact-cell MALDI-TOF mass spectrometry enabled rapid species identification of the lactobacilli with minimal pretreatment. However, it produced more than one identification result for 11.5% examined strains (mainly of the species L. johnsonii). ITS-PCR distinguished 12 genotypes among the isolates, but was not able to differentiate closely related strains, i.e. between Lactobacillus amylovorus and Lactobacillus kitasatonis and between Lactobacillus paracasei, Lactobacillus rhamnosus and Lactobacillus zeae. These species were differentiated by ITS-PCR/RFLP using the restriction enzymes TaqI and MseI. The results obtained indicate that ITS-PCR and ITS-PCR/RFLP assays could be used not only for interspecific, but also for intraspecific, typing. PMID:24607713

  8. Repetitive resonant railgun power supply

    DOEpatents

    Honig, E.M.; Nunnally, W.C.

    1985-06-19

    A repetitive resonant railgun power supply provides energy for repetitively propelling projectiles from a pair of parallel rails. The supply comprises an energy storage capacitor, a storage inductor to form a resonant circuit with the energy storage capacitor and a magnetic switch to transfer energy between the resonant circuit and the pair of parallel rails for the propelling of projectiles.

  9. Repetitive resonant railgun power supply

    DOEpatents

    Honig, Emanuel M.; Nunnally, William C.

    1988-01-01

    A repetitive resonant railgun power supply provides energy for repetitively propelling projectiles from a pair of parallel rails. The supply comprises an energy storage capacitor, a storage inductor to form a resonant circuit with the energy storage capacitor and a magnetic switch to transfer energy between the resonant circuit and the pair of parallel rails for the propelling of projectiles.

  10. NEUTRONIC REACTOR SHIELD AND SPACER CONSTRUCTION

    DOEpatents

    Wigner, E.P.; Ohlinger, L.A.

    1958-11-18

    Reactors of the heterogeneous, graphite moderated, fluid cooled type and shielding and spacing plugs for the coolant channels thereof are reported. In this design, the coolant passages extend horizontally through the moderator structure, accommodating the fuel elements in abutting end-to-end relationship, and have access openings through the outer shield at one face of the reactor to facilitate loading of the fuel elements. In the outer ends of the channels which extend through the shields are provided spacers and shielding plugs designed to offer minimal reslstance to coolant fluid flow while preventing emanation of harmful radiation through the access openings when closed between loadings.

  11. Perceptual Repetition Blindness Effects

    NASA Technical Reports Server (NTRS)

    Hochhaus, Larry; Johnston, James C.; Null, Cynthia H. (Technical Monitor)

    1994-01-01

    The phenomenon of repetition blindness (RB) may reveal a new limitation on human perceptual processing. Recently, however, researchers have attributed RB to post-perceptual processes such as memory retrieval and/or reporting biases. The standard rapid serial visual presentation (RSVP) paradigm used in most RB studies is, indeed, open to such objections. Here we investigate RB using a "single-frame" paradigm introduced by Johnston and Hale (1984) in which memory demands are minimal. Subjects made only a single judgement about whether one masked target word was the same or different than a post-target probe. Confidence ratings permitted use of signal detection methods to assess sensitivity and bias effects. In the critical condition for RB a precue of the post-target word was provided prior to the target stimulus (identity precue), so that the required judgement amounted to whether the target did or did not repeat the precue word. In control treatments, the precue was either an unrelated word or a dummy.

  12. [Repetition Strain Injury

    PubMed

    Ribeiro

    1997-01-01

    Muscular-skeletal disorders of the upper limbs resulting from work involving repetition strain (RSI) are now the most frequent work-related diseases in early or late industrialized countries. The author maintains that in addition to being work-related diseases, RSIs are symbolic illnesses revealing the contradictions and social pathogenesis of the new cycle of development and crisis in capitalist production. Discussing the social and historical dimensions of this process, the author insists that the low efficacy of technical interventions by labor engineering, ergonomics, and clinical medicine in the prevention, early and adequate diagnosis, and treatment of such post-modern illnesses and the difficulty in rehabilitating and reincorporating such workers reflect precisely a broader determination of health and illness, since the appropriation, incorporation, and use of technological innovations and the new forms of work management are defined according to the exclusive interests of capital. Thus, a growing contingent of young workers (mainly females) from different labor categories are losing or under threat of losing their health and work capacity, two essential and closely linked public values. The solution to the SRI issue must be political and collective. PMID:10886940

  13. Neural Basis of Repetition Priming during Mathematical Cognition: Repetition Suppression or Repetition Enhancement?

    ERIC Educational Resources Information Center

    Salimpoor, Valorie N.; Chang, Catie; Menon, Vinod

    2010-01-01

    We investigated the neural basis of repetition priming (RP) during mathematical cognition. Previous studies of RP have focused on repetition suppression as the basis of behavioral facilitation, primarily using word and object identification and classification tasks. More recently, researchers have suggested associative stimulus-response learning…

  14. [Repetitive work and psychosomatic complaints].

    PubMed

    Liebrich, J; Geiger, L; Rupp, M

    1978-08-01

    200 workers of the Swiss watch industry were examined in an interdisciplinary study on the effect of repetitive work on the wellbeing of the worker. Women doing repetitive work with little autonomy complained more often about psychosomatic problems than the male workers doing non-repetitive work. This difference is interpreted as a difference of sexe rather than one of the work situation. However, there is a significant difference in the complaint about nervosity between women being paid monthly and women who were paid by piece or by hour with a premium. PMID:706840

  15. Neural repetition suppression reflects fulfilled perceptual expectations

    PubMed Central

    Summerfield, Christopher; Monti, Jim M.P.; Trittschuh, Emily H.; Mesulam, M.-Marsel; Egner, Tobias

    2009-01-01

    Stimulus-evoked neural activity is attenuated upon stimulus repetition (‘repetition suppression’), a phenomenon attributed to largely automatic processes in sensory neurons. By manipulating the likelihood of stimulus repetition, we show that repetition suppression in the human brain is reduced when stimulus repetitions are improbable (and thus, unexpected). These data suggest that repetition suppression reflects a relative reduction in top-down perceptual ‘prediction error’ when processing an expected compared to an unexpected stimulus. PMID:19160497

  16. Exchange of Spacer Regions between Rrna Operons in Escherichia Coli

    PubMed Central

    Harvey, S.; Hill, C. W.

    1990-01-01

    The Escherichia coli rRNA operons each have one of two types of spacer separating the 16S and 23S coding regions. The spacers of four operons encode tRNA(Glu2) and the other three encode both tRNA(Ile) and tRNA(Ala 1 B). We have prepared a series of mutants in which the spacer region of a particular rrn operon has been replaced by the opposite type. Included among these were a mutant retaining only a single copy of the tRNA(Glu2) spacer (at rrnG) and another retaining only a single copy of the tRNA(Ile)-tRNA(Ala 1 B) spacer (at rrnA). While both mutants grew more slowly than controls, the mutant deficient in tRNA(Glu2) spacers was more severely affected. At a frequency of 6 X 10(-5), these mutants phenotypically reverted to faster growing types by increasing the copy number of the deficient spacer. In most of these phenotypic revertants, the deficient spacer type appeared in a rrn operon which previously contained the surplus type, bringing the ratio of spacer types closer to normal. In a few cases, these spacer changes were accompanied by an inversion of the chromosomal material between the donor and recipient rrn operons. Two examples of inversion of one-half of the E. coli chromosome between rrnG and rrnH were observed. The correlation of spacer change with inversion indicated that, in these particular cases, the change was due to an intrachromatid gene conversion event accompanied by a reciprocal crossover rather than reciprocal exchange between sister chromatids. PMID:2168847

  17. Emotional response to musical repetition.

    PubMed

    Livingstone, Steven R; Palmer, Caroline; Schubert, Emery

    2012-06-01

    Two experiments examined the effects of repetition on listeners' emotional response to music. Listeners heard recordings of orchestral music that contained a large section repeated twice. The music had a symmetric phrase structure (same-length phrases) in Experiment 1 and an asymmetric phrase structure (different-length phrases) in Experiment 2, hypothesized to alter the predictability of sensitivity to musical repetition. Continuous measures of arousal and valence were compared across music that contained identical repetition, variation (related), or contrasting (unrelated) structure. Listeners' emotional arousal ratings differed most for contrasting music, moderately for variations, and least for repeating musical segments. A computational model for the detection of repeated musical segments was applied to the listeners' emotional responses. The model detected the locations of phrase boundaries from the emotional responses better than from performed tempo or physical intensity in both experiments. These findings indicate the importance of repetition in listeners' emotional response to music and in the perceptual segmentation of musical structure. PMID:21707165

  18. Repetitively pumped electron beam device

    DOEpatents

    Schlitt, L.G.

    1979-07-24

    Disclosed is an apparatus for producing fast, repetitive pulses of controllable length of an electron beam by phased energy storage in a transmission line of length matched to the number of pulses and specific pulse lengths desired. 12 figs.

  19. Paucity of moderately repetitive sequences

    SciTech Connect

    Schmid, C.W.

    1991-01-01

    We examined clones of renatured repetitive human DNA to find novel repetitive DNAs. After eliminating known repeats, the remaining clones were subjected to sequence analysis. These clones also corresponded to known repeats, but with greater sequence diversity. This indicates that either these libraries were depleted of short interspersed repeats in construction, or these repeats are much less prevalent in the human genome than is indicated by data from {und Xenopus} or sea urchin studies. We directly investigated the sequence composition of human DNA through traditional renaturation techniques with the goal of estimating the limits of abundance of repetitive sequence classes in human DNA. Our results sharply limit the maximum possible abundance to 1--2% of the human genome. Our estimate, minus the known repeats in this fraction, leaves about 1% (3 {times} 10{sup 7} nucleotides) of the human genome for novel repetitive elements. 2 refs. (MHB)

  20. A Perceptual Repetition Blindness Effect

    NASA Technical Reports Server (NTRS)

    Hochhaus, Larry; Johnston, James C.; Null, Cynthia H. (Technical Monitor)

    1994-01-01

    Before concluding Repetition Blindness is a perceptual phenomenon, alternative explanations based on memory retrieval problems and report bias must be rejected. Memory problems were minimized by requiring a judgment about only a single briefly displayed field. Bias and sensitivity effects were empirically measured with an ROC-curve analysis method based on confidence ratings. Results from five experiments support the hypothesis that Repetition Blindness can be a perceptual phenomenon.

  1. Improvement of inhaler efficacy by home-made spacer.

    PubMed

    Sritara, P; Janvitayanuchit, S

    1993-12-01

    The delivery of aerosol from a metered dose inhaler (MDI) was reported to be more efficient with a spacer. Hence, a home-made spacer modified from a 950 ml low cost plastic bottle, was compared with a MDI and with a 750 ml imported spacer (Nebuhaler). On three consecutive days, at the same time of day, 20 adult patients with chronic asthma inhaled two puffs of terbutaline sulphate (0.5 mg), delivered from MDI alone, MDI with a 750 ml Nebuhlaer and MDI with a home-made spacer. The following measurements were made: forced expiratory volume in one second (FEV1), forced vital capacity (FVC) and pulse rate. These measurements were carried out immediately before and at 5, 20, 60 min after inhalation of terbutaline. FEV1 was significantly increased (P < 0.05) at 5, 20 and 60 min after administration of terbutaline with MDI via either spacers than with MDI alone but no significant difference was observed between Nebuhaler and the home-made spacer. FVC and pulse rate showed no significant change with each method of administration. In conclusion, terbutaline delivered by MDI and home-made spacer was more effective in bronchodilatation than by MDI alone and was just as effective as MDI and Nebuhaler. The home-made spacer therefore offers a simple, inexpensive and more effective method for delivering aerosol drug. PMID:7798822

  2. Orthognathic model surgery with LEGO key-spacer.

    PubMed

    Tsang, Alfred Chee-Ching; Lee, Alfred Siu Hong; Li, Wai Keung

    2013-12-01

    A new technique of model surgery using LEGO plates as key-spacers is described. This technique requires less time to set up compared with the conventional plaster model method. It also retains the preoperative setup with the same set of models. Movement of the segments can be measured and examined in detail with LEGO key-spacers. PMID:24045189

  3. Molecular recordings by directed CRISPR spacer acquisition.

    PubMed

    Shipman, Seth L; Nivala, Jeff; Macklis, Jeffrey D; Church, George M

    2016-07-29

    The ability to write a stable record of identified molecular events into a specific genomic locus would enable the examination of long cellular histories and have many applications, ranging from developmental biology to synthetic devices. We show that the type I-E CRISPR (clustered regularly interspaced short palindromic repeats)-Cas system of Escherichia coli can mediate acquisition of defined pieces of synthetic DNA. We harnessed this feature to generate records of specific DNA sequences into a population of bacterial genomes. We then applied directed evolution so as to alter the recognition of a protospacer adjacent motif by the Cas1-Cas2 complex, which enabled recording in two modes simultaneously. We used this system to reveal aspects of spacer acquisition, fundamental to the CRISPR-Cas adaptation process. These results lay the foundations of a multimodal intracellular recording device. PMID:27284167

  4. Associating disease-related genetic variants in intergenic regions to the genes they impact

    PubMed Central

    Ong, Cheng Soon

    2014-01-01

    We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In addition, we show the potential for this method to uncover relationships between intergenic SNPs and target genes across chromosomes. With more extensive chromatin conformation capture data becoming readily available, this method provides a way forward towards functional interpretation of SNPs in the context of the three dimensional structure of the genome in the nucleus. PMID:25374782

  5. Campylobacter jejuni acquire new host-derived CRISPR spacers when in association with bacteriophages harboring a CRISPR-like Cas4 protein

    PubMed Central

    Hooton, Steven P. T.; Connerton, Ian F.

    2015-01-01

    Campylobacter jejuni is a worldwide cause of human diarrhoeal disease. Clustered Repetitively Interspaced Palindromic Repeats (CRISPRs) and associated proteins allow Bacteria and Archaea to evade bacteriophage and plasmid infection. Type II CRISPR systems are found in association with combinations of genes encoding the CRISPR-associated Cas1, Cas2, Cas4 or Csn2, and Cas9 proteins. C. jejuni possesses a minimal subtype II-C CRISPR system containing cas1, cas2, and cas9 genes whilst cas4 is notably absent. Cas4 proteins possess 5′-3′ exonuclease activity to create recombinogenic-ends for spacer acquisition. Here we report a conserved Cas4-like protein in Campylobacter bacteriophages that creates a novel split arrangement between the bacteriophage and host that represents a new twist in the bacteriophage/host co-evolutionary arms race. The continuous association of bacteriophage and host in the carrier state life cycle of C. jejuni provided an opportunity to study spacer acquisition in this species. Remarkably all the spacer sequences observed were of host origin. We hypothesize that Campylobacter bacteriophages can use Cas4-like protein to activate spacer acquisition to use host DNA as an effective decoy to bacteriophage DNA. Bacteria that acquire self-spacers and escape phage infection must overcome CRISPR-mediated autoimmunity either by loss of the interference functions leaving them susceptible to foreign DNA incursion or tolerate changes in gene regulation. PMID:25601859

  6. [Analysis of the sequences of internal transcribed spacers ITS1, ITS2 and the 5.8S ribosomal gene of species of the Amaranthus genus].

    PubMed

    Slugina, M A; Torres Minho, K; Filiushin, M A

    2014-01-01

    Analysis of the sequence ITS1-5.8S-ITS2 in 11 samples of the amaranth species (Amaranthus caudatus, A. cruentus, A. hybridus, A. tricolor, A. paniculatus, A. hypohondriacus) was performed. It has been shown that the variability of the sequences of the intergenic spacers ITS1, ITS2 and 5.8S rRNA gene of the amaranth species analyzed is extremely low. A possible secondary structure of the 5.8S rRNA molecule was determined for the first time; three conservative motifs were identified. A single nucleotide substitution found in A. hybridus did not change the loop topology. In the sample of Celosia cristata taken as an external group, a four-nucleotide insertion in the 5'-end of the gene and a one-nucleotide deletion in the fourth hairpin not affecting the general topology of the 5.8S rRNA molecule were found. PMID:25739312

  7. Unintended imitation in nonword repetition.

    PubMed

    Kappes, Juliane; Baumgaertner, Annette; Peschke, Claudia; Ziegler, Wolfram

    2009-12-01

    Verbal repetition is conventionally considered to require motor-reproduction of only the phonologically relevant content of a perceived linguistic stimulus, while imitation of incidental acoustic properties of the stimulus is not an explicit part of this task. Exemplar-based theories of speech processing, however, would predict that imitation beyond linguistic reproduction may occur in word repetition. Five experiments were conducted in which verbal audio-motor translations had to be performed under different conditions. Nonwords varying in phonemic content, in vocal pitch (F(0)), and in speaking style (schwa-syllable expression) were presented. We experimentally varied the factors response delay (repetition vs. shadowing), intention-to-repeat (repetition vs. pseudo-naming), and phonological load (repetition vs. transformation). The responses of ten healthy participants were examined for phonemic accuracy and for traces of para-phonological imitation. Two aphasic patients with phonological impairments were also included, to find out if lesions to left anterior or posterior perisylvian cortex interfere with imitation. In the healthy participants, significant imitation of both F(0) and phonetic style was observed, with markedly stronger effects for the latter. Strong imitation was also found in an aphasic patient with a lesion to left anterior perisylvian cortex, whereas almost no imitation occurred in a patient with a lesion to the posterior language area. The degree of unintended imitation was modulated by each of the three independent factors introduced here. The results are discussed on the background of cognitive and neurolinguistic theories of imitation. PMID:19811813

  8. Pervasive generation of oppositely oriented spacers during CRISPR adaptation

    PubMed Central

    Shmakov, Sergey; Savitskaya, Ekaterina; Semenova, Ekaterina; Logacheva, Maria D.; Datsenko, Kirill A.; Severinov, Konstantin

    2014-01-01

    During the process of prokaryotic CRISPR adaptation, a copy of a segment of foreign deoxyribonucleic acid referred to as protospacer is added to the CRISPR cassette and becomes a spacer. When a protospacer contains a neighboring target interference motif, the specific small CRISPR ribonucleic acid (crRNA) transcribed from expanded CRISPR cassette can protect a prokaryotic cell from virus infection or plasmid transformation and conjugation. We show that in Escherichia coli, a vast majority of plasmid protospacers generate spacers integrated in CRISPR cassette in two opposing orientations, leading to frequent appearance of complementary spacer pairs in a population of cells that underwent CRISPR adaptation. When a protospacer contains a spacer acquisition motif AAG, spacer orientation that generates functional protective crRNA is strongly preferred. All other protospacers give rise to spacers oriented in both ways at comparable frequencies. This phenomenon increases the repertoire of available spacers and should make it more likely that a protective crRNA is formed as a result of CRISPR adaptation. PMID:24728991

  9. Repetitively pulsed plasma illumination sources

    NASA Astrophysics Data System (ADS)

    Root, Robert G.; Falkos, Paul

    1997-12-01

    The acoustic environment created by turbulence in aircraft flight tests demands that illumination sources for high speed photography of munitions drops be extremely rugged. A repetitive pulsed surface discharge system has been developed to provide wide angle illumination in a bomb bay for photography at 250 - 500 Hertz. The lamp has a simple construction suitable for adverse environments and produces 100 mJ of visible light per pulse. The discharge parameters were selected to minimize the size and complexity of the power supply. The system is also capable of operating at high repetition rates; preliminary tests demonstrated 1000 pulses at 1 kHz, 200 pulses at 1.5 kHz, and 13 pulses at 2 kHz. A simple power supply capable of providing several amperes at 450 V is being completed; it will be used to extend the run times and to explore extensions to higher repetition rate.

  10. Inhalational drug delivery from seven different spacer devices.

    PubMed Central

    Barry, P. W.; O'Callaghan, C.

    1996-01-01

    BACKGROUND: A study was performed to determine in vitro the difference in drug output of seven currently available spacer devices when used with different inhaled medications. METHODS: A glass multistage liquid impinger (MSLI) was used to determine the amount of disodium cromoglycate (DSCG, 5 mg), salbutamol (100 micrograms), or budesonide (200 micrograms) obtained in various particle size ranges from metered dose inhalers (MDIs) actuated directly into the MSLI or via one of seven different spacer devices; the Fisonair, Nebuhaler, Volumatic, Inspirease, Aerochamber, Aerosol Cloud Enhancer, and Dynahaler. RESULTS: In particles smaller than 5 microns in diameter the dose of DSCG recovered from the Fisonair and Nebuhaler was 118% and 124%, respectively, of that recovered using the MDI alone. The dose recovered from the smaller volume spacers was 90% (Inspirease), 36% (Aerochamber), 33% (Aerosol Cloud Enhancer), and 21% (Dynahaler) of that from the MDI alone. The Volumatic increased the amount of salbutamol in particles smaller than 5 microns to 117% of that from the MDI, and the Inspirease and Aerochamber spacers decreased it by nearly 50%. The amount of budesonide in small particles recovered after use of the Nebuhaler, Inspirease, and the Aerochamber was 92%, 101%, and 78%, respectively, of that from the MDI alone. CONCLUSIONS: Under the test conditions used, large volume spacers such as the Fisonair, Nebuhaler, and Volumatic delivered significantly more DSCG and salbutamol than the smaller spacers tested. The differences between spacers were less for budesonide than the other medications studied. This study shows that there are significant differences in the amount of drug available for inhalation when different spacers are used as inhalational aids with different drugs. Spacer devices need to be fully evaluated for each drug prescribed for them. Images PMID:8795674

  11. Preclinical Evaluation of Bioabsorbable Polyglycolic Acid Spacer for Particle Therapy

    SciTech Connect

    Akasaka, Hiroaki; Sasaki, Ryohei; Miyawaki, Daisuke; Mukumoto, Naritoshi; Sulaiman, Nor Shazrina Binti; Nagata, Masaaki; Yamada, Shigeru; Murakami, Masao; Demizu, Yusuke; Fukumoto, Takumi

    2014-12-01

    Purpose: To evaluate the efficacy and safety of a polyglycolic acid (PGA) spacer through physical and animal experiments. Methods and Materials: The spacer was produced with surgical suture material made of PGA, forming a 3-dimensional nonwoven fabric. For evaluation or physical experiments, 150-MeV proton or 320-MeV carbon-ion beams were used to generate 60-mm width of spread-out Bragg peak. For animal experiments, the abdomens of C57BL/6 mice, with or without the inserted PGA spacers, were irradiated with 20 Gy of carbon-ion beam (290 MeV) using the spread-out Bragg peak. Body weight changes over time were scored, and radiation damage to the intestine was investigated using hematoxylin and eosin stain. Blood samples were also evaluated 24 days after the irradiation. Long-term thickness retention and safety were evaluated using crab-eating macaques. Results: No chemical or structural changes after 100 Gy of proton or carbon-ion irradiation were observed in the PGA spacer. Water equivalency of the PGA spacer was equal to the water thickness under wet condition. During 24 days' observation after 20 Gy of carbon-ion irradiation, the body weights of mice with the PGA spacer were relatively unchanged, whereas significant weight loss was observed in those mice without the PGA spacer (P<.05). In mice with the PGA spacer, villus and crypt structure were preserved after irradiation. No inflammatory reactions or liver or renal dysfunctions due to placement of the PGA spacer were observed. In the abdomen of crab-eating macaques, thickness of the PGA spacer was maintained 8 weeks after placement. Conclusions: The absorbable PGA spacer had water-equivalent, bio-compatible, and thickness-retaining properties. Although further evaluation is warranted in a clinical setting, the PGA spacer may be effective to stop proton or carbon-ion beams and to separate normal tissues from the radiation field.

  12. Neural Basis of Repetition Priming during Mathematical Cognition: Repetition Suppression or Repetition Enhancement?

    PubMed Central

    Salimpoor, Valorie N.; Chang, Catie; Menon, Vinod

    2015-01-01

    We investigated the neural basis of repetition priming (RP) during mathematical cognition. Previous studies of RP have focused on repetition suppression as the basis of behavioral facilitation, primarily using word and object identification and classification tasks. More recently, researchers have suggested associative stimulus-response learning as an alternate model for behavioral facilitation. We examined the neural basis of RP during mathematical problem solving in the context of these two models of learning. Brain imaging and behavioral data were acquired from 39 adults during novel and repeated presentation of three-operand mathematical equations. Despite widespread decreases in activation during repeat, compared with novel trials, there was no direct relation between behavioral facilitation and the degree of repetition suppression in any brain region. Rather, RT improvements were directly correlated with repetition enhancement in the hippocampus and the postero-medial cortex [posterior cingulate cortex, precuneus, and retro-splenial cortex; Brodmann’s areas (BAs) 23, 7, and 30, respectively], regions known to support memory formation and retrieval, and in the SMA (BA 6) and the dorsal midcingulate (“motor cingulate”) cortex (BA 24d), regions known to be important for motor learning. Furthermore, improvements in RT were also correlated with increased functional connectivity of the hippocampus with both the SMA and the dorsal midcingulate cortex. Our findings provide novel support for the hypothesis that repetition enhancement and associated stimulus-response learning may facilitate behavioral performance during problem solving. PMID:19366289

  13. Unintended Imitation in Nonword Repetition

    ERIC Educational Resources Information Center

    Kappes, Juliane; Baumgaertner, Annette; Peschke, Claudia; Ziegler, Wolfram

    2009-01-01

    Verbal repetition is conventionally considered to require motor-reproduction of only the phonologically relevant content of a perceived linguistic stimulus, while imitation of incidental acoustic properties of the stimulus is not an explicit part of this task. Exemplar-based theories of speech processing, however, would predict that imitation…

  14. Constructive and Unconstructive Repetitive Thought

    ERIC Educational Resources Information Center

    Watkins, Edward R.

    2008-01-01

    The author reviews research showing that repetitive thought (RT) can have constructive or unconstructive consequences. The main unconstructive consequences of RT are (a) depression, (b) anxiety, and (c) difficulties in physical health. The main constructive consequences of RT are (a) recovery from upsetting and traumatic events, (b) adaptive…

  15. De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements.

    PubMed

    Schlesinger, Felix; Smith, Andrew D; Gingeras, Thomas R; Hannon, Gregory J; Hodges, Emily

    2013-10-01

    Deep sequencing of mammalian DNA methylomes has uncovered a previously unpredicted number of discrete hypomethylated regions in intergenic space (iHMRs). Here, we combined whole-genome bisulfite sequencing data with extensive gene expression and chromatin-state data to define functional classes of iHMRs, and to reconstruct the dynamics of their establishment in a developmental setting. Comparing HMR profiles in embryonic stem and primary blood cells, we show that iHMRs mark an exclusive subset of active DNase hypersensitive sites (DHS), and that both developmentally constitutive and cell-type-specific iHMRs display chromatin states typical of distinct regulatory elements. We also observe that iHMR changes are more predictive of nearby gene activity than the promoter HMR itself, and that expression of noncoding RNAs within the iHMR accompanies full activation and complete demethylation of mature B cell enhancers. Conserved sequence features corresponding to iHMR transcript start sites, including a discernible TATA motif, suggest a conserved, functional role for transcription in these regions. Similarly, we explored both primate-specific and human population variation at iHMRs, finding that while enhancer iHMRs are more variable in sequence and methylation status than any other functional class, conservation of the TATA box is highly predictive of iHMR maintenance, reflecting the impact of sequence plasticity and transcriptional signals on iHMR establishment. Overall, our analysis allowed us to construct a three-step timeline in which (1) intergenic DHS are pre-established in the stem cell, (2) partial demethylation of blood-specific intergenic DHSs occurs in blood progenitors, and (3) complete iHMR formation and transcription coincide with enhancer activation in lymphoid-specified cells. PMID:23811145

  16. De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements

    PubMed Central

    Schlesinger, Felix; Smith, Andrew D.; Gingeras, Thomas R.; Hannon, Gregory J.; Hodges, Emily

    2013-01-01

    Deep sequencing of mammalian DNA methylomes has uncovered a previously unpredicted number of discrete hypomethylated regions in intergenic space (iHMRs). Here, we combined whole-genome bisulfite sequencing data with extensive gene expression and chromatin-state data to define functional classes of iHMRs, and to reconstruct the dynamics of their establishment in a developmental setting. Comparing HMR profiles in embryonic stem and primary blood cells, we show that iHMRs mark an exclusive subset of active DNase hypersensitive sites (DHS), and that both developmentally constitutive and cell-type-specific iHMRs display chromatin states typical of distinct regulatory elements. We also observe that iHMR changes are more predictive of nearby gene activity than the promoter HMR itself, and that expression of noncoding RNAs within the iHMR accompanies full activation and complete demethylation of mature B cell enhancers. Conserved sequence features corresponding to iHMR transcript start sites, including a discernible TATA motif, suggest a conserved, functional role for transcription in these regions. Similarly, we explored both primate-specific and human population variation at iHMRs, finding that while enhancer iHMRs are more variable in sequence and methylation status than any other functional class, conservation of the TATA box is highly predictive of iHMR maintenance, reflecting the impact of sequence plasticity and transcriptional signals on iHMR establishment. Overall, our analysis allowed us to construct a three-step timeline in which (1) intergenic DHS are pre-established in the stem cell, (2) partial demethylation of blood-specific intergenic DHSs occurs in blood progenitors, and (3) complete iHMR formation and transcription coincide with enhancer activation in lymphoid-specified cells. PMID:23811145

  17. 14. TYPICAL WORK DECK SHOWING RING SPACERS, CABLE DRUMS AND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    14. TYPICAL WORK DECK SHOWING RING SPACERS, CABLE DRUMS AND OTHER SPECIALIZED HARDWARE; VIEW TO SOUTH. - Cape Canaveral Air Station, Launch Complex 17, Facility 28416, East end of Lighthouse Road, Cape Canaveral, Brevard County, FL

  18. Repetitive DNA in eukaryotic genomes.

    PubMed

    Biscotti, Maria Assunta; Olmo, Ettore; Heslop-Harrison, J S Pat

    2015-09-01

    Repetitive DNA--sequence motifs repeated hundreds or thousands of times in the genome--makes up the major proportion of all the nuclear DNA in most eukaryotic genomes. However, the significance of repetitive DNA in the genome is not completely understood, and it has been considered to have both structural and functional roles, or perhaps even no essential role. High-throughput DNA sequencing reveals huge numbers of repetitive sequences. Most bioinformatic studies focus on low-copy DNA including genes, and hence, the analyses collapse repeats in assemblies presenting only one or a few copies, often masking out and ignoring them in both DNA and RNA read data. Chromosomal studies are proving vital to examine the distribution and evolution of sequences because of the challenges of analysis of sequence data. Many questions are open about the origin, evolutionary mode and functions that repetitive sequences might have in the genome. Some, the satellite DNAs, are present in long arrays of similar motifs at a small number of sites, while others, particularly the transposable elements (DNA transposons and retrotranposons), are dispersed over regions of the genome; in both cases, sequence motifs may be located at relatively specific chromosome domains such as centromeres or subtelomeric regions. Here, we overview a range of works involving detailed characterization of the nature of all types of repetitive sequences, in particular their organization, abundance, chromosome localization, variation in sequence within and between chromosomes, and, importantly, the investigation of their transcription or expression activity. Comparison of the nature and locations of sequences between more, and less, related species is providing extensive information about their evolution and amplification. Some repetitive sequences are extremely well conserved between species, while others are among the most variable, defining differences between even closely relative species. These data suggest

  19. Mitochondrial intergenic COII/tRNA(Lys) 9-bp deletion, a biomarker for hepatocellular carcinoma?

    PubMed

    Ren, Weihua; Li, Yawei; Li, Rui; Feng, Hongbo; Wu, Shuangting; Mao, Yuhui; Huang, Lei

    2016-07-01

    The COII/tRNA(Lys) intergenic 9-bp deletion is one of the most commonly studied human mitochondrial DNA (mtDNA) polymorphisms. It consists of the loss of one of two tandemly repeated copies of the sequence CCCCCTCTA from a non-coding region located between cytochrome oxidase II (COII) and tRNA(Lys) gene. Most recently, case-control studies have shown a positive association between this deletion with hepatocellular cancer. In this study, we first performed a detailed analysis between this deletion and clinical diseases; moreover, we took the phylogenetic approach to examine the pathogenicity status of 9-bp deletion. PMID:26017042

  20. Spacer process and alignment assessment for SADP process

    NASA Astrophysics Data System (ADS)

    Lattard, L.; McCallum, M.; Morton, R.; Fujiwara, T.; Makino, K.; Tokui, A.; Takahashi, N.; Sasamoto, S.

    2012-03-01

    Self Aligned Double Patterning (SADP) is now widely accepted as a viable technology for the further extension of 193nm immersion lithography towards the 22nm /18nm technology nodes. SADP was primary introduced for the manufacturing of flash memory due to its 1D design geometry. However, SADP is now becoming a main stream technology for advanced technology nodes for logic product. SADP results in alignment marks with reduced image contrast after completion of spacer patterning. Consequently there is an elevated risk that the alignment performance of the cut lithography layer on the spacer [1] may be negatively impacted. Initial studies indicate that it may be necessary to consider new mark designs. In this paper, we will evaluate different types of SADP processes with the alignment system of the Nikon S620D and S621D immersion scanner. We will discuss the performances and the differences observed due to the SADP materials. Included in this study is an intensive characterization of the morphology of the spacer after SADP process. We will use for this a 3D-AFM from Insight, and characterize the spacer profile of the spacer. Using a standard AFM microscope, we can characterize the surface roughness in the inner and the outer part of the wafer. The self aligned spacer process results in asymmetric spacers. Two types of surface (inside and outside) of the spacer are formed. The impact of this asymmetry is also assessed. The roughness difference, between the two parts, will play an important roll in the alignment contrast.

  1. Nuclear reactor spacer grid and ductless core component

    DOEpatents

    Christiansen, David W.; Karnesky, Richard A.

    1989-01-01

    The invention relates to a nuclear reactor spacer grid member for use in a liquid cooled nuclear reactor and to a ductless core component employing a plurality of these spacer grid members. The spacer grid member is of the egg-shell type and is constructed so that the walls of the cell members of the grid member are formed of a single thickness of metal to avoid tolerance problems. Within each cell member is a hydraulic spring which laterally constrains the nuclear material bearing rod which passes through each cell member against a hardstop in response to coolant flow through the cell member. This hydraulic spring is also suitable for use in a water cooled nuclear reactor. A core component constructed of, among other components, a plurality of these spacer grid members, avoids the use of a full length duct by providing spacer sleeves about the sodium tubes passing through the spacer grid members at locations between the grid members, thereby maintaining a predetermined space between adjacent grid members.

  2. Sidewall spacer optimization for steep switching junctionless transistors

    NASA Astrophysics Data System (ADS)

    Gupta, Manish; Kranti, Abhinav

    2016-06-01

    In this work, we analyze the impact of a high permittivity (high-κ) sidewall spacer and gate dielectric on the occurrence of sub-60 mV/decade subthreshold swing (S-swing) in symmetrical junctionless (JL) double gate (DG) transistors. It is shown that steep S-swing values (≤10 mV/decade) can be achieved in JL devices with a combination of a high permittivity (high-κ) gate dielectric and a narrow low permittivity (low-κ) sidewall spacer. Implementation of a wider high-κ spacer will diminish the degree of impact ionization by the influence of the fringing component of the gate electric field, and will not be useful for steep off-to-on current transition. A wider spacer with low-κ and a narrow spacer with high-κ permittivity will be useful to limit the latching effect that can occur at lower temperatures (250 K). For high temperature operation, the decrease in the impact ionization rate can be compensated by designing a JL transistor with a thicker silicon film. The work demonstrates opportunities to enhance impact ionization at sub bandgap voltages, and proposes optimal guidelines for selecting a sidewall spacer to facilitate steep switching in JL transistors.

  3. Autoclaved metal-on-cement spacer versus static spacer in two-stage revision in periprosthetic knee infection

    PubMed Central

    Chen, Yu-Pin; Wu, Cheng-Chun; Ho, Wei-Pin

    2016-01-01

    Background: Periprosthetic knee infection is troublesome for Orthopedic surgeons and a catastrophy for patients. Reported rates of periprosthetic joint infection following primary total knee arthroplasty (TKA) are 0.39–2%. Two stage revision arthroplasty, which has success rates exceeding 90%, has been the gold standard for treating subacute and chronic periprosthetic infection following TKA. Antibiotic spacers, a well established means of delivering local antibiotic therapy, maintain soft tissue tension during two stage revision arthroplasty. However, controversy remains around whether static or mobile antibiotic impregnated spacers are superior for treating infection following TKA. Various mobile spacers are available, including cement-on-cement, cement-on-polyethylene and metal-on-polyethylene. In this study, the efficacy of the modified metal-on-cement spacer, consisting of reinsertion of the autoclaved femoral component and implantation of antibiotic-loaded cement in the proximal tibia, is assessed. Materials and Methods: Records of 19 patients diagnosed as periprosthetic knee infection were reviewed in this retrospective study. Among these patients, 10 patients received first stage debridement with the autoclaved metal-on-cement spacer and 8 patients with the static spacer, who eventually underwent two-stage re-implantation, were listed in the final comparison. Patient demographics, infection eradication rates, average range of motion (ROM), surgical time and blood loss during the second-stage of the surgery, and Knee Society (KS) knee scores at last followup after revision total knee replacement were clinically evaluated. Results: At a minimum of 2-year followup after re-implantation, infection eradication rates, surgical times, blood loss during the second-stage of the surgery, and KS knee score after re-implantation were similar for the two groups. Patients receiving autoclaved metal-on-cement spacers had superior ROM after re-implantation compared to

  4. The CASC15 Long Intergenic Noncoding RNA Locus Is Involved in Melanoma Progression and Phenotype Switching.

    PubMed

    Lessard, Laurent; Liu, Michelle; Marzese, Diego M; Wang, Hongwei; Chong, Kelly; Kawas, Neal; Donovan, Nicholas C; Kiyohara, Eiji; Hsu, Sandy; Nelson, Nellie; Izraely, Sivan; Sagi-Assif, Orit; Witz, Isaac P; Ma, Xiao-Jun; Luo, Yuling; Hoon, Dave S B

    2015-10-01

    In recent years, considerable advances have been made in the characterization of protein-coding alterations involved in the pathogenesis of melanoma. However, despite their growing implication in cancer, little is known about the role of long noncoding RNAs in melanoma progression. We hypothesized that copy number alterations (CNAs) of intergenic nonprotein-coding domains could help identify long intergenic noncoding RNAs (lincRNAs) associated with metastatic cutaneous melanoma. Among several candidates, our approach uncovered the chromosome 6p22.3 CASC15 (cancer susceptibility candidate 15) lincRNA locus as a frequently gained genomic segment in metastatic melanoma tumors and cell lines. The locus was actively transcribed in metastatic melanoma cells, and upregulation of CASC15 expression was associated with metastatic progression to brain metastasis in a mouse xenograft model. In clinical specimens, CASC15 levels increased during melanoma progression and were independent predictors of disease recurrence in a cohort of 141 patients with AJCC (American Joint Committee on Cancer) stage III lymph node metastasis. Moreover, small interfering RNA (siRNA) knockdown experiments revealed that CASC15 regulates melanoma cell phenotype switching between proliferative and invasive states. Accordingly, CASC15 levels correlated with known gene signatures corresponding to melanoma proliferative and invasive phenotypes. These findings support a key role for CASC15 in metastatic melanoma. PMID:26016895

  5. De Novo Identification of Regulatory Regions in Intergenic Spaces of Prokaryotic Genomes

    SciTech Connect

    Chain, P; Garcia, E; Mcloughlin, K; Ovcharenko, I

    2007-02-20

    This project was begun to implement, test, and experimentally validate the results of a novel algorithm for genome-wide identification of candidate transcription-factor binding sites in prokaryotes. Most techniques used to identify regulatory regions rely on conservation between different genomes or have a predetermined sequence motif(s) to perform a genome-wide search. Therefore, such techniques cannot be used with new genome sequences, where information regarding such motifs has not yet been discovered. This project aimed to apply a de novo search algorithm to identify candidate binding-site motifs in intergenic regions of prokaryotic organisms, initially testing the available genomes of the Yersinia genus. We retrofitted existing nucleotide pattern-matching algorithms, analyzed the candidate sites identified by these algorithms as well as their target genes to screen for meaningful patterns. Using properly annotated prokaryotic genomes, this project aimed to develop a set of procedures to identify candidate intergenic sites important for gene regulation. We planned to demonstrate this in Yersinia pestis, a model biodefense, Category A Select Agent pathogen, and then follow up with experimental evidence that these regions are indeed involved in regulation. The ability to quickly characterize transcription-factor binding sites will help lead to a better understanding of how known virulence pathways are modulated in biodefense-related organisms, and will help our understanding and exploration of regulons--gene regulatory networks--and novel pathways for metabolic processes in environmental microbes.

  6. Diversity of Salmonella Strains Isolated from the Aquatic Environment as Determined by Serotyping and Amplification of the Ribosomal DNA Spacer Regions

    PubMed Central

    Baudart, Julia; Lemarchand, Karine; Brisabois, Anne; Lebaron, Philippe

    2000-01-01

    Salmonella species are pathogenic bacteria often detected in sewage, freshwater, marine coastal water, and groundwater. Salmonella spp. can survive for long periods in natural waters, and the persistence of specific and epidemic strains is of great concern in public health. However, the diversity of species found in the natural environment remains unknown. The aim of this study was to investigate the diversity of Salmonella strains isolated from different natural aquatic systems within a Mediterranean coastal watershed (river, wastewater, and marine coastal areas). A total of 574 strains isolated from these natural environments were identified by both conventional serotyping and the ribosomal spacer-heteroduplex polymorphism (RS-HP) method (M. A. Jensen and N. Straus, PCR Methods Appl. 3:186–194, 1993). More than 40 different serotypes were found, and some serotypes probably mobilized from widespread animal-rearing activities were detected only during storm events. These serotypes may be good indicators of specific contamination sources. Furthermore, the RS-HP method based on the PCR amplification of the intergenic spacer region between the 16S and 23S rRNA genes can produce amplicon profiles allowing the discrimination of species at both serotype and intraserotype levels. This method represents a powerful tool that could be used for rapid typing of Salmonella isolates. PMID:10742240

  7. Cultivar-level phylogeny using chloroplast DNA barcode psbK-psbI spacers for identification of Emirati date palm (Phoenix dactylifera L.) varieties.

    PubMed

    Enan, M R; Ahmed, A

    2016-01-01

    The efficacy of genetic material for use as DNA barcodes is under constant evaluation and improvement as new barcodes offering better resolution and efficiency of amplification for specific species groups are identified. In this study, the chloroplast intergenic spacer psbK-psbI was evaluated for the first time as a DNA barcode for distinguishing date palm cultivars. Nucleotide sequences were aligned using MEGA 6.0 to calculate pairwise divergence among the cultivars. The analyzed data illustrated a considerable level of variability in the genetic pool of the selected cultivars (0.009). In fact, five haplotypes were detected among 30 cultivars examined, yielding a haplotype diversity of 0.685. An unweighted pair group method with arithmetic mean phylogenetic tree was constructed and shows a well-defined relationship among date palm cultivar varieties. On the other hand, selective neutrality investigations using Tajima test and Fu and Li tests were negative, providing evidence that date palm has been undergoing rapid expansion and recent population growth. Thus, we suggest that the psbK-psbI spacer can be successfully used to construct reliable phylogenetic trees for P. dactylifera. PMID:27525916

  8. Chromosome specific repetitive DNA sequences

    DOEpatents

    Moyzis, Robert K.; Meyne, Julianne

    1991-01-01

    A method is provided for determining specific nucleotide sequences useful in forming a probe which can identify specific chromosomes, preferably through in situ hybridization within the cell itself. In one embodiment, chromosome preferential nucleotide sequences are first determined from a library of recombinant DNA clones having families of repetitive sequences. Library clones are identified with a low homology with a sequence of repetitive DNA families to which the first clones respectively belong and variant sequences are then identified by selecting clones having a pattern of hybridization with genomic DNA dissimilar to the hybridization pattern shown by the respective families. In another embodiment, variant sequences are selected from a sequence of a known repetitive DNA family. The selected variant sequence is classified as chromosome specific, chromosome preferential, or chromosome nonspecific. Sequences which are classified as chromosome preferential are further sequenced and regions are identified having a low homology with other regions of the chromosome preferential sequence or with known sequences of other family me This invention is the result of a contract with the Department of Energy (Contract No. W-7405-ENG-36).

  9. Molecular Profiling of Microbial Communities from Contaminated Sources: Use of Subtractive Cloning Methods and rDNA Spacer Sequences

    SciTech Connect

    Robb, Frank T.

    2001-04-10

    The major objective of this research was to provide appropriate sequences and assemble a DNA array of oligonucleotides to be used for rapid profiling of microbial populations from polluted areas and other areas of interest. The sequences to be assigned to the DNA array were chosen from cloned genomic DNA taken from groundwater sites having well characterized pollutant histories at Hanford Nuclear Plant and Lawrence Livermore Site 300. Glass-slide arrays were made and tested; and a new multiplexed, bead-based method was developed that uses nucleic acid hybridization on the surface of microscopic polystyrene spheres to identify specific sequences in heterogeneous mixtures of DNA sequences. The test data revealed considerable strain variation between sample sites showing a striking distribution of sequences. It also suggests that diversity varies greatly with bioremediation, and that there are many bacterial intergenic spacer region sequences that can indicate its effects. The bead method exhibited superior sequence discrimination and has features for easier and more accurate measurement.

  10. Genome-Wide Analyses in Bacteria Show Small-RNA Enrichment for Long and Conserved Intergenic Regions

    PubMed Central

    Tsai, Chen-Hsun; Liao, Rick; Chou, Brendan; Palumbo, Michael

    2014-01-01

    Interest in finding small RNAs (sRNAs) in bacteria has significantly increased in recent years due to their regulatory functions. Development of high-throughput methods and more sophisticated computational algorithms has allowed rapid identification of sRNA candidates in different species. However, given their various sizes (50 to 500 nucleotides [nt]) and their potential genomic locations in the 5′ and 3′ untranslated regions as well as in intergenic regions, identification and validation of true sRNAs have been challenging. In addition, the evolution of bacterial sRNAs across different species continues to be puzzling, given that they can exert similar functions with various sequences and structures. In this study, we analyzed the enrichment patterns of sRNAs in 13 well-annotated bacterial species using existing transcriptome and experimental data. All intergenic regions were analyzed by WU-BLAST to examine conservation levels relative to species within or outside their genus. In total, more than 900 validated bacterial sRNAs and 23,000 intergenic regions were analyzed. The results indicate that sRNAs are enriched in intergenic regions, which are longer and more conserved than the average intergenic regions in the corresponding bacterial genome. We also found that sRNA-coding regions have different conservation levels relative to their flanking regions. This work provides a way to analyze how noncoding RNAs are distributed in bacterial genomes and also shows conserved features of intergenic regions that encode sRNAs. These results also provide insight into the functions of regions surrounding sRNAs and into optimization of RNA search algorithms. PMID:25313390

  11. Species markers for equine strongyles detected in intergenic rDNA by PCR-RFLP.

    PubMed

    Gasser, R B; Stevenson, L A; Chilton, N B; Nansen, P; Bucknell, D G; Beveridge, I

    1996-10-01

    Five species of equine strongyle belonging to the subfamily Strongylinae (Strongylus edentatus, S. equinus, S. vulgaris, Oesophagodontus robustus and Triodontophorus serratus) and 11 species belonging to the subfamily Cyathostominae (Poteriostomum imparidentatum, P. ratzii, Cylicocyclus insignis, Cc. leptostomus, Cc. nassatus, Cylicostephanus calicatus, Cs. longibursatus, Cs. goldi, Cyathostomum catinatum, Cy. labiatum and Cy. pateratum) were characterized using a polymerase chain reaction-linked restriction fragment length polymorphism technique (PCR-RFLP). Internal transcribed spacer ribosomal DNA was amplified from genomic DNA by polymerase chain reaction (PCR) using conserved primers, digested separately with six restriction endonucleases (AluI, BfaI, CfoI, Hae III, VSpI and XbaI) and the fragments separated by agarose gel electrophoresis. The PCR products of the three Strongylus species were approx. 90-100 bp smaller in size compared with those of the other 13 species. The PCR-RFLP analysis of the rDNA region spanning the first and second internal transcribed spacers plus the 5.85 rDNA gene (ITS+) produced characteristic patterns for each of the 16 species examined, and no variation in RFLP patterns was detected within the species Cy. catinatum, where multiple isolates were analysed. The study demonstrates that the internal transcribed spacer sequences provide genetic markers for the species identification of a range of equine strongyles. These markers will be of use for the identification of egg and larval stages, where morphological characters alone are unreliable. The results also indicate that the spacer sequences will be of use to study the systematics of equine strongyles. PMID:8910892

  12. Space Station Long Spacer Element begins processing at KSC

    NASA Technical Reports Server (NTRS)

    1998-01-01

    The Long Spacer, a component of the International Space Station, arrives and is moved to its test stand in the northeast corner of the high bay in KSC's Space Station Processing Facility. The Long Spacer provides structural support for the outboard Photovoltaic Modules that supply power to the station. Now just a structure, the Long Spacer will have attached to it as part of processing a heat dissipation radiator and two Pump and Flow Control subassemblies that circulate ammonia to cool the solar array electronics. Also to be mounted are ammonia fluid lines as part of the cooling system and the cabling necessary for power and control of the station. The Long Spacer becomes an integral part of a station truss segment when it is mated with the Integrated Equipment Assembly, which stores the electrical power generated by the solar arrays for use by the station modules. The Long Spacer is being processed in preparation for STS-97, currently planned for launch aboard Discovery in April 1999.

  13. Gas-insulated substation spacer surface degradation analysis

    SciTech Connect

    Chu, F.Y.; Braun, J.M. )

    1990-06-01

    The objective of the project was to develop surface analysis techniques which can correlate the performance of spacers in SF{sub 6} insulated switchgear with changes in their dielectric and chemical characteristics after exposure to SF{sub 6} arcing byproducts and low energy flashovers. Critical material parameters responsible for spacer performance were investigated by optical and scanning electron microscopy, electron spectroscopy for chemical analysis, thermogravimetric analysis and electrical surface resistance measurements. Results related to arc byproduct resistance and tracking resistance of seven types of filled epoxy spacer materials are presented. Degradation mechanisms have been proposed to explain the differing material behaviour. The study shows that the interaction of certain types of filler and resin systems with the SF{sub 6} spark and the decomposed gas is responsible for the degradation in impulse withstand performance. A practical technique using surface electrical resistance to detect degraded spacer after exposure to large quantities of arc byproducts has been developed and the construction of a probe for spacer surface assessment was described. 15 refs., 28 figs., 8 tabs.

  14. Impact of spacer thickness on biofouling in forward osmosis.

    PubMed

    Valladares Linares, R; Bucs, Sz S; Li, Z; AbuGhdeeb, M; Amy, G; Vrouwenvelder, J S

    2014-06-15

    Forward osmosis (FO) indirect desalination systems integrate wastewater recovery with seawater desalination. Niche applications for FO systems have been reported recently, due to the demonstrated advantages compared to conventional high-pressure membrane processes such as nanofiltration (NF) and reverse osmosis (RO). Among them, wastewater recovery has been identified to be particularly suitable for practical applications. However, biofouling in FO membranes has rarely been studied in applications involving wastewater effluents. Feed spacers separating the membrane sheets in cross-flow systems play an important role in biofilm formation. The objective of this study was to determine the influence of feed spacer thickness (28, 31 and 46 mil) on biofouling development and membrane performance in a FO system, using identical cross-flow cells in parallel studies. Flux development, biomass accumulation, fouling localization and composition were determined and analyzed. For all spacer thicknesses, operated at the same feed flow and the same run time, the same amount of biomass was found, while the flux reduction decreased with thicker spacers. These observations are in good agreement with biofouling studies for RO systems, considering the key differences between FO and RO. Our findings contradict previous cross-flow studies on particulate/colloidal fouling, where higher cross-flow velocities improved system performance. Thicker spacers reduced the impact of biofouling on FO membrane flux. PMID:24726992

  15. [Prostate-rectum spacers: optimization of prostate cancer irradiation].

    PubMed

    Zilli, T; Benz, E; Miralbell, R

    2014-06-01

    In the curative radiotherapy of localized prostate cancer, improvements in biochemical control observed with dose escalation have been counterbalanced by an increase in radiation-induced toxicity. The injection of biodegradable spacers between prostate and rectum represents a new frontier in the optimization of radiotherapy treatments for patients with localized disease. Transperineal injection of different types of spacers under transrectal ultrasound guidance allows creating a 7-to-20 mm additional space between the prostate and the anterior rectal wall lasting 3 to 12 months. Dosimetrically, a relative reduction in the rectal volume receiving at least 70 Gy (V70) in the order of 43% to 84% is observed with all types of spacers, regardless of the radiotherapy technique used. Preliminary clinical results show for all spacers a good tolerance and a possible reduction in the acute side effects rate. The aim of the present systematic review of the literature is to report on indications as well as dosimetric and clinical advantages of the different types of prostate-rectum spacers commercially available (hydrogel, hyaluronic acid, collagen, biodegradable balloon). PMID:24746454

  16. Genetic Diversity of Food-Isolated Salmonella Strains through Pulsed Field Gel Electrophoresis (PFGE) and Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR)

    PubMed Central

    Fendri, Imen; Ben Hassena, Amal; Grosset, Noel; Barkallah, Mohamed; Khannous, Lamia; Chuat, Victoria; Gautier, Michel; Gdoura, Radhouane

    2013-01-01

    All over the world, the incidence of Salmonella spp contamination on different food sources like broilers, clams and cow milk has increased rapidly in recent years. The multifaceted properties of Salomnella serovars allow the microorganism to grow and multiply in various food matrices, even under adverse conditions. Therefore, methods are needed to detect and trace this pathogen along the entire food supply network. In the present work, PFGE and ERIC-PCR were used to subtype 45 Salmonella isolates belonging to different serovars and derived from different food origins. Among these isolates, S. Enteritidis and S. Kentucky were found to be the most predominant serovars. The Discrimination Index obtained by ERIC-PCR (0.85) was slightly below the acceptable confidence value. The best discriminatory ability was observed when PFGE typing method was used alone (DI = 0.94) or combined with ERIC-PCR (DI = 0.93). A wide variety of profiles was observed between the different serovars using PFGE or/and ERIC-PCR. This diversity is particularly important when the sample origins are varied and even within the same sampling origin. PMID:24312546

  17. Wheeze in childhood: is the spacer good enough?

    PubMed Central

    Rajkumar, Veena; Rajendra, Barathi; How, Choon How; Ang, Seng Bin

    2014-01-01

    Max was treated with SABA using an MDI and spacer with facemask and responded well to the initial treatment. You explained to the parents that nebulisers are neither required nor recommended in the treatment of wheezing in their child’s situation. You advised the parents on the proper technique of MDI use with spacer and facemask, as well as care of the equipment. You also gave them a clearly written action plan regarding the efficient management of the next episode of wheeze with MDI and spacer. You further explained the side effects of oral bronchodilators and nebulisers, and why you refrained from using them. Max was given a follow-up appointment to assess his progress, and his parents were advised on the situations when they should go to a doctor or the emergency department. PMID:25631964

  18. Spacer effect on nanostructures and self-assembly in organogels via some bolaform cholesteryl imide derivatives with different spacers

    PubMed Central

    2013-01-01

    In this paper, new bolaform cholesteryl imide derivatives with different spacers were designed and synthesized. Their gelation behaviors in 23 solvents were investigated, and some of them were found to be low molecular mass organic gelators. The experimental results indicated that these as-formed organogels can be regulated by changing the flexible/rigid segments in spacers and organic solvents. Suitable combination of flexible/rigid segments in molecular spacers in the present cholesteryl gelators is favorable for the gelation of organic solvents. Scanning electron microscopy and atomic force microscopy observations revealed that the gelator molecules self-assemble into different aggregates, from wrinkle and belt to fiber with the change of spacers and solvents. Spectral studies indicated that there existed different H-bond formations between imide groups and assembly modes, depending on the substituent spacers in molecular skeletons. The present work may give some insight into the design and character of new organogelators and soft materials with special molecular structures. PMID:24083361

  19. Circuit considerations for repetitive railguns

    SciTech Connect

    Honih, E.M.

    1986-01-01

    Railgun electromagnetic launchers have significant military and scientific potential. They provide direct conversion of electrical energy to projectile kinetic energy, and they offer the hope of achieving projectile velocities greatly exceeding the limits of conventional guns. With over 10 km/sec already demonstrated, railguns are attracting attention for tactical and strategic weapons systems and for scientific equation-of-state research. The full utilization of railguns will require significant improvements in every aspect of system design - projectile, barrel, and power source - to achieve operation on a large scale. This paper will review fundamental aspects of railguns, with emphasis on circuit considerations and repetitive operation.

  20. Use of the Coat Protein (CP) and minor CP Intergene Sequence to Discriminate Severe Strains of Citrus tristeza virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A rapid assay is a needed to differentiate mild vs severe strains of Citrus tristeza virus (CTV). Multiple alignment performed on the coat protein (CP) and the minor coat protein (CPm) intergene sequences (~80-100 bp) from different CTV isolates revealed that severe strains generally associated wit...

  1. Intergenic Sequence Ribotyping using a region neighboring dkgB links genovar to Kauffman-White serotype of Salmonella enterica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Intergenic Sequence Ribotyping using a region neighboring dkgB links genovar to Kauffman-White serotype of Salmonella enterica Previous research identified that the 5S ribosomal (rrn) gene and associated flanking sequences that are closely linked to the dkgB gene of Salmonella enterica were highly ...

  2. Intergenic Sequence Ribotyping using a region neighboring dkgB links genovar to Kauffman-White serotype of Salmonella enterica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thirty six (36) unique sequences which varied in length from 258bp to 530bp were found for Salmonella enterica strains and isolates that are not present in public databases following BLAST analysis searches for similarity. The sequences were found by application of Intergenic Sequence Ribotyping (IS...

  3. Neuroimaging in repetitive brain trauma

    PubMed Central

    2014-01-01

    Sports-related concussions are one of the major causes of mild traumatic brain injury. Although most patients recover completely within days to weeks, those who experience repetitive brain trauma (RBT) may be at risk for developing a condition known as chronic traumatic encephalopathy (CTE). While this condition is most commonly observed in athletes who experience repetitive concussive and/or subconcussive blows to the head, such as boxers, football players, or hockey players, CTE may also affect soldiers on active duty. Currently, the only means by which to diagnose CTE is by the presence of phosphorylated tau aggregations post-mortem. Non-invasive neuroimaging, however, may allow early diagnosis as well as improve our understanding of the underlying pathophysiology of RBT. The purpose of this article is to review advanced neuroimaging methods used to investigate RBT, including diffusion tensor imaging, magnetic resonance spectroscopy, functional magnetic resonance imaging, susceptibility weighted imaging, and positron emission tomography. While there is a considerable literature using these methods in brain injury in general, the focus of this review is on RBT and those subject populations currently known to be susceptible to RBT, namely athletes and soldiers. Further, while direct detection of CTE in vivo has not yet been achieved, all of the methods described in this review provide insight into RBT and will likely lead to a better characterization (diagnosis), in vivo, of CTE than measures of self-report. PMID:25031630

  4. Molecular Analysis of Promoter and Intergenic Region Attenuator of the Vibrio vulnificus prx1ahpF Operon.

    PubMed

    Lee, Hyun Sung; Lim, Jong Gyu; Han, Kook; Lee, Younghoon; Choi, Sang Ho

    2015-08-01

    Prx1, an AhpF-dependent 2-Cys peroxiredoxin (Prx), was previously identified in Vibrio vulnificus, a facultative aerobic pathogen. In the present study, transcription of the V. vulnificus prx1ahpF genes, which are adjacently located on the chromosome, was evaluated by analyzing the promoter and intergenic region of the two genes. Northern blot analyses revealed that transcription of prx1ahpF results in two transcripts, the prx1 and prx1ahpF transcripts. Primer extension analysis and a point mutational analysis of the promoter region showed that the two transcripts are generated from a single promoter. In addition, the 3' end of the prx1 transcript at the prx1ahpF intergenic region was determined by a 3'RACE assay. These results suggested that the prx1ahpF genes are transcribed as an operon, and the prx1 transcript was produced by transcriptional termination in the intergenic region. RNA secondary structure prediction of the prx1ahpF intergenic region singled out a stem-loop structure without poly(U) tract, and a deletion analysis of the intergenic region showed that the atypical stem-loop structure acts as the transcriptional attenuator to result in the prx1 and prx1ahpF transcripts. The combined results demonstrate that the differential expression of prx1 and ahpF is accomplished by the cis-acting transcriptional attenuator located between the two genes and thereby leads to the production of a high level of Prx1 and a low level of AhpF. PMID:25824432

  5. CRISPR interference and priming varies with individual spacer sequences

    PubMed Central

    Xue, Chaoyou; Seetharam, Arun S.; Musharova, Olga; Severinov, Konstantin; J. Brouns, Stan J.; Severin, Andrew J.; Sashital, Dipali G.

    2015-01-01

    CRISPR–Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring ‘spacer’ sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destruction through CRISPR interference. Mutations in the protospacer adjacent motif (PAM) and seed regions block interference but promote rapid ‘primed’ adaptation. Here, we use multiple spacer sequences to reexamine the PAM and seed sequence requirements for interference and priming in the Escherichia coli Type I-E CRISPR–Cas system. Surprisingly, CRISPR interference is far more tolerant of mutations in the seed and the PAM than previously reported, and this mutational tolerance, as well as priming activity, is highly dependent on spacer sequence. We identify a large number of functional PAMs that can promote interference, priming or both activities, depending on the associated spacer sequence. Functional PAMs are preferentially acquired during unprimed ‘naïve’ adaptation, leading to a rapid priming response following infection. Our results provide numerous insights into the importance of both spacer and target sequences for interference and priming, and reveal that priming is a major pathway for adaptation during initial infection. PMID:26586800

  6. Filter holder assembly having extended collar spacer ring

    DOEpatents

    Alvin, Mary Anne; Bruck, Gerald J.

    2002-01-01

    A filter holder assembly is provided that utilizes a fail-safe regenerator unit with an annular spacer ring having an extended metal collar for containment and positioning of a compliant ceramic gasket used in the assembly. The filter holder assembly is disclosed for use with advanced composite, filament wound, and metal candle filters.

  7. Modeling repetitive, non-globular proteins.

    PubMed

    Basu, Koli; Campbell, Robert L; Guo, Shuaiqi; Sun, Tianjun; Davies, Peter L

    2016-05-01

    While ab initio modeling of protein structures is not routine, certain types of proteins are more straightforward to model than others. Proteins with short repetitive sequences typically exhibit repetitive structures. These repetitive sequences can be more amenable to modeling if some information is known about the predominant secondary structure or other key features of the protein sequence. We have successfully built models of a number of repetitive structures with novel folds using knowledge of the consensus sequence within the sequence repeat and an understanding of the likely secondary structures that these may adopt. Our methods for achieving this success are reviewed here. PMID:26914323

  8. Constructive and Unconstructive Repetitive Thought

    PubMed Central

    Watkins, Edward R.

    2008-01-01

    The author reviews research showing that repetitive thought (RT) can have constructive or unconstructive consequences. The main unconstructive consequences of RT are (a) depression, (b) anxiety, and (c) difficulties in physical health. The main constructive consequences of RT are (a) recovery from upsetting and traumatic events, (b) adaptive preparation and anticipatory planning, (c) recovery from depression, and (d) uptake of health-promoting behaviors. Several potential principles accounting for these distinct consequences of RT are identified within this review: (a) the valence of thought content, (b) the intrapersonal and situational context in which RT occurs, and (c) the level of construal (abstract vs. concrete processing) adopted during RT. Of the existing models of RT, it is proposed that an elaborated version of the control theory account provides the best theoretical framework to account for its distinct consequences. PMID:18298268

  9. Pressure rig for repetitive casting

    NASA Technical Reports Server (NTRS)

    Vasquez, Peter (Inventor); Hutto, William R. (Inventor); Philips, Albert R. (Inventor)

    1989-01-01

    The invention is a pressure rig for repetitive casting of metal. The pressure rig performs like a piston for feeding molten metal into a mold. Pressure is applied to an expandable rubber diaphragm which expands like a balloon to force the metal into the mold. A ceramic cavity which holds molten metal is lined with blanket-type insulating material, necessitating only a relining for subsequent use and eliminating the lengthy cavity preparation inherent in previous rigs. In addition, the expandable rubber diaphragm is protected by the insulating material thereby decreasing its vulnerability to heat damage. As a result of the improved design the life expectancy of the pressure rig contemplated by the present invention is more than doubled. Moreover, the improved heat protection has allowed the casting of brass and other alloys with higher melting temperatures than possible in the conventional pressure rigs.

  10. Information Density and Syntactic Repetition.

    PubMed

    Temperley, David; Gildea, Daniel

    2015-11-01

    In noun phrase (NP) coordinate constructions (e.g., NP and NP), there is a strong tendency for the syntactic structure of the second conjunct to match that of the first; the second conjunct in such constructions is therefore low in syntactic information. The theory of uniform information density predicts that low-information syntactic constructions will be counterbalanced by high information in other aspects of that part of the sentence, and high-information constructions will be counterbalanced by other low-information components. Three predictions follow: (a) lexical probabilities (measured by N-gram probabilities and head-dependent probabilities) will be lower in second conjuncts than first conjuncts; (b) lexical probabilities will be lower in matching second conjuncts (those whose syntactic expansions match the first conjunct) than nonmatching ones; and (c) syntactic repetition should be especially common for low-frequency NP expansions. Corpus analysis provides support for all three of these predictions. PMID:25557056

  11. [Repetitive DNA sequences as an indicator of the level of genetic isolation in fish].

    PubMed

    Shubina, E A; Ponomareva, E V; Klimov, A V; Klimova, A V; Kedrova, O S

    2015-01-01

    Although the functional role is still unknown for most types of nuclear noncoding repetitive sequences, some of them proved to provide adequate phylogenetic and taxonomic markers for studying the genetic relationships of organisms at the species and within-species levels. Several markers were used in this work. First, microsatellite markers were used to examine populations varying in the extent of genetic subdivision in marine and anadromous fish, including the Chilean jack mackerel Trachurus murphyi, anadromous brown trout Salmo trutta, and isolated and anadromous char populations. Locus polymorphism was proportional to the gene flow between populations in all cases. Second, satellite DNA was used to study the phylogenetic relationships within the genera Salmo, Oncorhynchus, Salvelinus, and Coregonus. Genetic distances agreed well with the taxonomic relationships based on morphological traits and various biochemical markers and correlated with the evolutionary ages estimated for the groups by other markers. Third, RAPD PCR with a set of 20-mer primers was performed to study the genus Coregonus and anadromous and isolated populations and species of the genus Salvelinus. The resulting phylogenetic trees may help to resolve some disputable taxonomic issues for the groups. A comparison showed that several RAPD-detected sequences contain conserved fragments of coding sequences and polymorphic repeats (minisatellites) from intergenic regions or introns. The finding point to a nonrandom nature of repetitive DNA divergence and may reflect the evolution of the fish groups examined. Heterochromatic satellite repeats were assumed to contribute to generating a reproductive barrier. PMID:26107893

  12. Effects of spacer length and terminal group on the crystallization and morphology of biscarbamates: a longer spacer does not reduce the melting temperature.

    PubMed

    Khan, Mostofa Kamal; Sundararajan, Pudupadi R

    2013-05-01

    The effects of alkyl side chain and spacer lengths and the type of terminal group on the morphology and crystallization of a homologous series of biscarbamates (model compounds for polyurethanes) were investigated. Biscarbamates were synthesized with alkyl side chains of various lengths ranging from C4 to C18 and an alkyl spacer group with 12 CH2 units (C12 spacer) between the two hydrogen bonding motifs. The crystallization and morphological features are compared with the previously studied biscarbamates with a C6 spacer. As a token example, we also studied a biscarbamate molecule in which the terminal methyl group was replaced by a phenyl group. We stress four important conclusions of the study: (1) A number of studies in the literature found that the longer alkyl spacers reduced the thermal transition temperatures of the molecules, and such behavior was attributed to an increase in the flexibility of the alkyl spacer. However, the results of the present study are to the contrary. With the biscarbamates studied here, the hydrogen-bonding groups on both sides of the C12 spacer act as "anchors", and the longer spacer does not reduce the melting temperatures compared with those with the C6 spacer. (2) The melt viscosity measurements show shear-thinning behavior, which has been mostly observed with polysaccharides and hydrogen-bonded polymers. (3) Avrami analysis shows a two-stage crystallization, which is not commonly observed in organic small molecule systems. (4) The phenyl end group does not add another self-assembly code in terms of π-stacking but acts as a defect. While formation of crystals was observed for biscarbamates with short alkyl side chains with a C6 spacer, an increase in spacer length to C12 induces spherulitic morphology. Although the overall sizes of the spherulites are the same for both spacers, the rate of spherulite growth was higher and the crystallization rate was lower with the C12 spacer compared with the C6 spacer. In contrast with the

  13. A Nonword Repetition Task for Speakers with Misarticulations: The Syllable Repetition Task (SRT)

    ERIC Educational Resources Information Center

    Shriberg, Lawrence D.; Lohmeier, Heather L.; Campbell, Thomas F.; Dollaghan, Christine A.; Green, Jordan R.; Moore, Christopher A.

    2009-01-01

    Purpose: Conceptual and methodological confounds occur when non(sense) word repetition tasks are administered to speakers who do not have the target speech sounds in their phonetic inventories or who habitually misarticulate targeted speech sounds. In this article, the authors (a) describe a nonword repetition task, the Syllable Repetition Task…

  14. Socio-Economic Status Affects Sentence Repetition, but Not Non-Word Repetition, in Chilean Preschoolers

    ERIC Educational Resources Information Center

    Balladares, Jaime; Marshall, Chloë; Griffiths, Yvonne

    2016-01-01

    Sentence repetition and non-word repetition tests are widely used measures of language processing which are sensitive to language ability. Surprisingly little previous work has investigated whether children's socio-economic status (SES) affects their sentence and non-word repetition accuracy. This study investigates sentence and non-word…

  15. Serial Position Effects in Nonword Repetition

    ERIC Educational Resources Information Center

    Gupta, P.; Lipinski, J.; Abbs, B.; Lin, P.H.

    2005-01-01

    A growing body of research has emphasized the linkage between performance in immediate serial recall of lists, nonword repetition, and word learning. Recently, it has been reported that primacy and recency effects are obtained in repetition of individual syllables within nonwords (Gupta, in press). Five experiments examined whether such…

  16. Disruption of a Large Intergenic Noncoding RNA in Subjects with Neurodevelopmental Disabilities

    PubMed Central

    Talkowski, Michael E.; Maussion, Gilles; Crapper, Liam; Rosenfeld, Jill A.; Blumenthal, Ian; Hanscom, Carrie; Chiang, Colby; Lindgren, Amelia; Pereira, Shahrin; Ruderfer, Douglas; Diallo, Alpha B.; Lopez, Juan Pablo; Turecki, Gustavo; Chen, Elizabeth S.; Gigek, Carolina; Harris, David J.; Lip, Va; An, Yu; Biagioli, Marta; MacDonald, Marcy E.; Lin, Michael; Haggarty, Stephen J.; Sklar, Pamela; Purcell, Shaun; Kellis, Manolis; Schwartz, Stuart; Shaffer, Lisa G.; Natowicz, Marvin R.; Shen, Yiping; Morton, Cynthia C.; Gusella, James F.; Ernst, Carl

    2012-01-01

    Large intergenic noncoding (linc) RNAs represent a newly described class of ribonucleic acid whose importance in human disease remains undefined. We identified a severely developmentally delayed 16-year-old female with karyotype 46,XX,t(2;11)(p25.1;p15.1)dn in the absence of clinically significant copy number variants (CNVs). DNA capture followed by next-generation sequencing of the translocation breakpoints revealed disruption of a single noncoding gene on chromosome 2, LINC00299, whose RNA product is expressed in all tissues measured, but most abundantly in brain. Among a series of additional, unrelated subjects referred for clinical diagnostic testing who showed CNV affecting this locus, we identified four with exon-crossing deletions in association with neurodevelopmental abnormalities. No disruption of the LINC00299 coding sequence was seen in almost 14,000 control subjects. Together, these subjects with disruption of LINC00299 implicate this particular noncoding RNA in brain development and raise the possibility that, as a class, abnormalities of lincRNAs may play a significant role in human developmental disorders. PMID:23217328

  17. In silico prediction of long intergenic non-coding RNAs in sheep.

    PubMed

    Bakhtiarizadeh, Mohammad Reza; Hosseinpour, Batool; Arefnezhad, Babak; Shamabadi, Narges; Salami, Seyed Alireza

    2016-04-01

    Long non-coding RNAs (lncRNAs) are transcribed RNA molecules >200 nucleotides in length that do not encode proteins and serve as key regulators of diverse biological processes. Recently, thousands of long intergenic non-coding RNAs (lincRNAs), a type of lncRNAs, have been identified in mammalians using massive parallel large sequencing technologies. The availability of the genome sequence of sheep (Ovis aries) has allowed us genomic prediction of non-coding RNAs. This is the first study to identify lincRNAs using RNA-seq data of eight different tissues of sheep, including brain, heart, kidney, liver, lung, ovary, skin, and white adipose. A computational pipeline was employed to characterize 325 putative lincRNAs with high confidence from eight important tissues of sheep using different criteria such as GC content, exon number, gene length, co-expression analysis, stability, and tissue-specific scores. Sixty-four putative lincRNAs displayed tissues-specific expression. The highest number of tissues-specific lincRNAs was found in skin and brain. All novel lincRNAs that aligned to the human and mouse lincRNAs had conserved synteny. These closest protein-coding genes were enriched in 11 significant GO terms such as limb development, appendage development, striated muscle tissue development, and multicellular organismal development. The findings reported here have important implications for the study of sheep genome. PMID:27002388

  18. Conservation and diversity among the three-dimensional folds of the Dicistroviridae intergenic region IRESes.

    PubMed

    Pfingsten, Jennifer S; Costantino, David A; Kieft, Jeffrey S

    2007-07-27

    Internal ribosome entry site (IRES) RNAs are necessary for successful infection of many pathogenic viruses, but the details of the RNA structure-based mechanism used to bind and manipulate the ribosome remain poorly understood. The IRES RNAs from the Dicistroviridae intergenic region (IGR) are an excellent model system to understand the fundamental tenets of IRES function, requiring no protein factors to manipulate the ribosome and initiate translation. Here, we explore the architecture of four members of the IGR IRESes, representative of the two divergent classes of these IRES RNAs. Using biochemical and structural probing methods, we show that despite sequence variability they contain a common three-dimensional fold. The three-dimensional architecture of the ribosome binding domain from these IRESes is organized around a core helical scaffold, around which the rest of the RNA molecule folds. However, subtle variation in the folds of these IRESes and the presence of an additional secondary structure element suggest differences in the details of their manipulation of the large ribosomal subunit. Overall, the results demonstrate how a conserved three-dimensional RNA fold governs ribosome binding and manipulation. PMID:17544444

  19. RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes.

    PubMed

    Pfingsten, Jennifer S; Kieft, Jeffrey S

    2008-07-01

    In eukaryotes, the canonical process of initiating protein synthesis on an mRNA depends on many large protein factors and the modified nucleotide cap on the 5' end of the mRNA. However, certain RNA sequences can bypass the need for these proteins and cap, using an RNA structure-based mechanism called internal initiation of translation. These RNAs are called internal ribosome entry sites (IRESes), and the cap-independent initiation pathway they support is critical for successful infection by many viruses of medical and economic importance. In this review, we briefly describe and compare mechanistic and structural groups of viral IRES RNAs, focusing on those IRESes that are capable of direct ribosome recruitment using specific RNA structures. We then discuss in greater detail some recent advances in our understanding of the intergenic region IRESes of the Dicistroviridae, which use the most streamlined ribosome-recruitment mechanism yet discovered. By combining these findings with knowledge of canonical translation and the behavior of other IRESes, mechanistic models of this RNA structure-based process are emerging. PMID:18515544

  20. Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes

    PubMed Central

    Kannan, Sivakumar; Chernikova, Diana; Rogozin, Igor B.; Poliakov, Eugenia; Managadze, David; Koonin, Eugene V.; Milanesi, Luciano

    2015-01-01

    Transposable elements (TEs) are abundant in mammalian genomes and appear to have contributed to the evolution of their hosts by providing novel regulatory or coding sequences. We analyzed different regions of long intergenic non-coding RNA (lincRNA) genes in human and mouse genomes to systematically assess the potential contribution of TEs to the evolution of the structure and regulation of expression of lincRNA genes. Introns of lincRNA genes contain the highest percentage of TE-derived sequences (TES), followed by exons and then promoter regions although the density of TEs is not significantly different between exons and promoters. Higher frequencies of ancient TEs in promoters and exons compared to introns implies that many lincRNA genes emerged before the split of primates and rodents. The content of TES in lincRNA genes is substantially higher than that in protein-coding genes, especially in exons and promoter regions. A significant positive correlation was detected between the content of TEs and evolutionary rate of lincRNAs indicating that inserted TEs are preferentially fixed in fast-evolving lincRNA genes. These results are consistent with the repeat insertion domains of LncRNAs hypothesis under which TEs have substantially contributed to the origin, evolution, and, in particular, fast functional diversification, of lincRNA genes. PMID:26106594

  1. A Novel Intergenic ETnII-β Insertion Mutation Causes Multiple Malformations in Polypodia Mice

    PubMed Central

    Lehoczky, Jessica A.; Thomas, Peedikayil E.; Patrie, Kevin M.; Owens, Kailey M.; Villarreal, Lisa M.; Galbraith, Kenneth; Washburn, Joe; Johnson, Craig N.; Gavino, Bryant; Borowsky, Alexander D.; Millen, Kathleen J.; Wakenight, Paul; Law, William; Van Keuren, Margaret L.; Gavrilina, Galina; Hughes, Elizabeth D.; Saunders, Thomas L.; Brihn, Lesil; Nadeau, Joseph H.; Innis, Jeffrey W.

    2013-01-01

    Mouse early transposon insertions are responsible for ∼10% of spontaneous mutant phenotypes. We previously reported the phenotypes and genetic mapping of Polypodia, (Ppd), a spontaneous, X-linked dominant mutation with profound effects on body plan morphogenesis. Our new data shows that mutant mice are not born in expected Mendelian ratios secondary to loss after E9.5. In addition, we refined the Ppd genetic interval and discovered a novel ETnII-β early transposon insertion between the genes for Dusp9 and Pnck. The ETn inserted 1.6 kb downstream and antisense to Dusp9 and does not disrupt polyadenylation or splicing of either gene. Knock-in mice engineered to carry the ETn display Ppd characteristic ectopic caudal limb phenotypes, showing that the ETn insertion is the Ppd molecular lesion. Early transposons are actively expressed in the early blastocyst. To explore the consequences of the ETn on the genomic landscape at an early stage of development, we compared interval gene expression between wild-type and mutant ES cells. Mutant ES cell expression analysis revealed marked upregulation of Dusp9 mRNA and protein expression. Evaluation of the 5′ LTR CpG methylation state in adult mice revealed no correlation with the occurrence or severity of Ppd phenotypes at birth. Thus, the broad range of phenotypes observed in this mutant is secondary to a novel intergenic ETn insertion whose effects include dysregulation of nearby interval gene expression at early stages of development. PMID:24339789

  2. DNA methylation signatures of long intergenic noncoding RNAs in porcine adipose and muscle tissues

    PubMed Central

    Zhou, Zhong-Yin; Li, Aimin; Wang, Li-Gang; Irwin, David M; Liu, Yan-Hu; Xu, Dan; Han, Xu-Man; Wang, Lu; Wu, Shi-Fang; Wang, Li-Xian; Xie, Hai-Bing; Zhang, Ya-Ping

    2015-01-01

    Long intergenic noncoding RNAs (lincRNAs) are one of the major unexplored components of genomes. Here we re-analyzed a published methylated DNA immunoprecipitation sequencing (MeDIP-seq) dataset to characterize the DNA methylation pattern of pig lincRNA genes in adipose and muscle tissues. Our study showed that the methylation level of lincRNA genes was higher than that of mRNA genes, with similar trends observed in comparisons of the promoter, exon or intron regions. Different methylation pattern were observed across the transcription start sites (TSS) of lincRNA and protein-coding genes. Furthermore, an overlap was observed between many lincRNA genes and differentially methylated regions (DMRs) identified among different breeds of pigs, which show different fat contents, sexes and anatomic locations of tissues. We identify a lincRNA gene, linc-sscg3623, that displayed differential methylation levels in backfat between Min and Large White pigs at 60 and 120 days of age. We found that a demethylation process occurred between days 150 and 180 in the Min and Large White pigs, which was followed by remethylation between days 180 and 210. These results contribute to our understanding of the domestication of domestic animals and identify lincRNA genes involved in adipogenesis and muscle development. PMID:26493951

  3. DNA methylation signatures of long intergenic noncoding RNAs in porcine adipose and muscle tissues.

    PubMed

    Zhou, Zhong-Yin; Li, Aimin; Wang, Li-Gang; Irwin, David M; Liu, Yan-Hu; Xu, Dan; Han, Xu-Man; Wang, Lu; Wu, Shi-Fang; Wang, Li-Xian; Xie, Hai-Bing; Zhang, Ya-Ping

    2015-01-01

    Long intergenic noncoding RNAs (lincRNAs) are one of the major unexplored components of genomes. Here we re-analyzed a published methylated DNA immunoprecipitation sequencing (MeDIP-seq) dataset to characterize the DNA methylation pattern of pig lincRNA genes in adipose and muscle tissues. Our study showed that the methylation level of lincRNA genes was higher than that of mRNA genes, with similar trends observed in comparisons of the promoter, exon or intron regions. Different methylation pattern were observed across the transcription start sites (TSS) of lincRNA and protein-coding genes. Furthermore, an overlap was observed between many lincRNA genes and differentially methylated regions (DMRs) identified among different breeds of pigs, which show different fat contents, sexes and anatomic locations of tissues. We identify a lincRNA gene, linc-sscg3623, that displayed differential methylation levels in backfat between Min and Large White pigs at 60 and 120 days of age. We found that a demethylation process occurred between days 150 and 180 in the Min and Large White pigs, which was followed by remethylation between days 180 and 210. These results contribute to our understanding of the domestication of domestic animals and identify lincRNA genes involved in adipogenesis and muscle development. PMID:26493951

  4. Comparative Expression Dynamics of Intergenic Long Noncoding RNAs in the Genus Drosophila.

    PubMed

    Nyberg, Kevin G; Machado, Carlos A

    2016-01-01

    Thousands of long noncoding RNAs (lncRNAs) have been annotated in eukaryotic genomes, but comparative transcriptomic approaches are necessary to understand their biological impact and evolution. To facilitate such comparative studies in Drosophila, we identified and characterized lncRNAs in a second Drosophilid-the evolutionary model Drosophila pseudoobscura Using RNA-Seq and computational filtering of protein-coding potential, we identified 1,589 intergenic lncRNA loci in D. pseudoobscura We surveyed multiple sex-specific developmental stages and found, like in Drosophila melanogaster, increasingly prolific lncRNA expression through male development and an overrepresentation of lncRNAs in the testes. Other trends seen in D. melanogaster, like reduced pupal expression, were not observed. Nonrandom distributions of female-biased and non-testis-specific male-biased lncRNAs between the X chromosome and autosomes are consistent with selection-based models of gene trafficking to optimize genomic location of sex-biased genes. The numerous testis-specific lncRNAs, however, are randomly distributed between the X and autosomes, and we cannot reject the hypothesis that many of these are likely to be spurious transcripts. Finally, using annotated lncRNAs in both species, we identified 134 putative lncRNA homologs between D. pseudoobscura and D. melanogaster and find that many have conserved developmental expression dynamics, making them ideal candidates for future functional analyses. PMID:27189981

  5. Comparative Expression Dynamics of Intergenic Long Noncoding RNAs in the Genus Drosophila

    PubMed Central

    Nyberg, Kevin G.; Machado, Carlos A.

    2016-01-01

    Thousands of long noncoding RNAs (lncRNAs) have been annotated in eukaryotic genomes, but comparative transcriptomic approaches are necessary to understand their biological impact and evolution. To facilitate such comparative studies in Drosophila, we identified and characterized lncRNAs in a second Drosophilid—the evolutionary model Drosophila pseudoobscura. Using RNA-Seq and computational filtering of protein-coding potential, we identified 1,589 intergenic lncRNA loci in D. pseudoobscura. We surveyed multiple sex-specific developmental stages and found, like in Drosophila melanogaster, increasingly prolific lncRNA expression through male development and an overrepresentation of lncRNAs in the testes. Other trends seen in D. melanogaster, like reduced pupal expression, were not observed. Nonrandom distributions of female-biased and non-testis-specific male-biased lncRNAs between the X chromosome and autosomes are consistent with selection-based models of gene trafficking to optimize genomic location of sex-biased genes. The numerous testis-specific lncRNAs, however, are randomly distributed between the X and autosomes, and we cannot reject the hypothesis that many of these are likely to be spurious transcripts. Finally, using annotated lncRNAs in both species, we identified 134 putative lncRNA homologs between D. pseudoobscura and D. melanogaster and find that many have conserved developmental expression dynamics, making them ideal candidates for future functional analyses. PMID:27189981

  6. The evolutionary landscape of intergenic trans-splicing events in insects

    PubMed Central

    Kong, Yimeng; Zhou, Hongxia; Yu, Yao; Chen, Longxian; Hao, Pei; Li, Xuan

    2015-01-01

    To explore the landscape of intergenic trans-splicing events and characterize their functions and evolutionary dynamics, we conduct a mega-data study of a phylogeny containing eight species across five orders of class Insecta, a model system spanning 400 million years of evolution. A total of 1,627 trans-splicing events involving 2,199 genes are identified, accounting for 1.58% of the total genes. Homology analysis reveals that mod(mdg4)-like trans-splicing is the only conserved event that is consistently observed in multiple species across two orders, which represents a unique case of functional diversification involving trans-splicing. Thus, evolutionarily its potential for generating proteins with novel function is not broadly utilized by insects. Furthermore, 146 non-mod trans-spliced transcripts are found to resemble canonical genes from different species. Trans-splicing preserving the function of ‘breakup' genes may serve as a general mechanism for relaxing the constraints on gene structure, with profound implications for the evolution of genes and genomes. PMID:26521696

  7. Epistasis in intra- and inter-gene pool crosses of the common bean.

    PubMed

    Borel, J C; Ramalho, M A P; Abreu, A F B

    2016-01-01

    Epistasis has been shown to have an important role in the genetic control of several quantitative traits in the common bean. This study aimed to investigate the occurrence of epistasis in intra- and inter-pool gene crosses of the common bean. Four elite lines adapted to Brazilian conditions were used as parents, two from the Andean gene pool (ESAL 686; BRS Radiante) and two from the Mesoamerican gene pool (BRSMG Majestoso; BRS Valente). Four F2 populations were obtained: "A" (ESAL 686 x BRS Radiante), "B" (BRSMG Majestoso x BRS Valente), "C" (BRS Radiante x BRSMG Majestoso), and "D" (BRS Valente x ESAL 686). A random sample of F2 plants from each population was backcrossed to parents and F1 individuals, according to the triple test cross. Three types of progenies from each population were evaluated in contiguous trials. Seed yield and 100-seed weight were evaluated. Dominance genetic variance was predominant in most cases. However, the estimates of genetic variance may be biased by the occurrence of linkage disequilibrium and epistasis. Epistasis was detected for both traits; however, the occurrence differed among the populations and between the two traits. The results of this study reinforce the hypothesis that epistasis is present in the genetic control of traits in the common bean and suggest that the phenomenon is more frequent in inter-gene pool crosses than in intra-gene pool crosses. PMID:26985920

  8. Repetition priming results in sensitivity attenuation

    PubMed Central

    Allenmark, Fredrik; Hsu, Yi-Fang; Roussel, Cedric; Waszak, Florian

    2015-01-01

    Repetition priming refers to the change in the ability to perform a task on a stimulus as a consequence of a former encounter with that very same item. Usually, repetition results in faster and more accurate performance. In the present study, we used a contrast discrimination protocol to assess perceptual sensitivity and response bias of Gabor gratings that are either repeated (same orientation) or alternated (different orientation). We observed that contrast discrimination performance is worse, not better, for repeated than for alternated stimuli. In a second experiment, we varied the probability of stimulus repetition, thus testing whether the repetition effect is due to bottom-up or top-down factors. We found that it is top-down expectation that determines the effect. We discuss the implication of these findings for repetition priming and related phenomena as sensory attenuation. This article is part of a Special Issue entitled SI: Prediction and Attention. PMID:25819554

  9. Fast repetition rate (FRR) flasher

    DOEpatents

    Kolber, Z.; Falkowski, P.

    1997-02-11

    A fast repetition rate (FRR) flasher is described suitable for high flash photolysis including kinetic chemical and biological analysis. The flasher includes a power supply, a discharge capacitor operably connected to be charged by the power supply, and a flash lamp for producing a series of flashes in response to discharge of the discharge capacitor. A triggering circuit operably connected to the flash lamp initially ionizes the flash lamp. A current switch is operably connected between the flash lamp and the discharge capacitor. The current switch has at least one insulated gate bipolar transistor for switching current that is operable to initiate a controllable discharge of the discharge capacitor through the flash lamp. Control means connected to the current switch for controlling the rate of discharge of the discharge capacitor thereby to effectively keep the flash lamp in an ionized state between successive discharges of the discharge capacitor. Advantageously, the control means is operable to discharge the discharge capacitor at a rate greater than 10,000 Hz and even up to a rate greater than about 250,000 Hz. 14 figs.

  10. Fast repetition rate (FRR) flasher

    DOEpatents

    Kolber, Zbigniew; Falkowski, Paul

    1997-02-11

    A fast repetition rate (FRR) flasher suitable for high flash photolysis including kinetic chemical and biological analysis. The flasher includes a power supply, a discharge capacitor operably connected to be charged by the power supply, and a flash lamp for producing a series of flashes in response to discharge of the discharge capacitor. A triggering circuit operably connected to the flash lamp initially ionizes the flash lamp. A current switch is operably connected between the flash lamp and the discharge capacitor. The current switch has at least one insulated gate bipolar transistor for switching current that is operable to initiate a controllable discharge of the discharge capacitor through the flash lamp. Control means connected to the current switch for controlling the rate of discharge of the discharge capacitor thereby to effectively keep the flash lamp in an ionized state between Successive discharges of the discharge capacitor. Advantageously, the control means is operable to discharge the discharge capacitor at a rate greater than 10,000 Hz and even up to a rate greater than about 250,000 Hz.

  11. SPACER: server for predicting allosteric communication and effects of regulation

    PubMed Central

    Goncearenco, Alexander; Mitternacht, Simon; Yong, Taipang; Eisenhaber, Birgit; Eisenhaber, Frank; Berezovsky, Igor N.

    2013-01-01

    The SPACER server provides an interactive framework for exploring allosteric communication in proteins with different sizes, degrees of oligomerization and function. SPACER uses recently developed theoretical concepts based on the thermodynamic view of allostery. It proposes easily tractable and meaningful measures that allow users to analyze the effect of ligand binding on the intrinsic protein dynamics. The server shows potential allosteric sites and allows users to explore communication between the regulatory and functional sites. It is possible to explore, for instance, potential effector binding sites in a given structure as targets for allosteric drugs. As input, the server only requires a single structure. The server is freely available at http://allostery.bii.a-star.edu.sg/. PMID:23737445

  12. Flows through sequential orifices with heated spacer reservoirs

    NASA Technical Reports Server (NTRS)

    Hendricks, R. C.; Stetz, T. T.

    1982-01-01

    Flow rates and pressure thermal profiles for two phase choked flows of fluid nitrogen were studied theoretically and experimentally in a four sequential orifice configuration. Both theory and experimental evidence demonstrate that heat addition in the first spacer-reservoir adjacent to the inlet orifice is most effective in reducing the flow rate and that heat addition in the last spacer-reservoir is least effective. The flows are choked at the exit orifice for large spacings and at the inlet orifice for small spacings. The moderate addition of heat available for this experiment did not materially alter this result for large spacings; however, significant heat addition for the small spacings tended to shift the choke point to the exit orifice. Nitrogen is used as the working fluid over a range of states from liquid to gas with a reduced inlet stagnation pressure range to P sub r, o = 2.

  13. Strategies for Using Repetition as a Powerful Teaching Tool

    ERIC Educational Resources Information Center

    Saville, Kirt

    2011-01-01

    Brain research indicates that repetition is of vital importance in the learning process. Repetition is an especially useful tool in the area of music education. The success of repetition can be enhanced by accurate and timely feedback. From "simple repetition" to "repetition with the addition or subtraction of degrees of freedom," there are many…

  14. Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures[OPEN

    PubMed Central

    Zhu, Bo; Zhang, Wenli; Jiang, Jiming

    2015-01-01

    Enhancers are important regulators of gene expression in eukaryotes. Enhancers function independently of their distance and orientation to the promoters of target genes. Thus, enhancers have been difficult to identify. Only a few enhancers, especially distant intergenic enhancers, have been identified in plants. We developed an enhancer prediction system based exclusively on the DNase I hypersensitive sites (DHSs) in the Arabidopsis thaliana genome. A set of 10,044 DHSs located in intergenic regions, which are away from any gene promoters, were predicted to be putative enhancers. We examined the functions of 14 predicted enhancers using the β-glucuronidase gene reporter. Ten of the 14 (71%) candidates were validated by the reporter assay. We also designed 10 constructs using intergenic sequences that are not associated with DHSs, and none of these constructs showed enhancer activities in reporter assays. In addition, the tissue specificity of the putative enhancers can be precisely predicted based on DNase I hypersensitivity data sets developed from different plant tissues. These results suggest that the open chromatin signature-based enhancer prediction system developed in Arabidopsis may serve as a universal system for enhancer identification in plants. PMID:26373455

  15. Improving electricity production in tubular microbial fuel cells through optimizing the anolyte flow with spiral spacers.

    PubMed

    Zhang, Fei; Ge, Zheng; Grimaud, Julien; Hurst, Jim; He, Zhen

    2013-04-01

    The use of spiral spacers to create a helical flow for improving electricity generation in microbial fuel cells (MFCs) was investigated in both laboratory and on-site tests. The lab tests found that the MFC with the spiral spacers produced more electricity than the one without the spiral spacers at different recirculation rates or organic loading rates, likely due to the improved transport/distribution of ions and electron mediators instead of the substrates because the organic removal efficiency was not obviously affected by the presence of the spiral spacers. The energy production in the MFC with the spiral spacers reached 0.071 or 0.073 kWh/kg COD in either vertical or horizontal installment. The examination of the MFCs installed in an aeration tank of a municipal wastewater treatment plant confirmed the advantage of using the spiral spacers. Those results demonstrate that spiral spacers could be an effective approach to improve energy production in MFCs. PMID:23500582

  16. Increased antibiotic release and equivalent biomechanics of a spacer cement without hard radio contrast agents.

    PubMed

    Bitsch, R G; Kretzer, J P; Vogt, S; Büchner, H; Thomsen, M N; Lehner, B

    2015-10-01

    We compared a novel calcium carbonate spacer cement (Copal® spacem) to well-established bone cements. Electron microscopic structure and elution properties of the antibiotics ofloxacin, vancomycin, clindamycin, and gentamicin were examined. A knee wear simulator model for articulating cement spacers was established. Mechanical tests for bending strength, flexural modulus, and compressive and fatigue strength were performed. The electron microscopic analysis showed a microporous structure of the spacer cement, and this promoted a significantly higher and longer antibiotic elution. All spacer cement specimens released the antibiotics for a period of up to 50days with the exception of the vancomycin loading. The spacer cement showed significantly less wear scars and fulfilled the ISO 5833 requirements. The newly developed spacer cement is a hydrophilic antibiotic carrier with an increased release. Cement without hard radio contrast agents can improve tribological behaviour of spacers, and this may reduce reactive wear particles and abrasive bone defects. PMID:26219491

  17. Structural design feasibility study of Space Station long spacer truss

    NASA Technical Reports Server (NTRS)

    Armand, Sasan C.; Funk, Gregory P.; Dohogne, Caroline A.

    1994-01-01

    The structural design and configuration feasibility of the long spacer truss assembly that will be used as part of the Space Station Freedom is the focus of this study. The structural analysis discussed herein is derived from the transient loading events presented in the Space Transportation System Interface Control Document (STS ICD). The transient loading events are liftoff, landing, and emergency landing loads. Quasi-static loading events were neglected in this study since the magnitude of the quasi-static acceleration factors is lower than that of the transient acceleration factors. Structural analysis of the proposed configuration of the long spacer truss with four longerons indicated that negative safety margins are possible. As a result, configuration changes were proposed. The primary configuration change suggested was to increase the number of truss longerons to six. The six-longeron truss appears to be a more promising structure than the four-longeron truss because it offers a positive margin of safety and more volume in its second bay (BAY2). This additional volume can be used for resupply of some of the orbital replacement units (such as a battery box). Note that the design effort on the long spacer truss has not fully begun and that calculations and reports of the negative safety margins are, to date, based on concept only.

  18. Spacers' role in the dynamics of hyperbranched polymers

    NASA Astrophysics Data System (ADS)

    Satmarel, C.; von Ferber, C.; Blumen, A.

    2006-05-01

    We investigate hyperbranched polymers (HBPs) and highlight the relation between their architecture and their viscoelastic behavior, while paying special attention to the role of the chainlike spacer segments between branching points. For this we study the dynamics of HBP in solution, based on the generalized Gaussian structure formalism, an extension of the Rouse model, which disregards hydrodynamical and excluded volume effects. For HBP the dynamical effects display, beside the obvious contributions of localized modes on the spacers, also remarkable features, as we highlight based on the exact renormalization procedure recently developed by us in J. Chem. Phys. 123, 034907 (2005). We exemplify these features by analyzing the dynamics of randomly linked star polymers and study the impact both of the length and of the spacers' mobility on the normal modes' spectra. We compute these modes both by numerical diagonalization and also by employing our renormalization procedure; the excellent agreement between these methods allows us to extend the range of investigations to very large HBP.

  19. Structural design feasibility study of Space Station long spacer truss

    NASA Astrophysics Data System (ADS)

    Armand, Sasan C.; Funk, Gregory P.; Dohogne, Caroline A.

    1994-02-01

    The structural design and configuration feasibility of the long spacer truss assembly that will be used as part of the Space Station Freedom is the focus of this study. The structural analysis discussed herein is derived from the transient loading events presented in the Space Transportation System Interface Control Document (STS ICD). The transient loading events are liftoff, landing, and emergency landing loads. Quasi-static loading events were neglected in this study since the magnitude of the quasi-static acceleration factors is lower than that of the transient acceleration factors. Structural analysis of the proposed configuration of the long spacer truss with four longerons indicated that negative safety margins are possible. As a result, configuration changes were proposed. The primary configuration change suggested was to increase the number of truss longerons to six. The six-longeron truss appears to be a more promising structure than the four-longeron truss because it offers a positive margin of safety and more volume in its second bay (BAY2). This additional volume can be used for resupply of some of the orbital replacement units (such as a battery box). Note that the design effort on the long spacer truss has not fully begun and that calculations and reports of the negative safety margins are, to date, based on concept only.

  20. Development and characterization of 3D-printed feed spacers for spiral wound membrane systems.

    PubMed

    Siddiqui, Amber; Farhat, Nadia; Bucs, Szilárd S; Linares, Rodrigo Valladares; Picioreanu, Cristian; Kruithof, Joop C; van Loosdrecht, Mark C M; Kidwell, James; Vrouwenvelder, Johannes S

    2016-03-15

    Feed spacers are important for the impact of biofouling on the performance of spiral-wound reverse osmosis (RO) and nanofiltration (NF) membrane systems. The objective of this study was to propose a strategy for developing, characterizing, and testing of feed spacers by numerical modeling, three-dimensional (3D) printing of feed spacers and experimental membrane fouling simulator (MFS) studies. The results of numerical modeling on the hydrodynamic behavior of various feed spacer geometries suggested that the impact of spacers on hydrodynamics and biofouling can be improved. A good agreement was found for the modeled and measured relationship between linear flow velocity and pressure drop for feed spacers with the same geometry, indicating that modeling can serve as the first step in spacer characterization. An experimental comparison study of a feed spacer currently applied in practice and a 3D printed feed spacer with the same geometry showed (i) similar hydrodynamic behavior, (ii) similar pressure drop development with time and (iii) similar biomass accumulation during MFS biofouling studies, indicating that 3D printing technology is an alternative strategy for development of thin feed spacers with a complex geometry. Based on the numerical modeling results, a modified feed spacer with low pressure drop was selected for 3D printing. The comparison study of the feed spacer from practice and the modified geometry 3D printed feed spacer established that the 3D printed spacer had (i) a lower pressure drop during hydrodynamic testing, (ii) a lower pressure drop increase in time with the same accumulated biomass amount, indicating that modifying feed spacer geometries can reduce the impact of accumulated biomass on membrane performance. The combination of numerical modeling of feed spacers and experimental testing of 3D printed feed spacers is a promising strategy (rapid, low cost and representative) to develop advanced feed spacers aiming to reduce the impact of

  1. Cross-modal nonspatial repetition inhibition.

    PubMed

    Wang, Lihui; Yue, Zhenzhu; Chen, Qi

    2012-07-01

    Although it has been well documented that the spatial inhibitory effect induced by repetition of location (i.e., spatial inhibition of return, or IOR) occurs cross-modally, we do not yet know whether nonspatial (e.g., color-based) repetition-induced inhibition occurs in a cross-modal fashion as well. In the present study, a novel cross-modal paradigm with regard to color-based repetition was adopted. An intervening neutral cue, whose semantic identity was different from those of both the prime and the target, was introduced between the prime and the target in a repetition-priming task. The modalities of the prime, the neutral cue, and the target could be either visual or auditory, and the prime and the target could refer either to the same or to different semantic identities. By adopting this paradigm, we aimed to answer two questions: (1) What are the specific conditions under which cross-modal semantic-based repetition inhibition occurs? (2) Are the representations inhibited in the semantic-based repetition inhibition effect supramodal or modality-specific? Our results suggested that semantic-based repetition inhibition occurs only when the prime and the neutral cue are from the same sensory modality, and it occurs irrespective of whether the modality of the target is cued and irrespective of whether the modality of the target is auditory or visual. Taken together, our results suggest that the occurrence of cross-modal nonspatial repetition inhibition is conditional and that the nonspatial representations inhibited by the repetition inhibition are supramodal. PMID:22415447

  2. Independent tuning of double plasmonic waves in a free-standing graphene-spacer-grating-spacer-graphene hybrid slab.

    PubMed

    Chen, Ying; Yao, Jin; Song, Zhengyong; Ye, Longfang; Cai, Guoxiong; Liu, Qing Huo

    2016-07-25

    The independent excitation and tuning of double plasmonic waves are realized in a free-standing graphene-spacer-grating-spacer-graphene (GSGSG) hybrid slab, which consists of two graphene field effect transistors placed back-to-back to each other. Resulted from the high transparency and the tight confinement of surface plasmonic mode for the graphene, double plasmonic waves can be independently excited by guided-mode resonances (GMRs). Theoretical and numerical investigations are performed in the mid-infrared band. Furthermore, the tuning of individual GMR resonant wavelengths with respect to the system parameters is studied. The results provide opportunities to engineer the proposed hybrid slab for wavelength selective and multiplexing applications. PMID:27464148

  3. Functional Implications of RNA Splicing for Human Long Intergenic Noncoding RNAs

    PubMed Central

    Chen, Feng-Chi; Pan, Chia-Lin; Lin, Hsuan-Yu

    2014-01-01

    Long intergenic noncoding RNAs (lincRNAs) have been suggested as playing important roles in human gene regulation. The majority of annotated human lincRNAs include multiple exons and are alternatively spliced. However, the connections between alternative RNA splicing (AS) and the functions/regulations of lincRNAs have remained elusive. In this study, we compared the sequence evolution and biological features between single-exonic lincRNAs and multi-exonic lincRNAs (SELs and MELs, respectively) that were present only in the hominoids (hominoid-specific) or conserved in primates (primate-conserved). The MEL exons were further classified into alternatively spliced exons (ASEs) and constitutively spliced exons (CSEs) for evolutionary analyses. Our results indicate that SELs and MELs differed significantly from each other. Firstly, in hominoid-specific lincRNAs, MELs (both CSEs and ASEs) evolved slightly more rapidly than SELs, which evolved approximately at the neutral rate. In primate-conserved lincRNAs, SELs and ASEs evolved slightly more slowly than CSEs and neutral sequences. The evolutionary path of hominid-specific lincRNAs thus seemed to have diverged from that of their more ancestral counterparts. Secondly, both of the exons and transcripts of SELs were significantly longer than those of MELs, and this was probably because SEL transcripts were more resistant to RNA splicing than MELs. Thirdly, SELs were physically closer to coding genes than MELs. Fourthly, SELs were more widely expressed in human tissues than MELs. These results suggested that SELs and MELs represented two biologically distinct groups of genes. In addition, the SEL–MEL and ASE–CSE differences implied that splicing might be important for the functionality or regulations of lincRNAs in primates. PMID:25574121

  4. Intergenic Sequence Comparison of Escherichia coli Isolates Reveals Lifestyle Adaptations but Not Host Specificity▿

    PubMed Central

    White, A. P.; Sibley, K. A.; Sibley, C. D.; Wasmuth, J. D.; Schaefer, R.; Surette, M. G.; Edge, T. A.; Neumann, N. F.

    2011-01-01

    Establishing the risk of human infection is one of the goals of public health. For bacterial pathogens, the virulence and zoonotic potential can often be related to their host source. Escherichia coli bacteria are common contaminants of water associated with human recreation and consumption, and many strains are pathogenic. In this study, we analyzed three promoter-containing intergenic regions from 284 diverse E. coli isolates in an attempt to identify molecular signatures associated with specific host types. Promoter sequences controlling production of curli fimbriae, flagella, and nutrient import yielded a phylogenetic tree with isolates clustered by established phylogenetic grouping (A, B1, B2, and D) but not by host source. Virulence genes were more prevalent in groups B2 and D isolates and in human isolates. Group B1 isolates, primarily from nonhuman sources, were the most genetically similar, indicating that they lacked molecular adaptations to specific host environments and were likely host generalists. Conversely, B2 isolates, primarily from human sources, displayed greater genetic distances and were more likely to be host adapted. In agreement with these hypotheses, prevalence of σS activity and the rdar morphotype, phenotypes associated with environmental survival, were significantly higher in B1 isolates than in B2 isolates. Based on our findings, we speculate that E. coli host specificity is not defined by genome-wide sequence changes but, rather, by the presence or absence of specific genes and associated promoter elements. Furthermore, the requirements for colonization of the human gastrointestinal tract may lead to E. coli lifestyle changes along with selection for increased virulence. PMID:21908635

  5. Not all repetition is alike: different benefits of repetition in amnesia and normal memory.

    PubMed

    Verfaellie, Mieke; Rajaram, Suparna; Fossum, Karen; Williams, Lisa

    2008-05-01

    While it is well known that repetition can enhance memory in amnesia, little is known about which forms of repetition are most beneficial. This study compared the effect on recognition memory of repetition of words in the same semantic context and in varied semantic contexts. To gain insight into the mechanisms by which these forms of repetition affect performance, participants were asked to make Remember/Know judgments during recognition. These judgments were used to make inferences about the contribution of recollection and familiarity to performance. For individuals with intact memory, the two forms of repetition were equally beneficial to overall recognition, and were associated with both enhanced Remember and Know responses. However, varied repetition was associated with a higher likelihood of Remember responses than was fixed repetition. The two forms of repetition also conferred equivalent benefits on overall recognition in amnesia, but in both cases, this enhancement was manifest exclusively in enhanced Know responses. We conclude that the repetition of information, and especially repetition in varied contexts, enhances recollection in individuals with intact memory, but exclusively affects familiarity in patients with severe amnesia. PMID:18419835

  6. Developmental Norms for the Sentence Repetition Test.

    ERIC Educational Resources Information Center

    Carmichael, John A.; MacDonald, John W.

    1984-01-01

    Obtained developmental norms for the Sentence Repetition Test from children (N=1,081) ranging in age from three to 13 years. Utilized a substanially larger number of children in each age group than previous reports. (Author/LLL)

  7. Repetitive sequence environment distinguishes housekeeping genes

    PubMed Central

    Eller, C. Daniel; Regelson, Moira; Merriman, Barry; Nelson, Stan; Horvath, Steve; Marahrens, York

    2007-01-01

    Housekeeping genes are expressed across a wide variety of tissues. Since repetitive sequences have been reported to influence the expression of individual genes, we employed a novel approach to determine whether housekeeping genes can be distinguished from tissue-specific genes their repetitive sequence context. We show that Alu elements are more highly concentrated around housekeeping genes while various longer (>400-bp) repetitive sequences ("repeats"), including Long Interspersed Nuclear Element 1 (LINE-1) elements, are excluded from these regions. We further show that isochore membership does not distinguish housekeeping genes from tissue-specific genes and that repetitive sequence environment distinguishes housekeeping genes from tissue-specific genes in every isochore. The distinct repetitive sequence environment, in combination with other previously published sequence properties of housekeeping genes, were used to develop a method of predicting housekeeping genes on the basis of DNA sequence alone. Using expression across tissue types as a measure of success, we demonstrate that repetitive sequence environment is by far the most important sequence feature identified to date for distinguishing housekeeping genes. PMID:17141428

  8. Compact, repetitive, 6. 5 kilojoule Marx generator

    SciTech Connect

    Lancaster, K.T.; Clark, R.S.; Buttram, M.T.

    1988-01-01

    Repetitive Marx generator technology developed has been actively pursued for many years at Sandia National Laboratories. Four repetitive Marx generators with voltages to 1 MV, energies to 20 kJ and repetition rates to 50 Hz have been built, tested, and used in on-line experiments. These devices have proven to be reliable pulsed power energy sources. The 440 kV, 6 kJ, 1 Hz Marx generator in this report was designed using this existing technology base. The repetitive Marx generator is an attractive power source for many applications for a variety of reasons. Circuit-wise a Marx is simple, being essentially a capacitor and inductor in series. This permits its use in a variety of configurations ranging from a pulse-forming line charger to an element of a pulse-forming network. At slow repetition rates (1 Hz to 10 Hz) Marx generators can be fabricated almost entirely from commercial components making them both inexpensive and quick to build. Generally they can be easily reconfigured as requirements change, making them a flexible laboratory tool. When designed conservatively, they are also useful for some commercial applications outside the laboratory. In this paper we illustrate the latter point by discussing the design and development of a compact field-transportable, repetitive Marx generator that was designed and built in three months. The authors also review the options considered before choosing the Marx design, and the use of commercially-available hardware in the Marx generator's construction.

  9. Molecular profiling of microbial communities from contaminated sources: Use of substractive cloning methods and rDNA spacer sequences. 1997 annual progress report

    SciTech Connect

    1997-12-01

    'This project is to develop molecular methods for rapid characterization of microbial communities in contaminated ecosystems. The authors are exploring the use of {sup 16}s ribosomal DNA intergenic spacer regions (ISRs) to profile community composition. The choice proves to be a good one: there are 200--550 bases of 1 to 3 variable regions from which to choose species-specific probes, as well as 2--4 stretches of conserved sequence from which to develop universal PCR (polymerase chain reaction) primers. Preliminary community characterization is complete, and several types of arrays are under development to determine the types of bacteria present and the status of the ground water. Profiling the community composition of polluted groundwater will impact the broad field of microbial ecology as well as mixed-waste bioremediation. Results The samples the authors have been analysing were provided by Dr. Fred Brockman from Pacific Northwest Laboratory, and were collected at the US DOE Hanford site, Washington state. The samples were microbial filtrates from ground water polluted with 2 mg/L carbon tetrachloride and 250 mg/L nitrate and subjected to enrichment (acetate + nitrate) and recirculation. This project is described in some detail in PNNL-11113, Accelerated In Situ Bioremediation of Groundwater, by M.J. Truex, B.S. Hooker, and D.B. Anderson, July 1996.'

  10. Aggregation behavior of a gemini surfactant with a tripeptide spacer.

    PubMed

    Wang, Meina; Han, Yuchun; Qiao, Fulin; Wang, Yilin

    2015-02-28

    A peptide gemini surfactant, 12-G(NH2)LG(NH2)-12, has been constructed with two dodecyl chains separately attached to the two terminals of a glutamic acid-lysine-glutamic acid peptide and the aggregation behavior of the surfactant was studied in aqueous solution. The 12-G(NH2)LG(NH2)-12 molecules form fiber-like precipitates around pH 7.0, and the precipitation range is widened on increasing the concentration. At pHs 3.0 and 11.0, 12-G(NH2)LG(NH2)-12 forms soluble aggregates because each molecule carries two positively charged amino groups at the two ends of the peptide spacer at pH 3.0, while each molecule carries one negatively charged carboxyl group in the middle of the peptide spacer at pH 11.0. 12-G(NH2)LG(NH2)-12 displays a similar concentration-dependent process at these two pHs: forming small micelles above the critical micelle concentration and transferring to fibers at pH 3.0 or twisted ribbons at pH 11.0 above the second critical concentration. The fibers formed at pH 3.0 tend to aggregate into bundles with twisted structure. Both the twisted fibers at pH 3.0 and the twisted ribbons at pH 11.0 contain β-sheet structure formed by the peptide spacer. PMID:25588349

  11. Enhancing Asthma Medication Delivery: Spacers and Valved Holding Chambers.

    PubMed

    Schoessler, Sally; Winders, Tonya

    2016-07-01

    Asthma is one of the most prevalent chronic diseases managed by school nurses, and its management often includes the administration of bronchodilators delivered via a metered dose inhaler (MDI). The use of an MDI requires coordination and mastery of steps that must be performed correctly and in the proper order. These steps are greatly enhanced, especially in the pediatric population, through the use of medical devices-spacers and valved holding chambers. The purpose of this article is to review the rationale and implications for the use of these devices in the school setting. PMID:27194239

  12. Simulation of Anti-Galloping Effects of Phase-to-Phase Spacers in Transmission Line

    NASA Astrophysics Data System (ADS)

    Liu, Chao-Qun; Chen, Hua-Ling; Liu, Bin; Liu, Cao-Lan; Sun, Na; Yang, Jia-Lun

    Currently, the application of phase-to-phase spacers can effectively prevent and control line faults caused by conductor galloping and is one of the most effective methods to prevent galloping of transmission lines. The installation layout scheme of phase-to-phase spacers directly affects the anti-galloping effect. Moreover, the common empirical formula can not accurately assess the anti-galloping effect of phase-to-phase spacers. In this paper, the nonlinear finite element method is employed to establish an accurate analysis model of phase-to-phase spacers for conductors. And the anti-galloping effects of phase-to-phase spacers installed in different ways are analyzed, with the aim of providing an effective method for the installation of phase-to-phase spacers used in practical transmission lines.

  13. Integrative Analysis of Normal Long Intergenic Non-Coding RNAs in Prostate Cancer.

    PubMed

    Bawa, Pushpinder; Zackaria, Sajna; Verma, Mohit; Gupta, Saurabh; Srivatsan, R; Chaudhary, Bibha; Srinivasan, Subhashini

    2015-01-01

    Recently, large numbers of normal human tissues have been profiled for non-coding RNAs and more than fourteen thousand long intergenic non-coding RNAs (lincRNAs) are found expressed in normal human tissues. The functional roles of these normal lincRNAs (nlincRNAs) in the regulation of protein coding genes in normal and disease biology are yet to be established. Here, we have profiled two RNA-seq datasets including cancer and matched non-neoplastic tissues from 12 individuals from diverse demography for both coding genes and nlincRNAs. We find 130 nlincRNAs significantly regulated in cancer, with 127 regulated in the same direction in the two datasets. Interestingly, according to Illumina Body Map, significant numbers of these nlincRNAs display baseline null expression in normal prostate tissues but are specific to other tissues such as thyroid, kidney, liver and testis. A number of the regulated nlincRNAs share loci with coding genes, which are either co-regulated or oppositely regulated in all cancer samples studied here. For example, in all cancer samples i) the nlincRNA, TCONS_00029157, and a neighboring tumor suppressor factor, SIK1, are both down regulated; ii) several thyroid-specific nlincRNAs in the neighborhood of the thyroid-specific gene TPO, are both up-regulated; and iii) the TCONS_00010581, an isoform of HEIH, is down-regulated while the neighboring EZH2 gene is up-regulated in cancer. Several nlincRNAs from a prostate cancer associated chromosomal locus, 8q24, are up-regulated in cancer along with other known prostate cancer associated genes including PCAT-1, PVT1, and PCAT-92. We observe that there is significant bias towards up-regulation of nlincRNAs with as high as 118 out of 127 up-regulated in cancer, even though regulation of coding genes is skewed towards down-regulation. Considering that all reported cancer associated lincRNAs (clincRNAs) are biased towards up-regulation, we conclude that this bias may be functionally relevant. PMID:25933431

  14. The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA

    SciTech Connect

    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

  15. Functional Characterization of MC1R-TUBB3 Intergenic Splice Variants of the Human Melanocortin 1 Receptor

    PubMed Central

    Herraiz, Cecilia; Olivares, Conchi; Castejón-Griñán, Maria; Abrisqueta, Marta; Jiménez-Cervantes, Celia; García-Borrón, José Carlos

    2015-01-01

    The melanocortin 1 receptor gene (MC1R) expressed in melanocytes is a major determinant of skin pigmentation. It encodes a Gs protein-coupled receptor activated by α-melanocyte stimulating hormone (αMSH). Human MC1R has an inefficient poly(A) site allowing intergenic splicing with its downstream neighbour Tubulin-β-III (TUBB3). Intergenic splicing produces two MC1R isoforms, designated Iso1 and Iso2, bearing the complete seven transmembrane helices from MC1R fused to TUBB3-derived C-terminal extensions, in-frame for Iso1 and out-of-frame for Iso2. It has been reported that exposure to ultraviolet radiation (UVR) might promote an isoform switch from canonical MC1R (MC1R-001) to the MC1R-TUBB3 chimeras, which might lead to novel phenotypes required for tanning. We expressed the Flag epitope-tagged intergenic isoforms in heterologous HEK293T cells and human melanoma cells, for functional characterization. Iso1 was expressed with the expected size. Iso2 yielded a doublet of Mr significantly lower than predicted, and impaired intracellular stability. Although Iso1- and Iso2 bound radiolabelled agonist with the same affinity as MC1R-001, their plasma membrane expression was strongly reduced. Decreased surface expression mostly resulted from aberrant forward trafficking, rather than high rates of endocytosis. Functional coupling of both isoforms to cAMP was lower than wild-type, but ERK activation upon binding of αMSH was unimpaired, suggesting imbalanced signaling from the splice variants. Heterodimerization of differentially labelled MC1R-001 with the splicing isoforms analyzed by co-immunoprecipitation was efficient and caused decreased surface expression of binding sites. Thus, UVR-induced MC1R isoforms might contribute to fine-tune the tanning response by modulating MC1R-001 availability and functional parameters. PMID:26657157

  16. Characterizations of the human parainfluenza type 2 virus gene encoding the L protein and the intergenic sequences.

    PubMed Central

    Kawano, M; Okamoto, K; Bando, H; Kondo, K; Tsurudome, M; Komada, H; Nishio, M; Ito, Y

    1991-01-01

    We cloned and determined the nucleotide sequences of cDNAs against genomic RNA encoding the L protein of human parainfluenza type 2 virus (PIV-2). The L gene is 6904 nucleotides long including the intergenic region at the HN-L junction and putative negative strand leader RNA, almost all of which is complementary to the positive strand leader RNA of PIV-2. The deduced L protein contains 2262 amino acids with a calculated molecular weight of 256,366. The L protein of PIV-2 shows 39.9, 28.9, 27.8 and 28.3% homologies with Newcastle disease virus (NDV), Sendai virus (SV), parainfluenza type 3 virus (PIV-3) and measles virus (MV), respectively. Although sequence data on other components of transcriptive complex, NP and P, suggested a closer relationship between PIV-2 and MV, as concerns the L protein, MV is closely related to another group as SV and PIV-3. From analysis of the alignment of the five l proteins, six blocks composed of conserved amino acids were found in the L proteins. The L protein of PIV-2 was detected in purified virions and virus-infected cells using antiserum directed against an oligopeptide corresponding to the amino terminal region. Primer extension analyses showed that the intergenic regions at the NP-P, P-M, M-F, F-HN and HN-L junctions are 4, 45, 28, 8 and 42 nucleotides long, respectively, indicating that the intergenic regions exhibit no conservation of length and sequence. Furthermore, the starting and ending sequences of paramyxoviruses were summarized. Images PMID:1645865

  17. Influence of hydrophobic and hydrophilic spacer-containing enzyme conjugates on functional parameters of steroid immunoassay.

    PubMed

    Nara, Seema; Tripathi, Vinay; Chaube, Shail K; Rangari, Kiran; Singh, Harpal; Kariya, Kiran P; Shrivastav, Tulsidas G

    2008-02-01

    Introduction of spacers in coating steroid antigen or enzyme conjugates or immunogen is known to exert an influence on the sensitivity of steroid enzyme immunoassays. We have introduced hydrophobic and hydrophilic spacers between enzyme and steroid moieties and studied their effects on functional parameters of enzyme immunoassays, using cortisol as a model steroid. Cortisol-3-O-carboxymethyloxime-bovine serum albumin (F-3-O-CMO-BSA) was used as immunogen to raise the antiserum in New Zealand white rabbits. Three enzyme conjugates were prepared using cortisol-21-hemisuccinate (F-21-HS) as carboxylic derivative of cortisol and horseradish peroxidase (HRP) as an enzyme label. These were F-21-HS-HRP (without spacer), F-21-HS-adipic acid dihydrazide-HRP (adipic acid dihydrazide as hydrophobic spacer), and F-21-HS-urea-HRP (urea as hydrophilic spacer). The influence of hydrophobic and hydrophilic spacers on the functional parameters of assays such as lower detection limit, ED50, and specificity was studied with reference to enzyme conjugate without spacer. The results of the present investigation revealed that the presence of a hydrophilic spacer in the enzyme conjugate decreases the lower detection limit, decreases the ED50, and marginally improves the specificity of assays. These improvements in functional parameters of assays may be due to the decreased magnitude of the overall hydrophobic interactions existing between the spacer in enzyme conjugate and the antigen binding site of the antibody. PMID:18023401

  18. Nanoparticles based brachytherapy spacers for delivery of localized combined chemo-radiation therapy

    PubMed Central

    Kumar, Rajiv; Belz, Jodi; Markovic, Stacey; Jadhav, Tej; Fowle, William; Niedre, Mark; Cormack, Robert; Makrigiorgos, Mike G; Sridhar, Srinivas

    2015-01-01

    Purpose In radiation therapy (RT), brachytherapy inert source spacers are commonly used in clinical practice to achieve high spatial accuracy. These implanted devices are critical technical components of precise radiation delivery but provide no direct therapeutic benefits. Materials and Methods Here we have fabricated Implantable Nanoplatforms or Chemo-Radiation Therapy (INCeRT) spacers loaded with silica nanoparticles (SNPs) conjugated containing a drug, to act as a slow release drug depot for simultaneous localized chemo-radiation therapy. The spacers are made of poly(lactic-coglycolic) acid (PLGA) as matrix, were physically identical (size) to the commercially available brachytherapy spacers (5mm×0.8mm). The silica nanoparticles with diameter 250nm conjugated with near infrared fluorophore Cy7.5 as a model drug and the INCeRT spacers were characterized in terms of size, morphology and composition using different instrumentation techniques. The spacers were further doped with anticancer drug, docetaxel. We have evaluated the in vivo stability, biocompatibility and biodegradation of these spacers in live mouse tissues. Results The electron microscopy studies showed that nanoparticles were distributed throughout the spacers. These INCeRT spacers remained stable and can be tracked using optical fluorescence. In vivo optical imaging studies showed a slow diffusion of nanoparticles from the spacer to the adjacent tissue as opposed to the control Cy7.5-PLGA spacer which showed rapid disintegration in a few days with a burst release of Cy7.5. The docetaxel spacers showed suppression of tumor growth as opposed to control mice over 16 days. Conclusions The imaging with the Cy7.5-spacer and therapeutic efficacy with docetaxel-spacers supports the hypothesis that INCeRT spacers can be used for delivering the drugs in slow, sustained manner in conjunction with brachytherapy, as opposed to rapid clearance of the drugs when administered systemically. The results demonstrate

  19. Nanoparticle-Based Brachytherapy Spacers for Delivery of Localized Combined Chemoradiation Therapy

    SciTech Connect

    Kumar, Rajiv; Belz, Jodi; Markovic, Stacey; Jadhav, Tej; Fowle, William; Niedre, Mark; Cormack, Robert; Makrigiorgos, Mike G.; Sridhar, Srinivas

    2015-02-01

    Purpose: In radiation therapy (RT), brachytherapy-inert source spacers are commonly used in clinical practice to achieve high spatial accuracy. These implanted devices are critical technical components of precise radiation delivery but provide no direct therapeutic benefits. Methods and Materials: Here we have fabricated implantable nanoplatforms or chemoradiation therapy (INCeRT) spacers loaded with silica nanoparticles (SNPs) conjugated containing a drug, to act as a slow-release drug depot for simultaneous localized chemoradiation therapy. The spacers are made of poly(lactic-co-glycolic) acid (PLGA) as matrix and are physically identical in size to the commercially available brachytherapy spacers (5 mm × 0.8 mm). The silica nanoparticles, 250 nm in diameter, were conjugated with near infrared fluorophore Cy7.5 as a model drug, and the INCeRT spacers were characterized in terms of size, morphology, and composition using different instrumentation techniques. The spacers were further doped with an anticancer drug, docetaxel. We evaluated the in vivo stability, biocompatibility, and biodegradation of these spacers in live mouse tissues. Results: The electron microscopy studies showed that nanoparticles were distributed throughout the spacers. These INCeRT spacers remained stable and can be tracked by the use of optical fluorescence. In vivo optical imaging studies showed a slow diffusion of nanoparticles from the spacer to the adjacent tissue in contrast to the control Cy7.5-PLGA spacer, which showed rapid disintegration in a few days with a burst release of Cy7.5. The docetaxel spacers showed suppression of tumor growth in contrast to control mice over 16 days. Conclusions: The imaging with the Cy7.5 spacer and therapeutic efficacy with docetaxel spacers supports the hypothesis that INCeRT spacers can be used for delivering the drugs in a slow, sustained manner in conjunction with brachytherapy, in contrast to the rapid clearance of the drugs when

  20. The Prevalence and Phenomenology of Repetitive Behavior in Genetic Syndromes

    ERIC Educational Resources Information Center

    Moss, Joanna; Oliver, Chris; Arron, Kate; Burbidge, Cheryl; Berg, Katy

    2009-01-01

    We investigated the prevalence and phenomenology of repetitive behavior in genetic syndromes to detail profiles of behavior. The Repetitive Behaviour Questionnaire (RBQ) provides fine-grained identification of repetitive behaviors. The RBQ was employed to examine repetitive behavior in Angelman (N = 104), Cornelia de Lange (N = 101), Cri-du-Chat…

  1. 21 CFR 882.5805 - Repetitive transcranial magnetic stimulation system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Repetitive transcranial magnetic stimulation....5805 Repetitive transcranial magnetic stimulation system. (a) Identification. A repetitive transcranial magnetic stimulation system is an external device that delivers transcranial repetitive pulsed...

  2. 21 CFR 882.5805 - Repetitive transcranial magnetic stimulation system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Repetitive transcranial magnetic stimulation....5805 Repetitive transcranial magnetic stimulation system. (a) Identification. A repetitive transcranial magnetic stimulation system is an external device that delivers transcranial repetitive pulsed...

  3. 21 CFR 882.5805 - Repetitive transcranial magnetic stimulation system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Repetitive transcranial magnetic stimulation....5805 Repetitive transcranial magnetic stimulation system. (a) Identification. A repetitive transcranial magnetic stimulation system is an external device that delivers transcranial repetitive pulsed...

  4. Current role of spacers for prostate cancer radiotherapy

    PubMed Central

    Pinkawa, Michael

    2015-01-01

    Radiotherapy is an established curative treatment method for prostate cancer. Optimal tumor control rates can only be achieved with high local doses, associated with a considerable risk of rectal toxicity. Apart from already widely adapted technical advances, as intensity-modulated radiation therapy, the application of spacers placed between the prostate and rectum has been increasingly used in the last years. Biodegradable spacers, including hydrogel, hyaluronic acid, collagen or an implantable balloon, can be injected or inserted in a short procedure under transrectal ultrasound guidance via a transperineal approach. A distance of about 1.0-1.5 cm is usually achieved between the rectum and prostate, excluding the rectal wall from the high isodoses. Several studies have shown well tolerated injection procedures and treatments. Apart from considerable reduction of rectal irradiation, a prospective randomized trial demonstrated a reduction of rectal toxicity after hydrogel injection in men undergoing prostate image-guided intensity-modulated radiation therapy. The results are encouraging for continuing evaluation in dose escalation, hypofractionation, stereotactic radiotherapy or re-irradiation trials in the future. PMID:26677428

  5. Predicting electrical measurements by applying scatterometry to complex spacer structures

    NASA Astrophysics Data System (ADS)

    Sendelbach, Matthew; Ayala, Javier; Herrera, Pedro

    2007-03-01

    The comparison of scatterometry measurements of complex spacer structures to electrical test measurements is discussed. Details of the NFET and PFET structures are presented, along with a summary of the scatterometry models used to represent the structures. Before comparison data are shown, a methodology and set of metrics are presented that assist in the analysis and interpretation of comparison data. The methodology, called Prediction Analysis, has its roots in TMU analysis, where both measurements are subject to error. But in Prediction Analysis, an "apples-to-apples" comparison of the measurements is not the goal, and the measurements may be reported in different units. The goal of Prediction Analysis is to analyze the components of error in a correlation and use this analysis to predict a measurement based on the knowledge of another measurement, such that the predicted measurement is bounded. This method is used in this work to determine how well scatterometry measurements of certain parameters correlate to electrical measurements of gate resistance, gate Lpoly, and transistor current Ion. Clear correlations are demonstrated, and physical explanations that explain these correlations are presented. Due to the correlations, the scatterometry measurements can be used as a predictor of electrical performance significantly before the electrical test occurs. Because of this, scatterometry can be a reliable measurement technique for improving spacer controls and reducing the mean time to detect (MTTD) some profile abnormalities.

  6. Manipulating Articulatory Demands in Non-Word Repetition: A "Late-8" Non-Word Repetition Task

    ERIC Educational Resources Information Center

    Moore, Michelle W.; Tompkins, Connie A.; Dollaghan, Christine A.

    2010-01-01

    The purpose of this paper was to examine the psychometric properties of a non-word repetition task (NRT), the Late-8 Non-word Repetition Task (L8NRT). This task was designed similarly to the NRT, but contains only Late-8 consonants to increase articulatory demands and avoid ceiling effects in studies with adolescents and adults. Thirty college…

  7. Cervical interfacet spacers and maintenance of cervical lordosis.

    PubMed

    Tan, Lee A; Straus, David C; Traynelis, Vincent C

    2015-05-01

    OBJECT The cervical interfacet spacer (CIS) is a relatively new technology that can increase foraminal height and area by facet distraction. These offer the potential to provide indirect neuroforaminal decompression while simultaneously enhancing fusion potential due to the relatively large osteoconductive surface area and compressive forces exerted on the grafts. These potential benefits, along with the relative ease of implantation during posterior cervical fusion procedures, make the CIS an attractive adjuvant in the management of cervical pathology. One concern with the use of interfacet spacers is the theoretical risk of inducing iatrogenic kyphosis. This work tests the hypothesis that interfacet spacers are associated with loss of cervical lordosis. METHODS Records from patients undergoing posterior cervical fusion at Rush University Medical Center between March 2011 and December 2012 were reviewed. The FacetLift CISs were used in all patients. Preoperative and postoperative radiographic data were reviewed and the Ishihara indices and cervical lordotic angles were measured and recorded. Statistical analyses were performed using STATA software. RESULTS A total of 64 patients were identified in whom 154 cervical levels were implanted with machined allograft interfacet spacers. Of these, 15 patients underwent anterior-posterior fusions, 4 underwent anterior-posterior-anterior fusions, and the remaining 45 patients underwent posterior-only fusions. In the 45 patients with posterior-only fusions, a total of 110 levels were treated with spacers. There were 14 patients (31%) with a single level treated, 16 patients (36%) with two levels treated, 5 patients (11%) with three levels treated, 5 patients (11%) with four levels treated, 1 patient (2%) with five levels treated, and 4 patients (9%) with six levels treated. Complete radiographic data were available in 38 of 45 patients (84%). On average, radiographic follow-up was obtained at 256.9 days (range 48-524 days

  8. Repetition Priming and Repetition Suppression: A Case for Enhanced Efficiency Through Neural Synchronization

    PubMed Central

    Gotts, Stephen J.; Chow, Carson C.; Martin, Alex

    2012-01-01

    Stimulus repetition in identification tasks leads to improved behavioral performance ("repetition priming") but attenuated neural responses ("repetition suppression") throughout task-engaged cortical regions. While it's clear that this pervasive brain-behavior relationship reflects some form of improved processing efficiency, the exact form that it takes remains elusive. In this Discussion Paper, we review four different theoretical proposals that have the potential to link repetition suppression and priming, with a particular focus on a proposal that stimulus repetition affects improved efficiency through enhanced neural synchronization. We argue that despite exciting recent work on the role of neural synchronization in cognitive processes such as attention and perception, similar studies in the domain of learning and memory - and priming, in particular - have been lacking. We emphasize the need for new studies with adequate spatiotemporal resolution, formulate several novel predictions, and discuss our ongoing efforts to disentangle the current proposals. PMID:23144664

  9. Distribution of Genes and Repetitive Elements in the Diabrotica virgifera virgifera Genome Estimated Using BAC Sequencing

    PubMed Central

    Coates, Brad S.; Alves, Analiza P.; Wang, Haichuan; Walden, Kimberly K. O.; French, B. Wade; Miller, Nicholas J.; Abel, Craig A.; Robertson, Hugh M.; Sappington, Thomas W.; Siegfried, Blair D.

    2012-01-01

    Feeding damage caused by the western corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with 104 ± 34.5 kb inserts was created, which has an ~4.56X genome coverage based upon a 2.58 Gb (2.80 pg) flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17 Mb of data (~0.05% genome coverage) and indicated ~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs). Sequencing genes within BAC full inserts demonstrated that TE densities are high within intergenic and intron regions and contribute to the increased gene size. Comparison of homologous genome regions cloned within different BAC clones indicated that TE movement may cause haplotype variation within the inbred strain. The data presented here indicate that the D. virgifera virgifera genome is large in size and contains a high proportion of repetitive sequence. These BAC sequencing methods that are applicable for characterization of genomes prior to sequencing may likely be valuable resources for genome annotation as well as scaffolding. PMID:22919272

  10. Distribution of genes and repetitive elements in the Diabrotica virgifera virgifera genome estimated using BAC sequencing.

    PubMed

    Coates, Brad S; Alves, Analiza P; Wang, Haichuan; Walden, Kimberly K O; French, B Wade; Miller, Nicholas J; Abel, Craig A; Robertson, Hugh M; Sappington, Thomas W; Siegfried, Blair D

    2012-01-01

    Feeding damage caused by the western corn rootworm, Diabrotica virgifera virgifera, is destructive to corn plants in North America and Europe where control remains challenging due to evolution of resistance to chemical and transgenic toxins. A BAC library, DvvBAC1, containing 109,486 clones with 104 ± 34.5 kb inserts was created, which has an ~4.56X genome coverage based upon a 2.58 Gb (2.80 pg) flow cytometry-estimated haploid genome size. Paired end sequencing of 1037 BAC inserts produced 1.17 Mb of data (~0.05% genome coverage) and indicated ~9.4 and 16.0% of reads encode, respectively, endogenous genes and transposable elements (TEs). Sequencing genes within BAC full inserts demonstrated that TE densities are high within intergenic and intron regions and contribute to the increased gene size. Comparison of homologous genome regions cloned within different BAC clones indicated that TE movement may cause haplotype variation within the inbred strain. The data presented here indicate that the D. virgifera virgifera genome is large in size and contains a high proportion of repetitive sequence. These BAC sequencing methods that are applicable for characterization of genomes prior to sequencing may likely be valuable resources for genome annotation as well as scaffolding. PMID:22919272

  11. Identification and Functional Prediction of Large Intergenic Noncoding RNAs (lincRNAs) in Rainbow Trout (Oncorhynchus mykiss).

    PubMed

    Wang, Jian; Fu, Liyuan; Koganti, Prasanthi P; Wang, Lei; Hand, Jacqelyn M; Ma, Hao; Yao, Jianbo

    2016-04-01

    Long noncoding RNAs (lncRNAs) have been recognized in recent years as key regulators of diverse cellular processes. Genome-wide large-scale projects have uncovered thousands of lncRNAs in many model organisms. Large intergenic noncoding RNAs (lincRNAs) are lncRNAs that are transcribed from intergenic regions of genomes. To date, no lincRNAs in non-model teleost fish have been reported. In this report, we present the first reference catalog of 9674 rainbow trout lincRNAs based on analysis of RNA-Seq data from 15 tissues. Systematic analysis revealed that lincRNAs in rainbow trout share many characteristics with those in other mammalian species. They are shorter and lower in exon number and expression level compared with protein-coding genes. They show tissue-specific expression pattern and are typically co-expressed with their neighboring genes. Co-expression network analysis suggested that many lincRNAs are associated with immune response, muscle differentiation, and neural development. The study provides an opportunity for future experimental and computational studies to uncover the functions of lincRNAs in rainbow trout. PMID:26864089

  12. All-Trans Retinoic Acid Induces Expression of a Novel Intergenic Long Noncoding RNA in Adult rat Primary Hippocampal Neurons.

    PubMed

    Kour, Sukhleen; Rath, Pramod C

    2016-02-01

    Around 90% of the mammalian genome undergoes pervasive transcription into various types of small and long regulatory noncoding RNAs, whereas only ∼ 1.5% codes for proteins. Long noncoding RNAs (lncRNAs) constitute diverse classes of sense- and antisense transcripts that are abundantly expressed in the mammalian central nervous system (CNS) in cell type- and developmental stage-specific manners. They are implicated in brain development, differentiation, neuronal plasticity, and other cognitive functions. Mammalian brain requires the vitamin A metabolite all-trans retinoic acid (atRA) for its normal development, differentiation, and cell-fate determination. However, its role in adult brain function is less understood. Here, we report atRA-mediated transcriptional upregulation of endogenous expression of a novel long intergenic noncoding RNA-rat brain expressed (LINC-RBE) in cultured primary hippocampal neurons from adult rat. We have previously reported LINC-RBE as an intergenic, simple repeat sequence containing lncRNA highly expressed in the rat brain. This is a first-time report of involvement of atRA in transcriptional upregulation of lncRNA expression in rat hippocampal neurons. Therefore, it may be involved in regulation of brain function and disease. PMID:26572536

  13. The CASC15 long intergenic non-coding RNA locus is involved in melanoma progression and phenotype-switching

    PubMed Central

    Lessard, Laurent; Liu, Michelle; Marzese, Diego M.; Wang, Hongwei; Chong, Kelly; Kawas, Neal; Donovan, Nicholas C; Kiyohara, Eiji; Hsu, Sandy; Nelson, Nellie; Izraely, Sivan; Sagi-Assif, Orit; Witz, Isaac P; Ma, Xiao-Jun; Luo, Yuling; Hoon, Dave SB

    2015-01-01

    In recent years, considerable advances have been made in the characterization of protein-coding alterations involved in the pathogenesis of melanoma. However, despite their growing implication in cancer, little is known about the role of long non-coding RNAs in melanoma progression. We hypothesized that copy number alterations of intergenic non-protein coding domains could help identify long intergenic non-coding RNAs (lincRNAs) associated with metastatic cutaneous melanoma. Among several candidates, our approach uncovered the chromosome 6p22.3 CASC15 lincRNA locus as a frequently gained genomic segment in metastatic melanoma tumors and cell lines. The locus was actively transcribed in metastatic melanoma cells, and up-regulation of CASC15 expression was associated with metastatic progression to brain metastasis in a mouse xenograft model. In clinical specimens, CASC15 levels increased during melanoma progression and were independent predictors of disease recurrence in a cohort of 141 patients with AJCC stage III lymph node metastasis. Moreover, siRNA knockdown experiments revealed that CASC15 regulates melanoma cell phenotype switching between proliferative and invasive states. Accordingly, CASC15 levels correlated with known gene signatures corresponding to melanoma proliferative and invasive phenotypes. These findings support a key role for CASC15 in metastatic melanoma. PMID:26016895

  14. Effect of Structure on the Mechanical Behaviors of Three-Dimensional Spacer Fabric Composites

    NASA Astrophysics Data System (ADS)

    Li, Min; Wang, Shaokai; Zhang, Zuoguang; Wu, Boming

    2009-02-01

    Three-dimensional (3-D) spacer fabric composite is a newly developed sandwich structure, the reinforcement of which is integrally woven by advanced textile technique. Two facesheets of 3-D spacer fabric are connected by continuous fibers, named pile in the core, providing excellent properties like outstanding integrity, debonding resistance, light weight, good designability and so on. Usually the 3-D spacer fabric composite without extra reinforcement is a kind of core material. In comparison with the facesheet reinforced spacer fabric composite, here the composite without additional weaves is called mono-spacer fabric composite. In this paper, two kinds of mono-spacer fabric composites with integrated hollow cores have been developed, one with 8-shaped piles and the other with corrugated piles. The mechanical characteristics and the damage modes of these mono-spacer fabric composites under different load conditions have been investigated. Besides, effects of pile height, pile distribution density and pile structure on the composites mechanical performances were analyzed. It is shown that the mechanical performances of mono-spacer fabric composites can be widely adapted to the respective requirements through the choice of the structural factors.

  15. Ertapenem Articulating Spacer for the Treatment of Polymicrobial Total Knee Arthroplasty Infection

    PubMed Central

    Marinkovic, Jugoslav

    2016-01-01

    Introduction. Periprosthetic joint infections (PJIs) are the primary cause of early failure of the total knee arthroplasty (TKA). Polymicrobial TKA infections are often associated with a higher risk of treatment failure. The aim of the study was to assess the efficacy of ertapenem loaded spacers in the treatment of polymicrobial PJI. Methods. There were 18 patients enrolled; nine patients with polymicrobial PJI treated with ertapenem loaded articulating spacers were compared to the group of 9 patients treated with vancomycin or ceftazidime loaded spacers. Results. Successful reimplantation with revision implants was possible in 66.67%. Ertapenem spacers were used in 6 cases in primary two-stage procedure and in 3 cases in secondary spacer exchange. Successful infection eradication was achieved in all cases; final reimplantation with revision knee arthroplasty implants was possible in 6 cases. Conclusion. Ertapenem can be successfully used as antimicrobial addition to the cement spacers in two-stage revision treatment of polymicrobial PJIs. However, this type of spacer may also be useful in the treatment of infections caused by monomicrobial extended spectrum beta-lactamases producing gram-negative bacilli. Further clinical studies are required to evaluate the efficacy and safety of ertapenem spacers in the treatment of polymicrobial and monomicrobial PJIs. PMID:27366173

  16. Mechanical behaviour of standardized, endoskeleton-including hip spacers implanted into composite femurs

    PubMed Central

    Thielen, T.; Maas, S.; Zuerbes, A.; Waldmann, D.; Anagnostakos, K.; Kelm, J.

    2009-01-01

    Two-stage reconstruction using an antibiotic loaded cement spacer is the preferred treatment method of late hip joint infections. Hip spacers maintain stability of the joint and length of the limb during treatment period. However, as the material strength of bone cement (PMMA) is limited, spacer fractures led to serious complications in the past. This study investigated the load capacity of custom made hip spacers, developed at the 'Klinik für Orthopädie und Orthopädische Chirurgie' (Universitätsklinikum des Saarlandes, Homburg / Saar, Germany), and implanted into composite femurs. In a quasi-static test, non-reinforced spacers tolerated hip joint loads of about 3000 N, whereas reinforced spacers with titanium-grade-two endoskeletons doubled this load up to 6000 N. Even for cyclic loading, endoskeleton-including hip spacers tolerated loads of >4500 N with 500,000 load cycles. Thus, an endoskeleton-including spacer should provide a mobile and functional joint through the treatment course. A generated FE-model was used to determine the fracture stresses and allows for further sensitivity analysis. PMID:19834594

  17. Effect of spacer length and type on the biological activity of peptide-polysaccharide matrices.

    PubMed

    Kumai, Jun; Hozumi, Kentaro; Yamada, Yuji; Katagiri, Fumihiko; Kikkawa, Yamato; Nomizu, Motoyoshi

    2016-11-01

    Peptide-polysaccharide matrices can mimic extracellular matrix structure and function and are useful for tissue and cell engineering. The spacer between the peptide and the polysaccharide is important for both peptide conformation and the interaction between the peptide and receptors. Here, the effect of a spacer on the biological activity of peptide-polysaccharide matrices using various lengths of spacers consisting of glycine, β-alanine, and ε-aminocaproic acid has been examined. Active laminin-derived peptides, including a syndecan-binding peptide (AG73: RKRLQVQLSIRT), an integrin αvβ3-binding peptide (A99a: ALRGDN), and an integrin α6β1-binding peptide (A2G10: SYWYRIEASRTG), were used as the peptide ligands and chitosan was used as a polysaccharide matrix. The spacers did not influence the biological activity of the AG73-chitosan matrix. In contrast, the integrin-binding peptide-chitosan matrices showed spacer-dependent activity. Hydrophobic spacers enhanced the cell attachment activity of the A99a-chitosan matrix. A four-glycine spacer showed the strongest effect for the biological activity of the A2G10-chitosan matrix. These results suggested that spacer-optimization for each peptide is important for designing effective peptide-polysaccharide matrices. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 512-520, 2016. PMID:26588050

  18. Patterning with amorphous carbon spacer for expanding the resolution limit of current lithography tool

    NASA Astrophysics Data System (ADS)

    Jung, Woo-Yung; Kim, Sang-Min; Kim, Choi-Dong; Sim, Guee-Hwang; Jeon, Sung-Min; Park, Sang-Wook; Lee, Byung-Seok; Park, Sung-Ki; Kim, Ji-Soo; Heon, Lee-Sang

    2007-03-01

    Double patterning technique using spacer which can avoid CD (Critical Dimension) uniformity problem mainly caused by overlay issue is one of the methods that could be applied to apply to manufacturing of memory devices. Though double exposure and etch technology (DEET) has comparative advantage in the number of process steps, it is required to dramatically improve overlay performance of current exposure tools for the realization of manufacturing. In this study, negative type-double pattering technique using spacer has been developed as the best way for the application of NAND flash memory device from the view point of CD uniformity and the number of mask layers used to complete double patterning. Negative type-double patterning technique using spacer consists of subsequent steps such as formation of poly line, spacer on sidewall of poly line, SOG gap fill into space between poly lines, SOG etch back, removal of spacer, and finally hard mask etch. We have used amorphous carbon as a spacer material to easily remove spacer from poly lines and adopted SOG material to easily fill in space between poly lines. When negative type-double patterning technique using spacer is applied to NAND flash memory device, we can expect that k1 factor of about 0.14~0.20 could be accomplished successfully.

  19. The Internal Transcribed Spacer Region of Belonolaimus (Nemata: Belonolaimidae)

    PubMed Central

    Cherry, T.; Szalanski, A. L.; Todd, T. C.; Powers, T. O.

    1997-01-01

    Belonolaimus isolates from six U.S. states were compared by restriction endonuclease digestion of amplified first internal transcribed spacer region (ITS1) of the nuclear ribosomal genes. Seven restriction enzymes were selected for evaluation based on restriction sites inferred from the nucleotide sequence of a South Carolina Belonolaimus isolate. Amplified product size from individuals of each isolate was approximately 700 bp. All Midwestern isolates gave distinct restriction digestion patterns. Isolates identified morphologically as Belonolaimus longicaudatus from Florida, South Carolina, and Palm Springs, California, were identical for ITS1 restriction patterns. The correlation between ITS1 restriction patterns and the distribution of B. longicaudatus isolates suggest that the California isolate is a relatively recent introduction into the state. PMID:19274130

  20. Modified Open-door Laminoplasty Using Hydroxyapatite Spacers and Miniplates

    PubMed Central

    Jin, Sung-Won; Kim, Bum-Joon; Choi, Jong-Il; Ha, Sung-Kon; Kim, Sang-Dae; Lim, Dong-Jun

    2014-01-01

    Objective Cervical laminoplasty has been widely accepted as one of the major treatments for cervical myelopathy and various modifications and supplementary procedures have been devised to achieve both proper decompression and stability of the cervical spine. We present the retrospectively analyzed results of a modified unilateral open-door laminoplasty using hydroxyapatite (HA) spacers and malleable titanium miniplates. Methods From June 2008 to May 2012, among patients diagnosed with cervical spondylotic myelopathy and ossification of posterior longitudinal ligament, the patients who received laminoplasty were reviewed. Clinical outcome was assessed using Frankel grade and Japanese Orthopaedic Association score. The radiologic parameters were obtained from plain films, 3-dimensional computed tomography and magnetic resonance images. Results A total of 125 cervical laminae were operated in 38 patients. 11 patients received 4-level laminoplasty and 27 patients received 3-level laminoplasty. Postoperatively, the mean Frankel grade and JOA score were significantly improved from 3.97 to 4.55 and from 12.76 to 14.63, respectively (p<0.001). Radiologically, cervical curvature was worsened from 19.09 to 15.60 (p=0.025). The percentage of range of motion preservation was 73.32±22.39%. The axial dimension of the operated spinal canal was increased from 1.75 to 2.70 cm2 (p<0.001). Conclusion In the presenting study, unilateral open-door laminoplasty using HA spacers and miniplates appears to be a safe, rapid and easy procedure to obtain an immediate and rigid stabilization of the posterior elements of the cervical spine. This modified laminoplasty method showed effective expansion of the spinal canal and favorable clinical outcomes. PMID:25346767

  1. Posterior dynamic stabilization: The interspinous spacer from treatment to prevention

    PubMed Central

    Nachanakian, Antoine; El Helou, Antonios; Alaywan, Moussa

    2016-01-01

    Introduction: Managements of lumbar stenosis evoluted over the time from decompression to dynamic stabilization preserving the motion segment passing by the rigid fixation. After long years of rigid fusion, adjacent segment disease became more and more frequent and the concept of dynamic stabilization emerged. Materials and Methods: We report our experience with posterior dynamic stabilization using an interspinous distracter (ISD). One hundred and eight patients were operated between September 2008 and January 2012 with different lumbar spine pathologies. The ages of our patients were between 45 years and 70 years, with a mean age of 55 years. With our growing experience, indication of ISD became narrowed and the interspinous spacer became an absolute tool for adjacent segment disease as a treatment as well as prophylactic with rigid stabilization. Results and Discussion: Overall clinical improvement was noted in ISD-treated patients, with considerable satisfaction in 77% of patients on average. The patient at first reported an improvement of their radicular pain with a mean reduction of 3.6/10 on visual analog scale. Post-operative walking distance progressively increased during the next 3 months. Whereas, a radiological evaluation at 3 months showed a mean of 42% improvement of the disc height. On the other hand, all patients operated with posterior dynamic stabilization (PDS) at the time of rigid stabilization showed no adjacent segment disease compared to those operated with posterior arthrodesis (P < 0.05). Conclusion: Interspinous spacer after surgical decompression for spinal stenosis by excision of Ligamentum flavum demonstrates excellent short-term and long-term results for improvement in back pain, neurogenic claudication, and patient satisfaction. It provides restoration of disc height, reduction of vertebral slip and it's a necessary tool in the management and the prevention of adjacent segment disease. PMID:27057211

  2. Single electron transistor with P-type sidewall spacer gates.

    PubMed

    Lee, Jung Han; Li, Dong Hua; Lee, Joung-Eob; Kang, Kwon-Chil; Kim, Kyungwan; Park, Byung-Gook

    2011-07-01

    A single-electron transistor (SET) is one of the promising solutions to overcome the scaling limit of the Metal-Oxide-Semiconductor Field Effect Transistor (MOSFET). Up to now, various kinds of SETs are being proposed and SETs with a dual gate (DG) structure using an electrical potential barrier have been demonstrated for room temperature operation. To operate DG-SETs, however, extra bias of side gates is necessary. It causes new problems that the electrode for side gates and the extra bias for electrical barrier increase the complexity in circuit design and operation power consumption, respectively. For the reason, a new mechanism using work function (WF) difference is applied to operate a SET at room temperature by three electrodes. Its structure consists of an undoped active region, a control gate, n-doped source/drain electrodes, and metal/silicide or p-type silicon side gates, and a SET with metal/silicide gates or p-type silicon gates forms tunnel barriers induced by work function between an undoped channel and grounded side gates. Via simulation, the effectiveness of the new mechanism is confirmed through various silicide materials that have different WF values. Furthermore, by considering the realistic conditions of the fabrication process, SET with p-type sidewall spacer gates was designed, and its brief fabrication process was introduced. The characteristics of its electrical barrier and the controllability of its control gate were also confirmed via simulation. Finally, a single-hole transistor with n-type sidewall spacer gates was designed. PMID:22121580

  3. Matriculation Research Report: Course Repetition Data & Analysis.

    ERIC Educational Resources Information Center

    Gerda, Joe

    Due to concerns that its policy on class repetition was not promoting student success, California's College of the Canyons (CoC) undertook a project to analyze student course-taking patterns and make recommendations to modify the policy. Existing college policy did not follow Section 58161 of the State Educational Code that allows colleges to…

  4. Using Repetition to Make Ideas Stick

    ERIC Educational Resources Information Center

    Lykins, Alicia N.

    2015-01-01

    In elementary school, the use of repetitive songs to help children remember concepts is commonplace and is usually very effective. Unfortunately for many students, this strategy is generally not used in later grades. A group of mathematics teachers at Westerville South High School in Westerville, Ohio, have taken this approach to a new creative…

  5. Repetition effects in human ERPs to faces.

    PubMed

    Schweinberger, Stefan R; Neumann, Markus F

    2016-07-01

    In the present paper, we review research conducted over the past 25 years addressing the effects of repeating various kinds of information in faces (e.g., pictorial, spatial configural, identity, semantic) on different components in human event-related brain potentials (ERPs). This body of evidence suggests that several ERP components are systematically linked to different functional components of face identity processing. Specifically, we argue (1) that repetition of the category of faces (categorical adaptation) strongly affects the occipitotemporal N170 amplitude, which is systematically suppressed when a face is preceded by another face, irrespective of its identity, whereas (2) the prototypicality of a face's second order spatial configuration has a prominent effect on the subsequent occipitotemporal P200. Longer-latency repetition effects are related to the processing of individual facial identities. These include (3) an ERP correlate of the transient activation of individual representations of repeated faces in the form of an enhanced occipitotemporal N250r as seen in repetition priming experiments, and (4) a correlate of the acquisition of individual face identity representations during learning as seen in a topographically similar long-lasting N250 effect. Finally, (5) the repetition of semantic information in familiar person recognition elicits a central-parietal N400 ERP effect. We hope that this overview will encourage researchers to further exploit the potential of ERPs to provide a continuous time window to neuronal correlates of multiple processes in face perception under comparatively natural viewing conditions. PMID:26672902

  6. FRB repetition and non-Poissonian statistics

    NASA Astrophysics Data System (ADS)

    Connor, Liam; Pen, Ue-Li; Oppermann, Niels

    2016-05-01

    We discuss some of the claims that have been made regarding the statistics of fast radio bursts (FRBs). In an earlier Letter, we conjectured that flicker noise associated with FRB repetition could show up in non-cataclysmic neutron star emission models, like supergiant pulses. We show how the current limits of repetition would be significantly weakened if their repeat rate really were non-Poissonian and had a pink or red spectrum. Repetition and its statistics have implications for observing strategy, generally favouring shallow wide-field surveys, since in the non-repeating scenario survey depth is unimportant. We also discuss the statistics of the apparent latitudinal dependence of FRBs, and offer a simple method for calculating the significance of this effect. We provide a generalized Bayesian framework for addressing this problem, which allows for direct model comparison. It is shown how the evidence for a steep latitudinal gradient of the FRB rate is less strong than initially suggested and simple explanations like increased scattering and sky temperature in the plane are sufficient to decrease the low-latitude burst rate, given current data. The reported dearth of bursts near the plane is further complicated if FRBs have non-Poissonian repetition, since in that case the event rate inferred from observation depends on observing strategy.

  7. Pressure wave charged repetitively pulsed gas laser

    DOEpatents

    Kulkarny, Vijay A.

    1982-01-01

    A repetitively pulsed gas laser in which a system of mechanical shutters bracketing the laser cavity manipulate pressure waves resulting from residual energy in the cavity gas following a lasing event so as to draw fresh gas into the cavity and effectively pump spent gas in a dynamic closed loop.

  8. Sentence Repetition: What Does the Task Measure?

    ERIC Educational Resources Information Center

    Polišenská, Kamila; Chiat, Shula; Roy, Penny

    2015-01-01

    Background: Sentence repetition is gaining increasing attention as a source of information about children's sentence-level abilities in clinical assessment, and as a clinical marker of specific language impairment. However, it is widely debated what the task is testing and therefore how informative it is. Aims: (1) To evaluate the effects of…

  9. Temporal Processing Capabilities in Repetition Conduction Aphasia

    ERIC Educational Resources Information Center

    Sidiropoulos, Kyriakos; Ackermann, Hermann; Wannke, Michael; Hertrich, Ingo

    2010-01-01

    This study investigates the temporal resolution capacities of the central-auditory system in a subject (NP) suffering from repetition conduction aphasia. More specifically, the patient was asked to detect brief gaps between two stretches of broadband noise (gap detection task) and to evaluate the duration of two biphasic (WN-3) continuous noise…

  10. Social Interaction and Repetitive Motor Behaviors

    ERIC Educational Resources Information Center

    Loftin, Rachel L.; Odom, Samuel L.; Lantz, Johanna F.

    2008-01-01

    Students with autism have difficulty initiating social interactions and may exhibit repetitive motor behavior (e.g., body rocking, hand flapping). Increasing social interaction by teaching new skills may lead to reductions in problem behavior, such as motor stereotypies. Additionally, self-monitoring strategies can increase the maintenance of…

  11. Reducing Repetitive Speech: Effects of Strategy Instruction.

    ERIC Educational Resources Information Center

    Dipipi, Caroline M.; Jitendra, Asha K.; Miller, Judith A.

    2001-01-01

    This article describes an intervention with an 18-year-old young woman with mild mental retardation and a seizure disorder, which focused on her repetitive echolalic verbalizations. The intervention included time delay, differential reinforcement of other behaviors, and self-monitoring. Overall, the intervention was successful in facilitating…

  12. Verbal Repetitions and Echolalia in Alzheimer's Discourse

    ERIC Educational Resources Information Center

    Da Cruz, Fernanda Miranda

    2010-01-01

    This article reports on an investigation of echolalic repetition in Alzheimer's disease (AD). A qualitative analysis of data from spontaneous conversations with MHI, a woman with AD, is presented. The data come from the DALI Corpus, a corpus of spontaneous conversations involving subjects with AD. This study argues that echolalic effects can be…

  13. Large-scale detection of repetitions

    PubMed Central

    Smyth, W. F.

    2014-01-01

    Combinatorics on words began more than a century ago with a demonstration that an infinitely long string with no repetitions could be constructed on an alphabet of only three letters. Computing all the repetitions (such as ⋯TTT⋯ or ⋯CGACGA⋯ ) in a given string x of length n is one of the oldest and most important problems of computational stringology, requiring time in the worst case. About a dozen years ago, it was discovered that repetitions can be computed as a by-product of the Θ(n)-time computation of all the maximal periodicities or runs in x. However, even though the computation is linear, it is also brute force: global data structures, such as the suffix array, the longest common prefix array and the Lempel–Ziv factorization, need to be computed in a preprocessing phase. Furthermore, all of this effort is required despite the fact that the expected number of runs in a string is generally a small fraction of the string length. In this paper, I explore the possibility that repetitions (perhaps also other regularities in strings) can be computed in a manner commensurate with the size of the output. PMID:24751872

  14. Nonword Repetition and Vocabulary Use in Toddlers

    ERIC Educational Resources Information Center

    Stokes, Stephanie F.; Moran, Catherine; George, Anjali

    2013-01-01

    Purpose: There is general consensus that the ability to repeat nonsense words is related to vocabulary size in young children, but there is considerable debate about the nature of the relationship and the mechanisms that underlie it. Research with adults has proposed a shared neural substrate for nonword repetition (NWR) and language production,…

  15. Large-scale detection of repetitions.

    PubMed

    Smyth, W F

    2014-05-28

    Combinatorics on words began more than a century ago with a demonstration that an infinitely long string with no repetitions could be constructed on an alphabet of only three letters. Computing all the repetitions (such as ∙∙∙TTT ∙∙∙ or ∙∙∙ CGACGA ∙∙∙ ) in a given string x of length n is one of the oldest and most important problems of computational stringology, requiring time in the worst case. About a dozen years ago, it was discovered that repetitions can be computed as a by-product of the Θ(n)-time computation of all the maximal periodicities or runs in x. However, even though the computation is linear, it is also brute force: global data structures, such as the suffix array, the longest common prefix array and the Lempel-Ziv factorization, need to be computed in a preprocessing phase. Furthermore, all of this effort is required despite the fact that the expected number of runs in a string is generally a small fraction of the string length. In this paper, I explore the possibility that repetitions (perhaps also other regularities in strings) can be computed in a manner commensurate with the size of the output. PMID:24751872

  16. Bystanders' Reactions to Witnessing Repetitive Abuse Experiences

    ERIC Educational Resources Information Center

    Janson, Gregory R.; Carney, JoLynn V.; Hazler, Richard J.; Oh, Insoo

    2009-01-01

    The Impact of Event Scale-Revised (D. S. Weiss & C. R. Marmar, 1997) was used to obtain self-reported trauma levels from 587 young adults recalling childhood or adolescence experiences as witnesses to common forms of repetitive abuse defined as bullying. Mean participant scores were in a range suggesting potential need for clinical assessment at…

  17. Nonword Repetition, Phonological Storage, and Multiple Determinations

    ERIC Educational Resources Information Center

    Gupta, Prahlad

    2006-01-01

    The proposals that (a) nonword repetition and word learning both rely on phonological storage and (b) both are multiply determined are two of the major foci of Gathercole's (2006) Keynote Article, which marshals considerable evidence in support of each. In my view, the importance of these proposals cannot be overstated: these two notions go to the…

  18. Synthesis and evaluation of new spacers for use as dsDNA endcaps

    PubMed Central

    Ng, Pei-Sze; Laing, Brian M.; Balasundarum, Ganesan; Pingle, Maneesh; Friedman, Alan; Bergstrom, Donald E.

    2010-01-01

    A series of aliphatic and aromatic spacer molecules designed to cap the ends of DNA duplexes have been synthesized. The spacers were converted into dimethoxytrityl protected phosphoramidites as synthons for oligonucleotides synthesis. The effect of the spacers on the stability of short DNA duplexes was assessed by melting temperature studies. Endcaps containing amide groups were found to be less stabilizing than the hexaethylene glycol spacer. Endcaps containing either a terthiophene or a naphthalene tetracarboxylic acid dimide were found to be significantly more stabilizing. The former showed a preference for stacking above an A•T base pair. Spacers containing only methylene (-CH2-) and amide (-CONH-) groups interact weakly with DNA and consequently may be optimal for applications that require minimal influence on DNA structure but require a way to hold the ends of double-stranded DNA together. PMID:20715857

  19. Preliminary analysis and design optimization of the short spacer truss of Space Station Freedom

    NASA Technical Reports Server (NTRS)

    Gendy, A. S.; Patnaik, S. N.; Hopkins, D. A.; Berke, L.

    1993-01-01

    The analysis, dynamic simulation, and design optimization of the short spacer truss of the Space Station Freedom are presented in this report. The short spacer truss will be positioned between the integrated equipment assembly (IEA) and another truss, called the long spacer truss, in the Space Station Freedom. During its launch in the Space Shuttle, the truss will be subjected to considerable in-span distributed inertia loads due to shuttle accelerations. The short spacer truss, therefore, has been modeled as a space frame to account for flexural response. Several parameters have been assumed, since the design specifications are in the process of development; hence the results presented should be considered preliminary. However, the automated analysis and design capabilities that have been developed can readily be used to generate an optimum design of the short spacer truss once the actual specifications have been determined. This report includes static and dynamic analyses of the short spacer truss, which have been obtained with the linear elastic code LE-HOST (in these analyses, LE-HOST data files have been automated to facilitate their future use for different design specifications of the short spacer truss); the dynamic animation of the short spacer truss, which has been carried out by using the results of the dynamic analysis and a post-processing feature of the modeling code PATRAN; and the optimum-weight design of the spacer truss, which was obtained under prescribed stress, displacement, and frequency constraints by using the design code COMETBOARDS. Examination of the analysis and design results revealed that the design could be improved if the configuration of the short spacer truss were modified to a certain extent. A modified configuration, which may simplify fabrication, has been suggested. The performance of this configuration has been evaluated and was found to be satisfactory under both static and dynamic conditions.

  20. A Nonword Repetition Task for Speakers with Misarticulations: The Syllable Repetition Task (SRT)

    PubMed Central

    Shriberg, Lawrence D.; Lohmeier, Heather L.; Campbell, Thomas F.; Dollaghan, Christine A.; Green, Jordan R.; Moore, Christopher A.

    2010-01-01

    Purpose Conceptual and methodological confounds occur when non(sense) repetition tasks are administered to speakers who do not have the target speech sounds in their phonetic inventories or who habitually misarticulate targeted speech sounds. We describe a nonword repetition task, the Syllable Repetiton Task (SRT) that eliminates this confound and report findings from three validity studies. Method Ninety-five preschool children with Speech Delay and 63 with Typical Speech, completed an assessment battery that included the Nonword Repetition Task (NRT: Dollaghan & Campbell, 1998) and the SRT. SRT stimuli include only four of the earliest occurring consonants and one early occurring vowel. Results Study 1 findings indicated that the SRT eliminated the speech confound in nonword testing with speakers who misarticulate. Study 2 findings indicated that the accuracy of the SRT to identify expressive language impairment was comparable to findings for the NRT. Study 3 findings illustrated the SRT’s potential to interrogate speech processing constraints underlying poor nonword repetition accuracy. Results supported both memorial and auditory-perceptual encoding constraints underlying nonword repetition errors in children with speech-language impairment. Conclusion The SRT appears to be a psychometrically stable and substantively informative nonword repetition task for emerging genetic and other research with speakers who misarticulate. PMID:19635944

  1. Genome-wide CpG island methylation and intergenic demethylation propensities vary among different tumor sites.

    PubMed

    Lee, Seung-Tae; Wiemels, Joseph L

    2016-02-18

    The epigenetic landscape of cancer includes both focal hypermethylation and broader hypomethylation in a genome-wide manner. By means of a comprehensive genomic analysis on 6637 tissues of 21 tumor types, we here show that the degrees of overall methylation in CpG island (CGI) and demethylation in intergenic regions, defined as 'backbone', largely vary among different tumors. Depending on tumor type, both CGI methylation and backbone demethylation are often associated with clinical, epidemiological and biological features such as age, sex, smoking history, anatomic location, histological type and grade, stage, molecular subtype and biological pathways. We found connections between CGI methylation and hypermutability, microsatellite instability, IDH1 mutation, 19p gain and polycomb features, and backbone demethylation with chromosomal instability, NSD1 and TP53 mutations, 5q and 19p loss and long repressive domains. These broad epigenetic patterns add a new dimension to our understanding of tumor biology and its clinical implications. PMID:26464434

  2. Capturing intergenerativity: the use of student reflective journals to identify learning within an undergraduate course in gerontological nursing.

    PubMed

    Davies, Susan M; Reitmaier, Amy B; Smith, Linda Reveling; Mangan-Danckwart, Deborah

    2013-03-01

    The benefits of intergenerational contact between older and young adults have been demonstrated; yet, nursing programs have underexplored the potential of such relationships for enhancing student learning. This article presents an analysis of student reflective journals as part of an evaluation of an undergraduate gerontological nursing course. The course aims to create positive learning experiences by involving older adults as partners in student learning. Older adults are recruited to receive visits from a designated student to share aspects of their life and experiences. Students write reflective journals based on these visits as a method of evaluating their learning. A framework analysis of 80 journals completed by 59 students identified four major themes representing the impact of these visits on student learning: becoming aware, making connections, seeing the unique person, and valuing intergenerational relationships. The analysis suggests the relevance of the concept of intergenerativity in illuminating shared benefits of the practicum experience. PMID:23402281

  3. Genome-wide CpG island methylation and intergenic demethylation propensities vary among different tumor sites

    PubMed Central

    Lee, Seung-Tae; Wiemels, Joseph L.

    2016-01-01

    The epigenetic landscape of cancer includes both focal hypermethylation and broader hypomethylation in a genome-wide manner. By means of a comprehensive genomic analysis on 6637 tissues of 21 tumor types, we here show that the degrees of overall methylation in CpG island (CGI) and demethylation in intergenic regions, defined as ‘backbone’, largely vary among different tumors. Depending on tumor type, both CGI methylation and backbone demethylation are often associated with clinical, epidemiological and biological features such as age, sex, smoking history, anatomic location, histological type and grade, stage, molecular subtype and biological pathways. We found connections between CGI methylation and hypermutability, microsatellite instability, IDH1 mutation, 19p gain and polycomb features, and backbone demethylation with chromosomal instability, NSD1 and TP53 mutations, 5q and 19p loss and long repressive domains. These broad epigenetic patterns add a new dimension to our understanding of tumor biology and its clinical implications. PMID:26464434

  4. Conservation of the Exon-Intron Structure of Long Intergenic Non-Coding RNA Genes in Eutherian Mammals.

    PubMed

    Chernikova, Diana; Managadze, David; Glazko, Galina V; Makalowski, Wojciech; Rogozin, Igor B

    2016-01-01

    The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA with those of protein-coding genes for which a large body of functional information is available. A prominent feature of mammalian protein-coding genes is the high evolutionary conservation of the exon-intron structure. Comparative analysis of putative intron positions in lincRNA genes from various mammalian genomes suggests that some lincRNA introns have been conserved for over 100 million years, thus the primary and/or secondary structure of these molecules is likely to be functionally important. PMID:27429005

  5. H2A.Z has a function reminiscent of an activator required for preferential binding to intergenic DNA

    PubMed Central

    Larochelle, Marc; Gaudreau, Luc

    2003-01-01

    H2A.Z has been shown to regulate transcription in yeast, and that function resides in its C-terminal region as the reciprocal portion of H2A cannot substitute for the latter. We show that fusion of a transcriptional activating region to the C-terminal region of H2A, which is substituted for that of H2A.Z, can allow the chimera to fulfil the special role of H2A.Z in positive gene regulation, as well as complement growth deficiencies of htz1Δ cells. We further show that the ‘transcription’ function of H2A.Z is linked to its ability to preferentially localize to certain intergenic DNA regions. Our results suggest that H2A.Z modulates functional interactions with transcription regulatory components, and thus increases its localization to promoters where it helps poise chromatin for gene activation. PMID:12941702

  6. Degradation of silica-filled epoxy spacers by arc contaminated gases in SF/sub 6/-insulated equipment

    SciTech Connect

    Stuckless, H.A.; Braun, J.M.; Chu, F.Y.

    1985-12-01

    The visual and electrical effects of arced SF/sub 6/ gas on epoxy spacers with various fillers are examined. Field experience and laboratory investigations into the dielectric degradation of epoxy spacers and maintenance techniques for identifying serious loss of dielectric withstand are discussed. Rehabilitation of damaged spacers is also discussed.

  7. Identification of Rhizobium-specific intergenic mosaic elements within an essential two-component regulatory system of Rhizobium species.

    PubMed Central

    Osterås, M; Stanley, J; Finan, T M

    1995-01-01

    Analysis of the DNA regions upstream of the phosphoenolpyruvate carboxykinase gene (pckA) in Rhizobium meliloti and Rhizobium sp. strain NGR234 identified an open reading frame which was highly homologous to the Agrobacterium tumefaciens chromosomal virulence gene product ChvI. A second gene product, 500 bp downstream of the chvI-like gene in R. meliloti, was homologous to the A. tumefaciens ChvG protein. The homology between the R. meliloti and A. tumefaciens genes was confirmed, because the R. meliloti chvI and chvG genes complemented A. tumefaciens chvI and chvG mutants for growth on complex media. We were unable to construct chvI or chvG insertion mutants of R. meliloti, whereas mutants carrying insertions outside of these genes were readily obtained. A 108-bp repeat element characterized by two large palindromes was identified in the chvI and chvG intergenic regions of both Rhizobium species. This element was duplicated in Rhizobium sp. strain NGR234. Another structurally similar element with a size of 109 bp was present in R. meliloti but not in Rhizobium sp. strain NGR234. These elements were named rhizobium-specific intergenic mosaic elements (RIMEs), because their distribution seems to be limited to members of the family Rhizobiaceae. A homology search in GenBank detected six more copies of the first element (RIME1), all in Rhizobium species, and three extra copies of the second element (RIME2), only in R. meliloti. Southern blot analysis with a probe specific to RIME1 showed the presence of several copies of the element in the genome of R. meliloti, Rhizobium sp. strain NGR234, Rhizobium leguminosarum, and Agrobacterium rhizogenes, but none was present in A. tumefaciens and Bradyrhizobium japonicum. PMID:7559334

  8. Genic and Intergenic SSR Database Generation, SNPs Determination and Pathway Annotations, in Date Palm (Phoenix dactylifera L.).

    PubMed

    Mokhtar, Morad M; Adawy, Sami S; El-Assal, Salah El-Din S; Hussein, Ebtissam H A

    2016-01-01

    The present investigation was carried out aiming to use the bioinformatics tools in order to identify and characterize, simple sequence repeats within the third Version of the date palm genome and develop a new SSR primers database. In addition single nucleotide polymorphisms (SNPs) that are located within the SSR flanking regions were recognized. Moreover, the pathways for the sequences assigned by SSR primers, the biological functions and gene interaction were determined. A total of 172,075 SSR motifs was identified on date palm genome sequence with a frequency of 450.97 SSRs per Mb. Out of these, 130,014 SSRs (75.6%) were located within the intergenic regions with a frequency of 499 SSRs per Mb. While, only 42,061 SSRs (24.4%) were located within the genic regions with a frequency of 347.5 SSRs per Mb. A total of 111,403 of SSR primer pairs were designed, that represents 291.9 SSR primers per Mb. Out of the 111,403, only 31,380 SSR primers were in the genic regions, while 80,023 primers were in the intergenic regions. A number of 250,507 SNPs were recognized in 84,172 SSR flanking regions, which represents 75.55% of the total SSR flanking regions. Out of 12,274 genes only 463 genes comprising 896 SSR primers were mapped onto 111 pathways using KEGG data base. The most abundant enzymes were identified in the pathway related to the biosynthesis of antibiotics. We tested 1031 SSR primers using both publicly available date palm genome sequences as templates in the in silico PCR reactions. Concerning in vitro validation, 31 SSR primers among those used in the in silico PCR were synthesized and tested for their ability to detect polymorphism among six Egyptian date palm cultivars. All tested primers have successfully amplified products, but only 18 primers detected polymorphic amplicons among the studied date palm cultivars. PMID:27434138

  9. Analysis of the CYP21A2 gene with intergenic recombination and multiple gene deletions in the RCCX module.

    PubMed

    Chang, Shwu-Fen; Lee, Hsien-Hsiung

    2011-01-01

    The most frequent bimodular RCCX module of the RP1-C4A-CYP21A1P-TNXA-RP2-C4B-CYP21A2-TNXB gene sequence is located on chromosome 6p21.3. To determine RCCX alterations, we used the polymerase chain reaction (PCR) product containing the tenascin B (TNXB) and CYP21A2 genes with TaqI digestion and Southern blot analysis with AseI and NdeI endonuclease digestion of genomic DNA from congenital adrenal hyperplasia patients with common mutations resulting from an intergenic conversion of CYP21A1P, such as an I2 splice, I172N, V281L, F306-L307insT, Q318X, and R356W, and dual mutations of I236N/V237E in the CYP21A2 gene. The results showed that a 3.7-kb fragment of the CYP21A2 gene was detected in each case, and 21.6- and 11.3-kb DNA fragments were found in the RCCX region by a Southern blot analysis with these corresponding mutations. However, the IVS2-12A/C- > G (I2 splice) haplotype in combination with the 707-714delGAGACTAC (without the P30L mutation) mutation produced a 3.2-kb TaqI fragment in the PCR product analysis and a specific 9.3-kb fragment by the Southern blot method. Therefore, we concluded that the rearrangement in the RCCX region resulting from processing of either an intergenic recombination or multiple gene deletions can be identified by the PCR analysis and Southern blot method based on a fragment-distinguishing configuration without a family study. PMID:21117955

  10. Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific.

    PubMed

    Redd, A J; Takezaki, N; Sherry, S T; McGarvey, S T; Sofro, A S; Stoneking, M

    1995-07-01

    Length changes in human mitochondrial DNA (mtDNA) are potentially useful markers for inferring the evolutionary history of populations. One such length change is a nine base pair (9-bp) deletion that is located in the intergenic region between the COII gene and the Lysine tRNA gene (COII/tRNALys intergenic region). This deletion has been used as a genetic marker to trace descent from peoples of East Asian origin. A geographic cline of the deletion frequency across modern Pacific Islander populations suggests that the deletion may be useful for tracing prehistoric Polynesian origins and affinities. Mitochondrial DNA sequence variation within two variable segments of the control region (CR) permits a number of inferences regarding the evolutionary history of the 9-bp deletion that cannot be determined from frequency data alone. We obtained CR sequences from 74 mtDNAs with the 9-bp deletion from Indonesia, coastal Papua New Guinea (PNG), and American Samoa. Phylogenetic and pairwise distribution analysis of these CR sequences pooled with previously published CR sequences reveals that the deletion arose independently in Africa and Asia and suggests possible multiple origins of the deletion in Asia. A clinal increase of the frequency of the 9-bp deletion across the three Pacific populations is associated with a decrease in CR sequence diversity, consistent with founder events. Furthermore, analysis of pairwise difference distributions indicates an expansion time of proto-Polynesians that began 5,500 yr ago from Southeast Asia. These results are consistent with the express train model of Polynesian origins. PMID:7659016

  11. Genic and Intergenic SSR Database Generation, SNPs Determination and Pathway Annotations, in Date Palm (Phoenix dactylifera L.)

    PubMed Central

    2016-01-01

    The present investigation was carried out aiming to use the bioinformatics tools in order to identify and characterize, simple sequence repeats within the third Version of the date palm genome and develop a new SSR primers database. In addition single nucleotide polymorphisms (SNPs) that are located within the SSR flanking regions were recognized. Moreover, the pathways for the sequences assigned by SSR primers, the biological functions and gene interaction were determined. A total of 172,075 SSR motifs was identified on date palm genome sequence with a frequency of 450.97 SSRs per Mb. Out of these, 130,014 SSRs (75.6%) were located within the intergenic regions with a frequency of 499 SSRs per Mb. While, only 42,061 SSRs (24.4%) were located within the genic regions with a frequency of 347.5 SSRs per Mb. A total of 111,403 of SSR primer pairs were designed, that represents 291.9 SSR primers per Mb. Out of the 111,403, only 31,380 SSR primers were in the genic regions, while 80,023 primers were in the intergenic regions. A number of 250,507 SNPs were recognized in 84,172 SSR flanking regions, which represents 75.55% of the total SSR flanking regions. Out of 12,274 genes only 463 genes comprising 896 SSR primers were mapped onto 111 pathways using KEGG data base. The most abundant enzymes were identified in the pathway related to the biosynthesis of antibiotics. We tested 1031 SSR primers using both publicly available date palm genome sequences as templates in the in silico PCR reactions. Concerning in vitro validation, 31 SSR primers among those used in the in silico PCR were synthesized and tested for their ability to detect polymorphism among six Egyptian date palm cultivars. All tested primers have successfully amplified products, but only 18 primers detected polymorphic amplicons among the studied date palm cultivars. PMID:27434138

  12. Diversification of the light-harvesting complex gene family via intra- and intergenic duplications in the coral symbiotic alga Symbiodinium.

    PubMed

    Maruyama, Shinichiro; Shoguchi, Eiichi; Satoh, Nori; Minagawa, Jun

    2015-01-01

    The light-harvesting complex (LHC) is an essential component in light energy capture and transduction to facilitate downstream photosynthetic reactions in plant and algal chloroplasts. The unicellular dinoflagellate alga Symbiodinium is an endosymbiont of cnidarian animals, including corals and sea anemones, and provides carbohydrates generated through photosynthesis to host animals. Although Symbiodinium possesses a unique LHC gene family, called chlorophyll a-chlorophyll c2-peridinin protein complex (acpPC), its genome-level diversity and evolutionary trajectories have not been investigated. Here, we describe a phylogenetic analysis revealing that many of the LHCs are encoded by highly duplicated genes with multi-subunit polyprotein structures in the nuclear genome of Symbiodinium minutum. This analysis provides an extended list of the LHC gene family in a single organism, including 80 loci encoding polyproteins composed of 145 LHC subunits recovered in the phylogenetic tree. In S. minutum, 5 phylogenetic groups of the Lhcf-type gene family, which is exclusively conserved in algae harboring secondary plastids of red algal origin, were identified. Moreover, 5 groups of the Lhcr-type gene family, of which members are known to be associated with PSI in red algal plastids and secondary plastids of red algal origin, were identified. Notably, members classified within a phylogenetic group of the Lhcf-type (group F1) are highly duplicated, which may explain the presence of an unusually large number of LHC genes in this species. Some gene units were homologous to other units within single loci of the polyprotein genes, whereas intergenic homologies between separate loci were conspicuous in other cases, implying that gene unit 'shuffling' by gene conversion and/or genome rearrangement might have been a driving force for diversification. These results suggest that vigorous intra- and intergenic gene duplication events have resulted in the genomic framework of

  13. Diversification of the Light-Harvesting Complex Gene Family via Intra- and Intergenic Duplications in the Coral Symbiotic Alga Symbiodinium

    PubMed Central

    Maruyama, Shinichiro; Shoguchi, Eiichi; Satoh, Nori; Minagawa, Jun

    2015-01-01

    The light-harvesting complex (LHC) is an essential component in light energy capture and transduction to facilitate downstream photosynthetic reactions in plant and algal chloroplasts. The unicellular dinoflagellate alga Symbiodinium is an endosymbiont of cnidarian animals, including corals and sea anemones, and provides carbohydrates generated through photosynthesis to host animals. Although Symbiodinium possesses a unique LHC gene family, called chlorophyll a-chlorophyll c2-peridinin protein complex (acpPC), its genome-level diversity and evolutionary trajectories have not been investigated. Here, we describe a phylogenetic analysis revealing that many of the LHCs are encoded by highly duplicated genes with multi-subunit polyprotein structures in the nuclear genome of Symbiodinium minutum. This analysis provides an extended list of the LHC gene family in a single organism, including 80 loci encoding polyproteins composed of 145 LHC subunits recovered in the phylogenetic tree. In S. minutum, 5 phylogenetic groups of the Lhcf-type gene family, which is exclusively conserved in algae harboring secondary plastids of red algal origin, were identified. Moreover, 5 groups of the Lhcr-type gene family, of which members are known to be associated with PSI in red algal plastids and secondary plastids of red algal origin, were identified. Notably, members classified within a phylogenetic group of the Lhcf-type (group F1) are highly duplicated, which may explain the presence of an unusually large number of LHC genes in this species. Some gene units were homologous to other units within single loci of the polyprotein genes, whereas intergenic homologies between separate loci were conspicuous in other cases, implying that gene unit ‘shuffling’ by gene conversion and/or genome rearrangement might have been a driving force for diversification. These results suggest that vigorous intra- and intergenic gene duplication events have resulted in the genomic framework of

  14. The Annular Two-phase Flow on Rod Bundle: The Effects of Spacers

    NASA Astrophysics Data System (ADS)

    Kunugi, Tomoaki; Pham, Son; Kawara, Zensaku; Yokomine, Takehiko

    2013-11-01

    The annular two-phase flow on rod bundle keeps an important role in many heat exchange systems but our knowledge about it, especially the interaction between the liquid film flowing on the rods' surfaces and the spacers is very limited. This study is aimed to the investigation of how the spacer affects the disturbance waves of the flow in a 3 × 3 simulating BWR fuel rod bundle test section. Firstly, the characteristics of the disturbance waves at both upstream and downstream locations of the spacer were obtained by using reflected light arrangement with a high speed camera Phantom V7.1 (Vision Research Inc.) and a Nikon macro lens 105mm f/2.8. The data showed that the parameters such as frequency and circumferential coherence of the disturbance waves are strongly modified when they go through the spacer. Then, the observations at the locations right before and after the spacer were performed by using the back light arrangement with the same high speed camera and a Cassegrain optical system (Seika Cooperation). The obtained images at micro-scale of time and space provided the descriptions of the wavy interface behaviors right before and after the spacer as well as different droplets creation processes caused by the presence of this spacer.

  15. Antibiotic-impregnated articulating cement spacer for infected total knee arthroplasty

    PubMed Central

    Garg, Parag; Ranjan, Rajeev; Bandyopadhyay, Utpal; Chouksey, Shiv; Mitra, SR; Gupta, Samar K

    2011-01-01

    Background: Standard treatment of chronic infected total knee arthroplasty (TKA) is a two-stage revision, the first step being placement of an antibiotic-impregnated cement spacer. Here we describe the results of a new technique (modification of the Goldstien's technique) for intraoperative manufacture of a customized articulating spacer at minimal cost and with relatively good conformity and longevity. Materials and Methods: Thirty-six infected knees underwent this procedure from June 2002 to May 2007. The technique consists of using the freshened femur and tibia interface as molds wrapped in a tin foil for manufacturing the two components of the spacer with antibiotic-impregnated methyl methycrylate cement. We used the spacer and the femoral component of the trial set of a TKA system to mold them to perfect articulation. We also reinforced the spacer with a K-wire scaffold to prevent fracture of the cement mantle in the last 21 cases. Results: All 36 knees showed excellent results in terms of infection control, mobility, and stability. There was significant improvement in the WOMAC and Knee Society Scores (20 and 39 points respectively). There were two fractures of the spacers in the initial 15 cases that did not have K-wire scaffolding but none in the last 21 that had reinforcement. Conclusion: This technique provides a more conforming spacer, with good range of motion and stability. The reinforcement helps in preventing the fracture of the cement mantle and is cost effective. PMID:22144747

  16. Serotonin levels influence patterns of repetition priming.

    PubMed

    Burgund, E Darcy; Marsolek, Chad J; Luciana, Monica

    2003-01-01

    Repetition priming in a word-stem completion task was examined in a group of control subjects and in a group of experimental subjects under conditions of acute tryptophan depletion (T-) and tryptophan augmentation (T+). Experimental subjects ingested amino acid compounds that depleted or loaded the body with tryptophan, and word-stem completion priming performance was measured. Results indicate differential effects of T- and T+ manipulations on word-stem completion priming. In the control group, both specific-visual and amodal priming were observed. Conversely, in the T+ condition, specific-visual priming, but no amodal priming, was observed, whereas in the T- condition, amodal priming, but no specific-visual priming, was observed. The authors conclude that serotonin (5-hydroxytryptamine) plays a critical role in repetition priming by helping to modulate which neural systems contribute to priming effects. PMID:12597085

  17. Repetitive Elements in Genomes of Parasitic Protozoa

    PubMed Central

    Wickstead, Bill; Ersfeld, Klaus; Gull, Keith

    2003-01-01

    Repetitive DNA elements have been a part of the genomic fauna of eukaryotes perhaps since their very beginnings. Millions of years of coevolution have given repeats central roles in chromosome maintenance and genetic modulation. Here we review the genomes of parasitic protozoa in the context of the current understanding of repetitive elements. Particular reference is made to repeats in five medically important species with ongoing or completed genome sequencing projects: Plasmodium falciparum, Leishmania major, Trypanosoma brucei, Trypanosoma cruzi, and Giardia lamblia. These organisms are used to illustrate five thematic classes of repeats with different structures and genomic locations. We discuss how these repeat classes may interact with parasitic life-style and also how they can be used as experimental tools. The story which emerges is one of opportunism and upheaval which have been employed to add genetic diversity and genomic flexibility. PMID:12966140

  18. Evaluation of a dkgB linked intergenic sequence ribotyping (ISR) method for assigning serotype to Salmonella enterica isolated from poultry environmental samples.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Kauffman White (KW) serotyping method requires more than 250 antisera to characterize more than 2,500 Salmonella serovars. The complexity of serotyping could be overcome using molecular methods. In this study, a dkgB-linked intergenic sequence ribotyping (ISR) method that generates sequence occu...

  19. A cis-regulatory sequence from a short intergenic region gives rise to a strong microbe-associated molecular pattern-responsive synthetic promoter.

    PubMed

    Lehmeyer, Mona; Hanko, Erik K R; Roling, Lena; Gonzalez, Lilian; Wehrs, Maren; Hehl, Reinhard

    2016-06-01

    The high gene density in Arabidopsis thaliana leaves only relatively short intergenic regions for potential cis-regulatory sequences. To learn more about the regulation of genes harbouring only very short upstream intergenic regions, this study investigates a recently identified novel microbe-associated molecular pattern (MAMP)-responsive cis-sequence located within the 101 bp long intergenic region upstream of the At1g13990 gene. It is shown that the cis-regulatory sequence is sufficient for MAMP-responsive reporter gene activity in the context of its native promoter. The 3' UTR of the upstream gene has a quantitative effect on gene expression. In context of a synthetic promoter, the cis-sequence is shown to achieve a strong increase in reporter gene activity as a monomer, dimer and tetramer. Mutation analysis of the cis-sequence determined the specific nucleotides required for gene expression activation. In transgenic A. thaliana the synthetic promoter harbouring a tetramer of the cis-sequence not only drives strong pathogen-responsive reporter gene expression but also shows a high background activity. The results of this study contribute to our understanding how genes with very short upstream intergenic regions are regulated and how these regions can serve as a source for MAMP-responsive cis-sequences for synthetic promoter design. PMID:26833485

  20. A repetitive elements perspective in Polycomb epigenetics

    PubMed Central

    Casa, Valentina; Gabellini, Davide

    2012-01-01

    Repetitive elements comprise over two-thirds of the human genome. For a long time, these elements have received little attention since they were considered non-functional. On the contrary, recent evidence indicates that they play central roles in genome integrity, gene expression, and disease. Indeed, repeats display meiotic instability associated with disease and are located within common fragile sites, which are hotspots of chromosome re-arrangements in tumors. Moreover, a variety of diseases have been associated with aberrant transcription of repetitive elements. Overall this indicates that appropriate regulation of repetitive elements’ activity is fundamental. Polycomb group (PcG) proteins are epigenetic regulators that are essential for the normal development of multicellular organisms. Mammalian PcG proteins are involved in fundamental processes, such as cellular memory, cell proliferation, genomic imprinting, X-inactivation, and cancer development. PcG proteins can convey their activity through long-distance interactions also on different chromosomes. This indicates that the 3D organization of PcG proteins contributes significantly to their function. However, it is still unclear how these complex mechanisms are orchestrated and which role PcG proteins play in the multi-level organization of gene regulation. Intriguingly, the greatest proportion of Polycomb-mediated chromatin modifications is located in genomic repeats and it has been suggested that they could provide a binding platform for Polycomb proteins. Here, these lines of evidence are woven together to discuss how repetitive elements could contribute to chromatin organization in the 3D nuclear space. PMID:23060903

  1. Repetition probability effects for inverted faces.

    PubMed

    Grotheer, Mareike; Hermann, Petra; Vidnyánszky, Zoltán; Kovács, Gyula

    2014-11-15

    It has been shown, that the repetition related reduction of the blood-oxygen level dependent (BOLD) signal is modulated by the probability of repetitions (P(rep)) for faces (Summerfield et al., 2008), providing support for the predictive coding (PC) model of visual perception (Rao and Ballard, 1999). However, the stage of face processing where repetition suppression (RS) is modulated by P(rep) is still unclear. Face inversion is known to interrupt higher level configural/holistic face processing steps and if modulation of RS by P(rep) takes place at these stages of face processing, P(rep) effects are expected to be reduced for inverted when compared to upright faces. Therefore, here we aimed at investigating whether P(rep) effects on RS observed for face stimuli originate at the higher-level configural/holistic stages of face processing by comparing these effects for upright and inverted faces. Similarly to previous studies, we manipulated P(rep) for pairs of stimuli in individual blocks of fMRI recordings. This manipulation significantly influenced repetition suppression in the posterior FFA, the OFA and the LO, independently of stimulus orientation. Our results thus reveal that RS in the ventral visual stream is modulated by P(rep) even in the case of face inversion and hence strongly compromised configural/holistic face processing. An additional whole-brain analysis could not identify any areas where the modulatory effect of probability was orientation specific either. These findings imply that P(rep) effects on RS might originate from the earlier stages of face processing. PMID:25123974

  2. Can predictive coding explain repetition suppression?

    PubMed

    Grotheer, Mareike; Kovács, Gyula

    2016-07-01

    While in earlier work various local or bottom-up neural mechanisms were proposed to give rise to repetition suppression (RS), current theories suggest that top-down processes play a role in determining the repetition related reduction of the neural responses. In the current review we summarise those results, which support the role of these top-down processes, concentrating on the Bayesian models of predictive coding (PC). Such models assume that RS is related to the statistical probabilities of prior stimulus occurrences and to the future predictability of these stimuli. Here we review the current results that support or argue against this explanation. We point out that the heterogeneity of experimental manipulations that are thought to reflect predictive processes are likely to measure different processing steps, making their direct comparison difficult. In addition we emphasize the importance of identifying these sub-processes and clarifying their role in explaining RS. Finally, we propose a two-stage model for explaining the relationships of repetition and expectation phenomena in the human cortex. PMID:26861559

  3. Lsh, an epigenetic guardian of repetitive elements.

    PubMed

    Huang, Jiaqiang; Fan, Tao; Yan, Qingsheng; Zhu, Heming; Fox, Stephen; Issaq, Haleem J; Best, Lionel; Gangi, Lisa; Munroe, David; Muegge, Kathrin

    2004-01-01

    The genome is burdened with repetitive sequences that are generally embedded in silenced chromatin. We have previously demonstrated that Lsh (lymphoid-specific helicase) is crucial for the control of heterochromatin at pericentromeric regions consisting of satellite repeats. In this study, we searched for additional genomic targets of Lsh by examining the effects of Lsh deletion on repeat regions and single copy gene sequences. We found that the absence of Lsh resulted in an increased association of acetylated histones with repeat sequences and transcriptional reactivation of their silenced state. In contrast, selected single copy genes displayed no change in histone acetylation levels, and their transcriptional rate was indistinguishable compared to Lsh-deficient cells and wild-type controls. Microarray analysis of total RNA derived from brain and liver tissues revealed that <0.4% of the 15 247 examined loci were abnormally expressed in Lsh-/-embryos and almost two-thirds of these deregulated sequences contained repeats, mainly retroviral LTR (long terminal repeat) elements. Chromatin immunoprecipitation analysis demonstrated a direct interaction of Lsh with repetitive sites in the genome. These data suggest that the repetitive sites are direct targets of Lsh action and that Lsh plays an important role as 'epigenetic guardian' of the genome to protect against deregulation of parasitic retroviral elements. PMID:15448183

  4. The Dfam database of repetitive DNA families.

    PubMed

    Hubley, Robert; Finn, Robert D; Clements, Jody; Eddy, Sean R; Jones, Thomas A; Bao, Weidong; Smit, Arian F A; Wheeler, Travis J

    2016-01-01

    Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download. PMID:26612867

  5. Overview of repetitively pulsed photolytic iodine lasers

    NASA Astrophysics Data System (ADS)

    Schlie, L. A. V.

    1996-02-01

    The performance of a repetitively pulsed, 70 joule, closed cycle 1.3 (mu) M photolytic atomic iodine laser with excellent beam quality (BQ equals 1.15) is presented. This BQ was exhibited in the fundamental mode from a M equals 3.1 confocal unstable resonator at a 0.5 Hz repetition rate. A closed cycle scrubber/laser fuel system consisting of a condensative- evaporative section, two Cu wool I2 reactor regions, and an internal turbo-blower enabled the laser to operate very reliably with low maintenance. The fuel system provided C3F7I gas at 10 - 60 torr absent of the photolytic quenching by-product I2. Using a turbo- molecular blower longitudinal flow velocities greater than 10 m/s were achieved through the 150 cm long by 7.5 multiplied by 7.5 cm2 cross sectional photolytic iodine gain region. In addition to the high laser output and excellent BQ, the resulting 8 - 12 microsecond laser pulse had a coherence length greater than 45 meters and polarization extinction ratio better than 100:1. Projections from this pulsed photolytic atomic iodine laser technology to larger energies, higher repetition rates, and variable pulse widths are discussed.

  6. The Dfam database of repetitive DNA families

    PubMed Central

    Hubley, Robert; Finn, Robert D.; Clements, Jody; Eddy, Sean R.; Jones, Thomas A.; Bao, Weidong; Smit, Arian F.A.; Wheeler, Travis J.

    2016-01-01

    Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org. Seed alignments, profile HMMs, hit lists and other underlying data are available for download. PMID:26612867

  7. Repetition Blindness: An Emergent Property of Inter-Item Competition

    ERIC Educational Resources Information Center

    Morris, Alison L.; Still, Mary L.; Caldwell-Harris, Catherine L.

    2009-01-01

    Repeating an item in a brief or rapid display usually produces faster or more accurate identification of the item (repetition priming), but sometimes produces the opposite effect (repetition blindness). We present a theory of short-term repetition effects, the "competition hypothesis," which explains these paradoxical outcomes. The central tenet…

  8. Lingual Kinematics during Rapid Syllable Repetition in Parkinson's Disease

    ERIC Educational Resources Information Center

    Wong, Min Ney; Murdoch, Bruce E.; Whelan, Brooke-Mai

    2012-01-01

    Background: Rapid syllable repetition tasks are commonly used in the assessment of motor speech disorders. However, little is known about the articulatory kinematics during rapid syllable repetition in individuals with Parkinson's disease (PD). Aims: To investigate and compare lingual kinematics during rapid syllable repetition in dysarthric…

  9. Optimization of Radiation Therapy Techniques for Prostate Cancer With Prostate-Rectum Spacers: A Systematic Review

    SciTech Connect

    Mok, Gary; Benz, Eileen; Vallee, Jean-Paul; Miralbell, Raymond; Zilli, Thomas

    2014-10-01

    Dose-escalated radiation therapy for localized prostate cancer improves disease control but is also associated with worse rectal toxicity. A spacer placed between the prostate and rectum can be used to displace the anterior rectal wall outside of the high-dose radiation regions and potentially minimize radiation-induced rectal toxicity. This systematic review focuses on the published data regarding the different types of commercially available prostate-rectum spacers. Dosimetric results and preliminary clinical data using prostate-rectum spacers in patients with localized prostate cancer treated by curative radiation therapy are compared and discussed.

  10. Experimental Study of Two Phase Flow Behavior Past BWR Spacer Grids

    SciTech Connect

    Ratnayake, Ruwan K.; Hochreiter, L.E.; Ivanov, K.N.; Cimbala, J.M.

    2002-07-01

    Performance of best estimate codes used in the nuclear industry can be significantly improved by reducing the empiricism embedded in their constitutive models. Spacer grids have been found to have an important impact on the maximum allowable Critical Heat Flux within the fuel assembly of a nuclear reactor core. Therefore, incorporation of suitable spacer grids models can improve the critical heat flux prediction capability of best estimate codes. Realistic modeling of entrainment behavior of spacer grids requires understanding the different mechanisms that are involved. Since visual information pertaining to the entrainment behavior of spacer grids cannot possibly be obtained from operating nuclear reactors, experiments have to be designed and conducted for this specific purpose. Most of the spacer grid experiments available in literature have been designed in view of obtaining quantitative data for the purpose of developing or modifying empirical formulations for heat transfer, critical heat flux or pressure drop. Very few experiments have been designed to provide fundamental information which can be used to understand spacer grid effects and phenomena involved in two phase flow. Air-water experiments were conducted to obtain visual information on the two-phase flow behavior both upstream and downstream of Boiling Water Reactor (BWR) spacer grids. The test section was designed and constructed using prototypic dimensions such as the channel cross-section, rod diameter and other spacer grid configurations of a typical BWR fuel assembly. The test section models the flow behavior in two adjacent sub channels in the BWR core. A portion of a prototypic BWR spacer grid accounting for two adjacent channels was used with industrial mild steel rods for the purpose of representing the channel internals. Symmetry was preserved in this practice, so that the channel walls could effectively be considered as the channel boundaries. Thin films were established on the rod surfaces

  11. Titanium-copper-nitride coated spacers for two-stage revision of infected total hip endoprostheses

    PubMed Central

    Ellenrieder, Martin; Haenle, Maximilian; Lenz, Robert; Bader, Rainer; Mittelmeier, Wolfram

    2011-01-01

    Within the first two years after total hip arthroplasty implant-associated infection has become the second most common reason for a revision surgery. Two-stage implant exchange is frequently conducted using temporary spacers made of antibiotic-loaded cement in order to prevent a bacterial colonization on the spacer. Avoiding several disadvantages of cement spacers, a conventional hemi-endoprosthesis was equipped with a copper-containing implant coating for inhibition of bacterial biofilms. In the present paper details of this novel treatment concept are presented including a case report. PMID:22242097

  12. Increase of the electron mobility in HEMT heterostructures with composite spacers containing AlAs nanolayers

    SciTech Connect

    Vinichenko, A. N. Gladkov, V. P.; Kargin, N. I.; Strikhanov, M. N.; Vasil’evskii, I. S.

    2014-12-15

    The effect of the hybridization of quantum states on electron transport in a two-barrier quantum well δ-doped through a spacer layer at the limit of heavy doping is shown theoretically and experimentally. A method for increasing the electron mobility in the quantum well by suppressing the tunnel coupling with the donor region through the introduction of an AlAs nanobarrier into the spacer layer is proposed. It is experimentally shown that, in the samples with a shallow quantum well, the AlAs nanobarrier introduced into the spacer layer provides a larger than threefold increase in the electron mobility at low temperatures.

  13. Preventing mechanical complications of hip spacer implantation: technical tips and pearls.

    PubMed

    Barreira, Pedro; Leite, Pedro; Neves, Pedro; Soares, Daniel; Sousa, Ricardo

    2015-06-01

    Periprosthetic joint infection is a frequent complication after total hip replacement. Two-stage exchange with the use of a temporary cement spacer is commonplace. Several complications are possible with its use. In addition to infection persistence, mechanical complications such as dislocation or fractures are among the most common. Several risk factors can and should be addressed during first stage or spacer implantation surgery in order to minimize complications. Technical aspects as well as practical tips and pearls to overcome common nuisances such as spacer instability or femoral and acetabular bone loss will be discussed. PMID:26280978

  14. Modulation of porphyrin photoluminescence by nanoscale spacers on silicon substrates

    NASA Astrophysics Data System (ADS)

    Fang, Y. C.; Zhang, Y.; Gao, H. Y.; Chen, L. G.; Gao, B.; He, W. Z.; Meng, Q. S.; Zhang, C.; Dong, Z. C.

    2013-11-01

    We investigate photoluminescence (PL) properties of quasi-monolayered tetraphenyl porphyrin (TPP) molecules on silicon substrates modulated by three different nanoscale spacers: native oxide layer (NOL), hydrogen (H)-passivated layer, and Ag nanoparticle (AgNP) thin film, respectively. In comparison with the PL intensity from the TPP molecules on the NOL-covered silicon, the fluorescence intensity from the molecules on the AgNP-covered surface was greatly enhanced while that for the H-passivated surface was found dramatically suppressed. Time-resolved fluorescence spectra indicated shortened lifetimes for TPP molecules in both cases, but the decay kinetics is believed to be different. The suppressed emission for the H-passivated sample was attributed to the weaker decoupling effect of the monolayer of hydrogen atoms as compared to the NOL, leading to increased nonradiative decay rate; whereas the enhanced fluorescence with shortened lifetime for the AgNP-covered sample is attributed not only to the resonant excitation by local surface plasmons, but also to the increased radiative decay rate originating from the emission enhancement in plasmonic "hot-spots".

  15. Apparatus and methods for aligning holes through wheels and spacers and stacking the wheels and spacers to form a turbine rotor

    DOEpatents

    Berry, Robert Randolph; Palmer, Gene David; Wilson, Ian David

    2000-01-01

    A gas turbine rotor stacking fixture includes upstanding bolts for reception in aligned bolt holes in superposed aft disk, wheels and spacers and upstanding alignment rods received in openings of the disk, wheels and spacers during the rotor stacking assembly. The axially registering openings enable insertion of thin-walled tubes circumferentially about the rim of the rotor, with tight tolerances to the openings to provide supply and return steam for cooling buckets. The alignment rods have radial dimensions substantially less than their dimensions in a circumferential direction to allow for radial opening misalignment due to thermal expansion, tolerance stack-up and wheel-to-spacer mismatch due to rabbet mechanical growth. The circumferential dimension of the alignment rods affords tightly toleranced alignment of the openings through which the cooling tubes are installed.

  16. The Adult Repetitive Behaviours Questionnaire-2 (RBQ-2A): A Self-Report Measure of Restricted and Repetitive Behaviours

    ERIC Educational Resources Information Center

    Barrett, Sarah L.; Uljarevic, Mirko; Baker, Emma K.; Richdale, Amanda L.; Jones, Catherine R. G.; Leekam, Susan R.

    2015-01-01

    In two studies we developed and tested a new self-report measure of restricted and repetitive behaviours (RRB) suitable for adults. In Study 1, The Repetitive Behaviours Questionnaire-2 for adults (RBQ-2A) was completed by a sample of 163 neurotypical adults. Principal components analysis revealed two components: Repetitive Motor Behaviours and…

  17. Manufacturing and Process-based Property Analysis of Textile-Reinforced Thermoplastic Spacer Composites

    NASA Astrophysics Data System (ADS)

    Hufenbach, Werner; Adam, Frank; Füßel, René; Krahl, Michael; Weck, Daniel

    2012-12-01

    Novel woven spacer fabrics based on hybrid yarns are suitable for an efficient fabrication of three-dimensional composite structures in high volume production. In this paper, an innovative manufacturing process with short cycle times and high automatisation is introduced for textile-reinforced thermoplastic spacer structures suited for bending load cases. The different process steps hybrid yarn fabrication, weaving technology for three-dimensional textile preforms and consolidation with unique kinematics and hot pressing technology are described in detail. The bending properties of the manufactured spacer structures are evaluated by means of experiments as well as finite element simulations. Numerical parametric studies are performed in order to validate the influence of manufacturing tolerances on the bending stiffness of the spacer structures.

  18. Enhanced charge trapping in bipolar spacer oxides during low-dose-rate irradiation

    SciTech Connect

    Fleetwood, D.M.; Reber, R.A. Jr.; Winokur, P.S.; Kosier, S.L.; Schrimpf, R.D.; Nowlin, R.N.; Pease, R.L.; DeLaus, M.

    1994-03-01

    Thermally-stimulated-current and capacitance-voltage measurements reveal enhanced hole trapping in bipolar spacer-oxide capacitors irradiated at 0 V at low dose rates. Possible mechanisms and implications for bipolar low-rate response are discussed.

  19. Method of forming a spacer for field emission flat panel displays

    DOEpatents

    Bernhardt, A.F.; Contolini, R.J.

    1997-08-19

    Spacers are disclosed for applications such as field emission flat panel displays and vacuum microelectronics, and which involves the application of aerogel/xerogel technology to the formation of the spacer. In a preferred approach the method uses a mold and mold release agent wherein the gel precursor is a liquid which can be applied to the mold filling holes which expose the substrate (either the baseplate or the faceplate). A release agent is applied to the mold prior to precursor application to ease removal of the mold after formation of the dielectric spacer. The shrinkage of the gel during solvent extraction also improves mold removal. The final spacer material is a good dielectric, such as silica, secured to the substrate. 3 figs.

  20. Spacer defined double patterning for sub-72 nm pitch logic technology

    NASA Astrophysics Data System (ADS)

    Kim, Ryoung-Han; Mclellan, Erin; Yin, Yunpeng; Arnold, John; Kanakasabapathy, Sivananda; Mehta, Sanjay; Ma, Yuansheng; Burkhardt, Martin; Cain, Jason; McIntyre, Greg; Colburn, Matthew E.; Levinson, Harry J.

    2010-04-01

    In order to extend the optical lithography into sub-72 nm pitch regime, spacer defined double patterning as a self-aligning process option was investigated. In the sidewall defined spacer process, spacer material was deposited directly on the resist to achieve process simplification and cost effectiveness. For the spacer defined double patterning, core mandrel CD uniformity is proven to be a main contributor to pitch-walking and defined a new lithographic process window. Here, the aerial image log-slope is shown to be a measurable predictor of CD uniformity and sidewall angle of the resist pattern. Through resist screening and illumination optimization, resist core-mandrel of 2.5 nm CD uniformity across a focus range more than 200 nm with +/- 3.5 % exposure latitude was developed having sidewall control close to the normal. Finally etch revealed that pitch-walking post pitch split can be suppressed below 2 nm within +/- 2.5 % exposure latitude.

  1. Spacer geometry and particle deposition in spiral wound membrane feed channels.

    PubMed

    Radu, A I; van Steen, M S H; Vrouwenvelder, J S; van Loosdrecht, M C M; Picioreanu, C

    2014-11-01

    Deposition of microspheres mimicking bacterial cells was studied experimentally and with a numerical model in feed spacer membrane channels, as used in spiral wound nanofiltration (NF) and reverse osmosis (RO) membrane systems. In-situ microscopic observations in membrane fouling simulators revealed formation of specific particle deposition patterns for different diamond and ladder feed spacer orientations. A three-dimensional numerical model combining fluid flow with a Lagrangian approach for particle trajectory calculations could describe very well the in-situ observations on particle deposition in flow cells. Feed spacer geometry, positioning and cross-flow velocity sensitively influenced the particle transport and deposition patterns. The deposition patterns were not influenced by permeate production. This combined experimental-modeling approach could be used for feed spacer geometry optimization studies for reduced (bio)fouling. PMID:25055226

  2. CRISPR Spacer Arrays for Detection of Viral Signatures from Acidic Hot Springs

    NASA Astrophysics Data System (ADS)

    Snyder, J. C.; Bateson, M. M.; Suciu, D.; Young, M. J.

    2010-04-01

    Viruses are the most abundant life-like entities on the planet Earth. Using CRISPR spacer sequences, we have developed a microarray-based approach to detecting viral signatures in the acidic hot springs of Yellowstone.

  3. Method of forming a spacer for field emission flat panel displays

    DOEpatents

    Bernhardt, Anthony F.; Contolini, Robert J.

    1997-01-01

    Spacers for applications such as field emission flat panel displays and vacuum microelectronics, and which involves the application of aerogel/xerogel technology to the formation of the spacer. In a preferred approach the method uses a mold and mold release agent wherein the gel precursor is a liquid which can be applied to the mold filling holes which expose the substrate (either the baseplate or the faceplate). A release agent is applied to the mold prior to precursor application to ease removal of the mold after formation of the dielectric spacer. The shrinkage of the gel during solvent extraction also improves mold removal. The final spacer material is a good dielectric, such as silica, secured to the substrate.

  4. Effects of spacer layers on the Wigner function simulation of resonant tunneling diodes

    NASA Astrophysics Data System (ADS)

    García-García, J. J.; Oriols, X.; Martín, F.; Suñé, J.

    1998-06-01

    The effects of spacer layer width and asymmetry on the simulation of quantum transport in resonant tunneling diodes are studied. The results show that these layers significantly influence the I-V characteristic, which presents important differences under direct or reverse bias polarity in devices with asymmetric spacer layers. These differences are interpreted in terms of potential profile comparisons of the simulated structures and are in qualitative agreement with experimental data.

  5. [Guidelines for redesigning jobs with repetitive tasks].

    PubMed

    Colombini, D; Occhipinti, E; Meroni, M; Menoni, O; Bergamasco, R; Girola, C; Grea, V; Vendola, D

    1996-01-01

    Preventive measures aimed at minimising the occurrence of work-related musculo-skeletal disorders of the upper limbs (WMSDs) associated with repetitive tasks can be divided into 3 categories: structural, organisational and educational. Whenever specific risk and injury assessments have shown the need for preventive action, this is most often implemented within the framework of a range of assorted measures. In particular, structural measures pertain to optimising the layout of the work area and furnishings, and the "ergonomic" properties of work tools and equipment. Such measures serve to alleviate the problems caused by the use of excessive force and improper postures. The authors refer to the principles guiding such structural measures, in the light of the extensive literature that has been published on the subject. Organisational (or re-organisational) measures essentially relate to job design (i.e. distribution of tasks, speeds and pauses). They serve to alleviate problems connected with highly repetitive and frequent actions, excessively lengthy tasks and inadequate recovery periods. Very few relevant findings are available: the authors therefore illustrate in some detail a practical trial conducted in a major engineering firm. The objective was to lower to acceptable limits the frequency of certain repetitive tasks performed by workers using their upper limbs. The trial made it possible to identify a suitable plan and schedule of measures taking into due consideration the impact of the plan on production levels (and costs). The fundamental principles guiding the adoption of specific educational and training programmes for the workers and their supervisors are presented and discussed. PMID:9148129

  6. The Effect of Spacer Morphology on the Aerosolization Performance of Metered-Dose Inhalers

    PubMed Central

    Momeni, Sepideh; Nokhodchi, Ali; Ghanbarzadeh, Saeed; Hamishehkar, Hamed

    2016-01-01

    Purpose: Respiratory drug delivery has been attracted great interest for the past decades, because of the high incidence of pulmonary diseases. However, despite its invaluable benefits, there are some major drawbacks in respiratory drug delivery, mainly due to the relatively high drug deposition in undesirable regions. One way to improve the efficiency of respiratory drug delivery through metered-dose inhalers (MDI) is placing a respiratory spacer between the inhaler exit and the mouth. The aim of this study was to assess the effect of type and shape of spacer on the aerosolization performance of MDIs. Methods: A commercial Beclomethasone Dipropionate (BDP) MDI alone or equipped with two different spacer devices (roller and pear type) widely distributed in the world pharmaceutical market was used. The effect of spacers was evaluated by calculating aerosolization indexes such as fine particle fraction (FPF), mass median aerodynamic diameters (MMAD) and geometric standard deviation (GSD) using the next generation impactor. Results: Although one of the spacers resulted in superior outcomes than the other one, but it was not statistically significant. Conclusion: The results confirmed that the type and shape of spacer did not substantially influence the aerosolization performance of MDIs. PMID:27478789

  7. Using scatterometry to improve process control during the spacer pitch splitting process

    NASA Astrophysics Data System (ADS)

    Corboy, Scott; MacNaughton, Craig; Gubiotti, Thomas; Wollenweber, Marcus

    2009-03-01

    In an effort to keep scaling at the speed of Moore's law, novel methods are being developed to facilitate advanced semiconductor manufacturing at the 32nm node and beyond. One such method for enabling the creation of dense pitches beyond the current lithography resolution limit is spacer pitch splitting. This method typically involves patterning a sacrificial gate pattern, then performing a standard spacer deposition and etch back process, after which the sacrificial gate is removed and the remaining spacers themselves are used as the effective mask for the pattern transfer. Some of the key advantages of this process are the ability to create sub-resolution lines and also the improvement in Line Edge Roughness seen on the final pattern. However, there are certain limitations with this process, namely the ability to only pattern lines in one dimension, and also the complexity of the metrology, where the final Critical Dimension result is a function of the lithography condition from the sacrificial gate patterning, and also the various film layer depositions as well as the spacer etch back process. Given this complexity, the accurate measurement of not only the spacer width but also the spacer shape is important. In this work we investigate the use of scatterometry techniques to enable these measurements on leading edge devices.

  8. Gate Spacer Width Monitoring Study with Scatterometry Based on Spectroscopic Ellipsometry

    NASA Astrophysics Data System (ADS)

    Vachellerie, V.; Kremer, S.; Elazami, A.; Morin, P.; Julien, C.; Duca, D.; Guiheux, D.; Bicais, N.; Pokrant, S.

    2005-09-01

    Critical Dimension (CD) control of Gate Spacers is key to achieve in well controlled implantations and a tight distribution of Vt for transistors on semiconductors devices. Presently, historical methods for CD control (top-down low-voltage Scanning Electron Microscopy, Atomic Force Microscopy, Transmission Electron Microscopy or Electrical CD measurement) are facing limitations with regards to precision, matching, throughput or sample damage. So, with the reduction of design rules approaching the 65nm technology node, the need for a fast, precise and versatile "in-line" (at the process step) measurement of the spacer width and profile becomes critical, in order to shorten the spacer process development phase and the response time to production excursions. In this paper, we investigate the metrology performances and limitations (sensitivity, precision and accuracy) of Scatterometry (SCD) based on Spectroscopic Ellipsometry (SE) for this application using a KLA-TENCOR SpectraCD system. We show that it will be suitable for, at least, a simple oxide-nitride spacer configuration. We also explore its capability to measure more complex structures like the double-spacer configuration (LDD offset & S/D spacer). Finally, we show how additional information provided by Scatterometry helps in understanding process variations and how they correlate to end of line parametric test results.

  9. AUTOSIM: An automated repetitive software testing tool

    NASA Technical Reports Server (NTRS)

    Dunham, J. R.; Mcbride, S. E.

    1985-01-01

    AUTOSIM is a software tool which automates the repetitive run testing of software. This tool executes programming tasks previously performed by a programmer with one year of programming experience. Use of the AUTOSIM tool requires a knowledge base containing information about known faults, code fixes, and the fault diagnosis-correction process. AUTOSIM can be considered as an expert system which replaces a low level of programming expertise. Reference information about the design and implementation of the AUTOSIM software test tool provides flowcharts to assist in maintaining the software code and a description of how to use the tool.

  10. Software reliability: Repetitive run experimentation and modeling

    NASA Technical Reports Server (NTRS)

    Nagel, P. M.; Skrivan, J. A.

    1982-01-01

    A software experiment conducted with repetitive run sampling is reported. Independently generated input data was used to verify that interfailure times are very nearly exponentially distributed and to obtain good estimates of the failure rates of individual errors and demonstrate how widely they vary. This fact invalidates many of the popular software reliability models now in use. The log failure rate of interfailure time was nearly linear as a function of the number of errors corrected. A new model of software reliability is proposed that incorporates these observations.

  11. Animal models of restricted repetitive behavior in autism

    PubMed Central

    Lewis, Mark H.; Tanimura, Yoko; Lee, Linda W.; Bodfish, James W.

    2013-01-01

    Restricted, repetitive behavior, along with deficits in social reciprocity and communication, is diagnostic of autism. Animal models relevant to this domain generally fall into three classes: repetitive behavior associated with targeted insults to the CNS; repetitive behavior induced by pharmacological agents; and repetitive behavior associated with restricted environments and experience. The extant literature provides potential models of the repetitive behavioral phenotype in autism rather than attempts to model the etiology or pathophysiology of restricted, repetitive behavior, as these are poorly understood. This review focuses on our work with deer mice which exhibit repetitive behaviors associated with environmental restriction. Repetitive behaviors are the most common category of abnormal behavior observed in confined animals and larger, more complex environments substantially reduce the development and expression of such behavior. Studies with this model, including environmental enrichment effects, suggest alterations in cortical-basal ganglia circuitry in the development and expression of repetitive behavior. Considerably more work needs to be done in this area, particularly in modeling the development of aberrant repetitive behavior. As mutant mouse models continue to proliferate, there should be a number of promising genetic models to pursue. PMID:16997392

  12. Investigation of a repetitive pulsed electrothermal thruster

    NASA Technical Reports Server (NTRS)

    Burton, R. L.; Fleischer, D.; Goldstein, S. A.; Tidman, D. A.; Winsor, N. K.

    1986-01-01

    A pulsed electrothermal (PET) thruster with 1000:1 ratio nozzle is tested in a repetitive mode on water propellant. The thruster is driven by a 60J pulse forming network at repetition rates up to 10 Hz (600W). The pulse forming network has a .31 ohm impedance, well matched to the capillary discharge resistance of .40 ohm, and is directly coupled to the thruster electrodes without a switch. The discharge is initiated by high voltage breakdown, typically at 2500V, through the water vapor in the interelectrode gap. Water is injected as a jet through a .37 mm orifice on the thruster axis. Thruster voltage, current and impulse bit are recorded for several seconds at various power supply currents. Thruster to power ratio is typically T/P = .07 N/kW. Tank background pressure precludes direct measurement of exhaust velocity which is inferred from calculated pressure and temperature in the discharge to be about 14 km/sec. Efficiency, based on this velocity and measured T/P is .54 + or - .07. Thruster ablation is zero at the throat and becomes measurable further upstream, indicating that radiative ablation is occurring late in the pulse.

  13. Episodic repetitive thought: dimensions, correlates, and consequences.

    PubMed

    Segerstrom, Suzanne C; Stanton, Annette L; Flynn, Sarah McQueary; Roach, Abbey R; Testa, Jamie J; Hardy, Jaime K

    2012-01-01

    Repetitive thought (RT) - attentive, prolonged, or frequent thought about oneself and one's world - plays an important role in many models of psychological and physical ill health (e.g., rumination and worry), as well as models of recovery and well-being (e.g., processing and reminiscing). In these models, repetitive thought is typically treated as stable or trait-like. In contrast, episodic RT reflects what people have "on their minds" at a particular point in time. In four studies, young women (N=94), college students (N=166), first-year law students (N=73), and older adults (N=174) described their episodic RT, which was then rated for qualities including valence, purpose, and theme. Episodic RT valence was associated with mood and depressive symptoms both between (Studies 1-4) and within people (Studies 3-4), and it mediated the effects of dispositional coping through emotional approach (Study 1). The effect of episodic RT valence in turn was moderated by other properties of episodic RT, including purpose, "trait" valence, and theme (Studies 1-4). The study of episodic RT complements that of trait RT and allows for observations of how RT and psychological adjustment change in concert and in context, as well as examining how the RT qualities that are not reflected in trait measures affect adjustment. PMID:21861772

  14. Pull-production in repetitive remanufacturing

    SciTech Connect

    McCaskey, D.W. Jr.

    1992-09-01

    In the past, production activity control practices in most repetitive remanufacturing facilities resembled those used in intermittent production operations. These operations were characterized by large amounts of work-in-process (WIP), frequent work stoppages due to part shortages, excessive overtime, low product velocity, informal scheduling between dependent operations, low employee and management moral, and a lot of wasted time, material, labor, and space. Improvement in production activity control (PAC) methods for repetitive remanufactures has been hampered by uncertainty in: supply of incoming assets, configuration of assets, process times to refurbish assets, and yields in reclamation processes. collectively these uncertainties make shop floor operations seem uncontrollable. However, one United States Army depot has taken on the challenge. Through management supported, cross-functional teams, the Tooele Army Depot has designed and implemented pull-production systems for two of its major products, with several others to follow. This article presents a generalized version of Tooele`s pull-production system and highlights design characteristics which are specific to remanufacturing applications.

  15. Pull-production in repetitive remanufacturing

    SciTech Connect

    McCaskey, D.W. Jr.

    1992-09-01

    In the past, production activity control practices in most repetitive remanufacturing facilities resembled those used in intermittent production operations. These operations were characterized by large amounts of work-in-process (WIP), frequent work stoppages due to part shortages, excessive overtime, low product velocity, informal scheduling between dependent operations, low employee and management moral, and a lot of wasted time, material, labor, and space. Improvement in production activity control (PAC) methods for repetitive remanufactures has been hampered by uncertainty in: supply of incoming assets, configuration of assets, process times to refurbish assets, and yields in reclamation processes. collectively these uncertainties make shop floor operations seem uncontrollable. However, one United States Army depot has taken on the challenge. Through management supported, cross-functional teams, the Tooele Army Depot has designed and implemented pull-production systems for two of its major products, with several others to follow. This article presents a generalized version of Tooele's pull-production system and highlights design characteristics which are specific to remanufacturing applications.

  16. Episodic Repetitive Thought: Dimensions, Correlates, and Consequences

    PubMed Central

    Segerstrom, Suzanne C.; Stanton, Annette L.; Flynn, Sarah McQueary; Roach, Abbey R.; Testa, Jamie J.; Hardy, Jaime K.

    2011-01-01

    Repetitive thought (RT) – attentive, prolonged, or frequent thought about oneself and one’s world – plays an important role in many models of psychological and physical ill health (e.g., rumination and worry), as well as models of recovery and well-being (e.g., processing and reminiscing). In these models, repetitive thought is typically treated as stable or trait-like. In contrast, episodic RT reflects what people have “on their minds” at a particular point in time. In four studies, young women (N = 94), college students (N = 166), first-year law students (N = 73), and older adults (N = 174) described their episodic RT, which was then rated for qualities including valence, purpose, and theme. Episodic RT valence was associated with mood and depressive symptoms both between (Studies 1–4) and within people (Studies 3–4), and it mediated the effects of dispositional coping through emotional approach (Study 1). The effect of episodic RT valence in turn was moderated by other properties of episodic RT, including purpose, “trait” valence, and theme (Studies 1–4). The study of episodic RT complements that of trait RT and allows for observations of how RT and psychological adjustment change in concert and in context, as well as examining the RT qualities that are not reflected in trait measures affecting adjustment. PMID:21861772

  17. Regulation of miR-200c/141 expression by intergenic DNA-looping and transcriptional read-through.

    PubMed

    Batista, Luciana; Bourachot, Brigitte; Mateescu, Bogdan; Reyal, Fabien; Mechta-Grigoriou, Fatima

    2016-01-01

    The miR-200 family members have been implicated in stress responses and ovarian tumorigenesis. Here, we find that miR-200c/141 transcription is intimately linked to the transcription of the proximal upstream gene PTPN6 (SHP1) in all physiological conditions tested. PTPN6 and miR-200c/141 are transcriptionally co-regulated by two complementary mechanisms. First, a bypass of the regular PTPN6 polyadenylation signal allows the transcription of the downstream miR-200c/141. Second, the promoters of the PTPN6 and miR-200c/141 transcription units physically interact through a 3-dimensional DNA loop and exhibit similar epigenetic regulation. Our findings highlight that transcription of intergenic miRNAs is a novel outcome of transcriptional read-through and reveal a yet unexplored type of DNA loop associating two closely located promoters. These mechanisms have significant relevance in ovarian cancers and stress response, pathophysiological conditions in which miR-200c/141 exert key functions. PMID:26725650

  18. The Xis2d protein of CTnDOT binds to the intergenic region between the mob and tra operons.

    PubMed

    Hopp, Crystal M; Gardner, Jeffrey F; Salyers, Abigail A

    2015-09-01

    CTnDOT is a 65kbp integrative and conjugative element (ICE) that carries genes encoding both tetracycline and erythromycin resistances. The excision operon of this element encodes Xis2c, Xis2d, and Exc proteins involved in the excision of CTnDOT from host chromosomes. These proteins are also required in the complex transcriptional regulation of the divergently transcribed transfer (tra) and mobilization (mob) operons of CTnDOT. Transcription of the tra operon is positively regulated by Xis2c and Xis2d, whereas, transcription of the mob operon is positively regulated by Xis2d and Exc. Xis2d is the only protein that is involved in the excision reaction, as well as the transcriptional regulation of both the mob and tra operons. This paper helps establish how Xis2d binds the DNA in the mob and tra region. Unlike other excisionase proteins, Xis2d binds a region of dyad symmetry. The binding site is located in the intergenic region between the mob and tra promoters, and once bound Xis2d induces a bend in the DNA. Xis2d binding to this region could be the preliminary step for the activation of both operons. Then the other proteins, like Exc, can interact with Xis2d and form higher order complexes. PMID:26212728

  19. Identification of chimeric TSNAX-DISC1 resulting from intergenic splicing in endometrial carcinoma through high-throughput RNA sequencing.

    PubMed

    Li, Na; Zheng, Jian; Li, Hua; Deng, Jieqiong; Hu, Min; Wu, Hongchun; Li, Wei; Li, Fang; Lan, Xun; Lu, Jiachun; Zhou, Yifeng

    2014-12-01

    Gene fusion is among the primary processes that generate new genes and has been well characterized as potent pathway of oncogenesis. Here, by high-throughput RNA sequencing in nine paired human endometrial carcinoma (EC) and matched non-cancerous tissues, we obtained that chimeric translin-associated factor X-disrupted-in-schizophrenia 1 (TSNAX-DISC1) occurred significantly upregulated in multiple EC samples. Experimental investigation showed that TSNAX-DISC1 appears to be formed by splicing without chromosomal rearrangement. The chimera expression inversely correlated with the binding of CCCTC-binding factor (CTCF) to the insulators. Subsequent investigations indicate that long intergenic non-coding RNA lincRNA-NR_034037, separating TSNAX from DISC1, regulates TSNAX -DISC1 production and TSNAX/DISC1 expression levels by extricating CTCF from insulators. Dysregulation of TSNAX influences steroidogenic factor-1-stimulated transcription on the StAR promoter, altering progesterone actions, implying the association with cancer. Together, these results advance our understanding of the mechanism in which lincRNA-NR_034037 regulates TSNAX-DISC1 formation programs that tightly regulate EC development. PMID:25239642

  20. A New Intergenic α-Globin Deletion (α-α(Δ125)) Found in a Kabyle Population.

    PubMed

    Rabbind Singh, Amrathlal; Lacan, Philippe; Cadet, Estelle; Bignet, Patricia; Dumesnil, Cécile; Vannier, Jean-Pierre; Joly, Philippe; Rochette, Jacques

    2016-03-01

    We have identified a deletion of 125 bp (α-α(Δ125)) (NG_000006.1: g.37040_37164del) in the α-globin gene cluster in a Kabyle population. A combination of singlex and multiplex polymerase chain reaction (PCR)-based assays have been used to identify the molecular defect. Sequencing of the abnormal PCR amplification product revealed a novel α1-globin promoter deletion. The endpoints of the deletion were characterized by sequencing the deletion junctions of the mutated allele. The observed deletion was located 378 bp upstream of the α1-globin gene transcription initiation site and leaves the α2 gene intact. In some patients, the α-α(Δ125) deletion was shown to segregate with Hb S (HBB: c.20A>T) and/or Hb C (HBB: c.19G>A) or a β-thalassemic allele. The α-α(Δ125) deletion has no discernible effect on red cell indices when inherited with no other abnormal globin genes. The family study demonstrated that the deletion is heritable. This is the only example of an intergenic α2-α1 non coding DNA deletion, leaving the α2-globin gene and the α1 coding part intact. PMID:26911300

  1. Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network

    PubMed Central

    Xu, Xi-Wen; Zhou, Xiong-Hui; Wang, Rui-Ru; Peng, Wen-Lei; An, Yue; Chen, Ling-Ling

    2016-01-01

    Long intergenic non-coding RNAs (lincRNAs) may play widespread roles in gene regulation and other biological processes, however, a systematic examination of the functions of lincRNAs in the biological responses of rice to phosphate (Pi) starvation has not been performed. Here, we used a computational method to predict the functions of lincRNAs in Pi-starved rice. Overall, 3,170 lincRNA loci were identified using RNA sequencing data from the roots and shoots of control and Pi-starved rice. A competing endogenous RNA (ceRNA) network was constructed for each tissue by considering the competing relationships between lincRNAs and genes, and the correlations between the expression levels of RNAs in ceRNA pairs. Enrichment analyses showed that most of the communities in the networks were related to the biological processes of Pi starvation. The lincRNAs in the two tissues were individually functionally annotated based on the ceRNA networks, and the differentially expressed lincRNAs were biologically meaningful. For example, XLOC_026030 was upregulated from 3 days after Pi starvation, and its functional annotation was ‘cellular response to Pi starvation’. In conclusion, we systematically annotated lincRNAs in rice and identified those involved in the biological response to Pi starvation. PMID:26860696

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

    PubMed

    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. PMID:26776159

  3. Comparison of Sequences from the Ribosomal DNA Intergenic Region of Meloidogyne mayaguensis and Other Major Tropical Root-Knot Nematodes

    PubMed Central

    Blok, V. C.; Phillips, M. S.; Fargette, M.

    1997-01-01

    The unusual arrangement of the 5S ribosomal gene within the intergenic sequence (IGS) of the ribosomal cistron, previously reported for Meloidogyne arenaria, was also found in the ribosomal DNA of two other economically important species of tropical root-knot nematodes, M, incognita and M. javanica. This arrangement also was found in M. hapla, which is important in temperate regions, and M. mayaguensis, a virulent species of concern in West Africa. Amplification of the region between the 5S and 18S genes by PCR yielded products of three different sizes such that M. mayaguensis could be readily differentiated from the other species in this study. This product can be amplified from single juveniles, females, or egg masses. The sequences obtained in this region for one line of each of M. incognita, M. arenaria, and M. javanica were very similar, reflecting the close relationships of these lineages. The M. mayaguensis sequence for this region had a number of small deletions and insertions of various sizes, including possible sequence duplications. PMID:19274129

  4. A functional analysis of the spacer of V(D)J recombination signal sequences.

    PubMed

    Lee, Alfred Ian; Fugmann, Sebastian D; Cowell, Lindsay G; Ptaszek, Leon M; Kelsoe, Garnett; Schatz, David G

    2003-10-01

    During lymphocyte development, V(D)J recombination assembles antigen receptor genes from component V, D, and J gene segments. These gene segments are flanked by a recombination signal sequence (RSS), which serves as the binding site for the recombination machinery. The murine Jbeta2.6 gene segment is a recombinationally inactive pseudogene, but examination of its RSS reveals no obvious reason for its failure to recombine. Mutagenesis of the Jbeta2.6 RSS demonstrates that the sequences of the heptamer, nonamer, and spacer are all important. Strikingly, changes solely in the spacer sequence can result in dramatic differences in the level of recombination. The subsequent analysis of a library of more than 4,000 spacer variants revealed that spacer residues of particular functional importance are correlated with their degree of conservation. Biochemical assays indicate distinct cooperation between the spacer and heptamer/nonamer along each step of the reaction pathway. The results suggest that the spacer serves not only to ensure the appropriate distance between the heptamer and nonamer but also regulates RSS activity by providing additional RAG:RSS interaction surfaces. We conclude that while RSSs are defined by a "digital" requirement for absolutely conserved nucleotides, the quality of RSS function is determined in an "analog" manner by numerous complex interactions between the RAG proteins and the less-well conserved nucleotides in the heptamer, the nonamer, and, importantly, the spacer. Those modulatory effects are accurately predicted by a new computational algorithm for "RSS information content." The interplay between such binary and multiplicative modes of interactions provides a general model for analyzing protein-DNA interactions in various biological systems. PMID:14551903

  5. A phonetic approach to consonant repetition in early words.

    PubMed

    Kim, Namhee; Davis, Barbara L

    2015-08-01

    The goal of this study was to evaluate movement-based principles for understanding early speech output patterns. Consonant repetition patterns within children's actual productions of word forms were analyzed using spontaneous speech data from 10 typically developing American-English learning children between 12 and 36 months of age. Place of articulation, word level patterns, and developmental trends in CVC and CVCV repeated word forms were evaluated. Labial and coronal place repetitions dominated. Regressive repetition (e.g., [gag] for "dog") occurred frequently in CVC but not in CVCV word forms. Consonant repetition decreased over time. However, the children produced sound types available reported as being within young children's production system capabilities in consonant repetitions in all time periods. Findings suggest that a movement-based approach can provide a framework for comprehensively characterizing consonant place repetition patterns in early speech development. PMID:26176184

  6. Combining denaturing gradient gel electrophoresis of 16S rDNA V3 region and 16S-23S rDNA spacer region polymorphism analyses for the identification of staphylococci from Italian fermented sausages.

    PubMed

    Blaiotta, Giuseppe; Pennacchia, Carmelina; Ercolini, Danilo; Moschetti, Giancarlo; Villani, Francesco

    2003-09-01

    Separation of amplified V3 region from 16S rDNA by denaturing gradient gel electrophoresis (PCR-DGGE) and 16S-23S rDNA intergenic spacer region polymorphism (ISR-PCR) analyses were tested as tool for differentiation of staphylococcal strains commonly isolated from fermented sausages. Variable V3 regions of 25 staphylococcal reference strains and 96 wild strains of species belonging to the genera Staphylococcus, Micrococcus and Kocuria were analyzed. PCR-DGGE profiles obtained were species-specific for S. sciuri, S. haemolyticus, S. hominis, S. auricularis, S. condimenti, S. kloosi, S. vitulus, S. succinus, S. pasteuri, S. capitis and S. (Macrococcus) caseolyticus. Moreover, 7 groups could be distinguished gathering the remaining species as result of the separation of the V3 rDNA amplicons in DGGE. Furthermore, the combination of the results obtained by PCR-DGGE and ISR-PCR analyses allowed a clear differentiation of all the staphylococcal species analysed, with exception of the pairs S. equorum-S. cohnii and S. carnosus-S. schleiferi. The suitability of both molecular techniques and of the combination their results for the identification of staphylococci was validated analysing partial nucleotide sequence of the 16S rDNA of a representative number of wild strains. PMID:14529185

  7. Use of Repetitive DNA Sequences and the PCR To Differentiate Escherichia coli Isolates from Human and Animal Sources

    PubMed Central

    Dombek, Priscilla E.; Johnson, LeeAnn K.; Zimmerley, Sara T.; Sadowsky, Michael J.

    2000-01-01

    The rep-PCR DNA fingerprint technique, which uses repetitive intergenic DNA sequences, was investigated as a way to differentiate between human and animal sources of fecal pollution. BOX and REP primers were used to generate DNA fingerprints from Escherichia coli strains isolated from human and animal sources (geese, ducks, cows, pigs, chickens, and sheep). Our initial studies revealed that the DNA fingerprints obtained with the BOX primer were more effective for grouping E. coli strains than the DNA fingerprints obtained with REP primers. The BOX primer DNA fingerprints of 154 E. coli isolates were analyzed by using the Jaccard band-matching algorithm. Jackknife analysis of the resulting similarity coefficients revealed that 100% of the chicken and cow isolates and between 78 and 90% of the human, goose, duck, pig, and sheep isolates were assigned to the correct source groups. A dendrogram constructed by using Jaccard similarity coefficients almost completely separated the human isolates from the nonhuman isolates. Multivariate analysis of variance, a form of discriminant analysis, successfully differentiated the isolates and placed them in the appropriate source groups. Taken together, our results indicate that rep-PCR performed with the BOX A1R primer may be a useful and effective tool for rapidly determining sources of fecal pollution. PMID:10831440

  8. A review of neuroimaging findings in repetitive brain trauma.

    PubMed

    Koerte, Inga K; Lin, Alexander P; Willems, Anna; Muehlmann, Marc; Hufschmidt, Jakob; Coleman, Michael J; Green, Isobel; Liao, Huijun; Tate, David F; Wilde, Elisabeth A; Pasternak, Ofer; Bouix, Sylvain; Rathi, Yogesh; Bigler, Erin D; Stern, Robert A; Shenton, Martha E

    2015-05-01

    Chronic traumatic encephalopathy (CTE) is a neurodegenerative disease confirmed at postmortem. Those at highest risk are professional athletes who participate in contact sports and military personnel who are exposed to repetitive blast events. All neuropathologically confirmed CTE cases, to date, have had a history of repetitive head impacts. This suggests that repetitive head impacts may be necessary for the initiation of the pathogenetic cascade that, in some cases, leads to CTE. Importantly, while all CTE appears to result from repetitive brain trauma, not all repetitive brain trauma results in CTE. Magnetic resonance imaging has great potential for understanding better the underlying mechanisms of repetitive brain trauma. In this review, we provide an overview of advanced imaging techniques currently used to investigate brain anomalies. We also provide an overview of neuroimaging findings in those exposed to repetitive head impacts in the acute/subacute and chronic phase of injury and in more neurodegenerative phases of injury, as well as in military personnel exposed to repetitive head impacts. Finally, we discuss future directions for research that will likely lead to a better understanding of the underlying mechanisms separating those who recover from repetitive brain trauma vs. those who go on to develop CTE. PMID:25904047

  9. The use of repetition suppression paradigms in developmental cognitive neuroscience.

    PubMed

    Nordt, Marisa; Hoehl, Stefanie; Weigelt, Sarah

    2016-07-01

    Repetition suppression paradigms allow a more detailed look at brain functioning than classical paradigms and have been applied vigorously in adult cognitive neuroscience. These paradigms are well suited for studies in the field of developmental cognitive neuroscience as they can be applied without collecting a behavioral response and across all age groups. Furthermore, repetition suppression paradigms can be employed in various neuroscience techniques, such as functional magnetic resonance imaging (fMRI), functional near-infrared spectroscopy (fNIRS), electroencephalography (EEG) and magnetoencephalography (MEG). In the present article we review studies using repetition suppression paradigms in developmental cognitive neuroscience covering the age range from infancy to adolescence. Our first goal is to point out characteristics of developmental repetition suppression effects. In doing so, we discuss the relationship of the direction of repetition effects (suppression vs enhancement) with developmental factors, and address the question how the direction of repetition effects might be related to looking-time effects in behavioral infant paradigms, the most prominently used behavioral measure in infant research. To highlight the potential of repetition suppression paradigms, our second goal is to provide an overview on the insights recently obtained by applying repetition paradigms in neurodevelopmental studies, including research on children with autism spectrum disorders (ASDs). We conclude that repetition suppression paradigms are valuable tools for investigating neurodevelopmental processes, while at the same time we highlight the necessity for further studies that disentangle methodological and developmental factors. PMID:27161033

  10. Low-Intensity Repetitive Exercise Induced Rhabdomyolysis

    PubMed Central

    Tran, Mina; Hayden, Nicholas; Garcia, Brandon; Tucci, Veronica

    2015-01-01

    Rhabdomyolysis is a rare condition caused by the proteins of damaged muscle cells entering the bloodstream and damaging the kidneys. Common symptoms of rhabdomyolysis are muscle pain and fatigue in conjunction with dark urine; kidney damage is a common symptom among these patients. We present a case of a 23-year-old woman who displayed myalgia in the upper extremities caused by low-intensity and high-repetition exercise. She was successfully diagnosed and treated for exertional rhabdomyolysis. This patient had no significant medical history that would induce this condition. We urge the emergency medical community to observe and monitor patients that complain of myalgia to ensure they are not suffering from rhabdomyolysis even in atypical cases. PMID:26693360

  11. Repetitive DNA sequences in Mycoplasma pneumoniae.

    PubMed Central

    Wenzel, R; Herrmann, R

    1988-01-01

    Two types of different repetitive DNA sequences called RepMP1 and RepMP2 were identified in the genome of Mycoplasma pneumoniae. The number of these repeated elements, their nucleotide sequence and their localization on a physical map of the M. pneumoniae genome were determined. The results show that RepMP1 appears at least 10 times and RepMP2 at least 8 times in the genome. The repeated elements are dispersed on the chromosome and, in three cases, linked to each other by a homologous DNA sequence of 400 bp. The elements themselves are 300 bp (for RepMP1) and 150 bp (for RepMP2) long showing a high degree of homology. One copy of RepMP2 is a translated part of the gene for the major cytadhesin protein P1 which is responsible for the adsorption of M. pneumoniae to its host cell. Images PMID:3138660

  12. Context and repetition in word learning

    PubMed Central

    Horst, Jessica S.

    2013-01-01

    Young children learn words from a variety of situations, including shared storybook reading. A recent study by Horst et al. (2011a) demonstrates that children learned more new words during shared storybook reading if they were read the same stories repeatedly than if they were read different stories that had the same number of target words. The current paper reviews this study and further examines the effect of contextual repetition on children's word learning in both shared storybook reading and other situations, including fast mapping by mutual exclusivity. The studies reviewed here suggest that the same cognitive mechanisms support word learning in a variety of situations. Both practical considerations for experimental design and directions for future research are discussed. PMID:23580347

  13. Visual identity and uncertainty in repetition blindness.

    PubMed

    Brill, Gary A; Glass, Arnold L; Rashid, Hanin; Hussey, Erika

    2008-01-01

    Repetition blindness (RB) was investigated in 6 experiments. In the first 3 experiments participants detected vowel targets in 11-letter sequences. When all letters were uppercase, detection was poorer for same (e.g., AA) than for different (e.g., AO) targets. However, when one target was uppercase and the other lowercase, RB was found only for targets visually identical except for size (e.g., Oo), not for visually different pairs (e.g., Aa). Experiment 4 found RB for visually identical versus different consonant-vowel-consonant words. Experiments 5 and 6 replicated Kanwisher's (1987) experiment in which RB was insensitive to word case but revealed these effects to be artifacts of poor recognition of 5-letter words coupled with a biased guessing strategy. Overall, these experiments found RB only at a low level of visual information processing. PMID:18792718

  14. Development of an innovative spacer grid model utilizing computational fluid dynamics within a subchannel analysis tool

    NASA Astrophysics Data System (ADS)

    Avramova, Maria

    In the past few decades the need for improved nuclear reactor safety analyses has led to a rapid development of advanced methods for multidimensional thermal-hydraulic analyses. These methods have become progressively more complex in order to account for the many physical phenomena anticipated during steady state and transient Light Water Reactor (LWR) conditions. The advanced thermal-hydraulic subchannel code COBRA-TF (Thurgood, M. J. et al., 1983) is used worldwide for best-estimate evaluations of the nuclear reactor safety margins. In the framework of a joint research project between the Pennsylvania State University (PSU) and AREVA NP GmbH, the theoretical models and numerics of COBRA-TF have been improved. Under the name F-COBRA-TF, the code has been subjected to an extensive verification and validation program and has been applied to variety of LWR steady state and transient simulations. To enable F-COBRA-TF for industrial applications, including safety margins evaluations and design analyses, the code spacer grid models were revised and substantially improved. The state-of-the-art in the modeling of the spacer grid effects on the flow thermal-hydraulic performance in rod bundles employs numerical experiments performed by computational fluid dynamics (CFD) calculations. Because of the involved computational cost, the CFD codes cannot be yet used for full bundle predictions, but their capabilities can be utilized for development of more advanced and sophisticated models for subchannel-level analyses. A subchannel code, equipped with improved physical models, can be then a powerful tool for LWR safety and design evaluations. The unique contributions of this PhD research are seen as development, implementation, and qualification of an innovative spacer grid model by utilizing CFD results within a framework of a subchannel analysis code. Usually, the spacer grid models are mostly related to modeling of the entrainment and deposition phenomena and the heat

  15. Enhanced spacer-is-dielectric (sid) decomposition flow with model-based verification

    NASA Astrophysics Data System (ADS)

    Du, Yuelin; Song, Hua; Shiely, James; Wong, Martin D. F.

    2013-03-01

    Self-aligned double patterning (SADP) lithography is a leading candidate for 14nm node lower-metal layer fabrication. Besides the intrinsic overlay-tolerance capability, the accurate spacer width and uniformity control enables such technology to fabricate very narrow and dense patterns. Spacer-is-dielectric (SID) is the most popular flavor of SADP with higher flexibility in design. In the SID process, due to uniform spacer deposition, the spacer shape gets rounded at convex mandrel corners, and disregarding the corner rounding issue during SID decomposition may result in severe residue artifacts on device patterns. Previously, SADP decomposition was merely verified by Boolean operations on the decomposed layers, where the residue artifacts are not even identifiable. This paper proposes a model-based verification method for SID decomposition to identify the artifacts caused by spacer corner rounding. Then targeting residue artifact removal, an enhanced SID decomposition flow is introduced. Simulation results show that residue artifacts are removed effectively through the enhanced SID decomposition strategy.

  16. Ternary DNA chip based on a novel thymine spacer group chemistry.

    PubMed

    Yang, Yanli; Yildiz, Umit Hakan; Peh, Jaime; Liedberg, Bo

    2015-01-01

    A novel thymine-based surface chemistry suitable for label-free electrochemical DNA detection is described. It involves a simple two-step sequential process: immobilization of 9-mer thymine-terminated probe DNAs followed by backfilling with 9-mer thymine-based spacers (T9). As compared to commonly used organic spacer groups like 2-mercaptoethanol, 3-mercapto-1-propanol and 6-mercapto-1-hexanol, the 9-mer thymine-based spacers offer a 10-fold improvement in discriminating between complementary and non-complementary target hybridization, which is due mainly to facilitated transport of the redox probes through the probe-DNA/T9 layers. Electrochemical measurements, complemented with Surface Plasmon Resonance (SPR) and Quartz Crystal Microbalance (QCM-D) binding analyses, reveal that optimum selectivity between complementary and non-complementary hybridization is obtained for a sensing surface prepared using probe-DNA and backfiller T9 at equimolar concentration (1:1). At this particular ratio, the probe-DNAs are preferentially oriented and easily accessible to yield a sensing surface with favorable hybridization and electron transfer characteristics. Our findings suggest that oligonucleotide-based spacer groups offer an attractive alternative to short organic thiol spacers in the design of future DNA biochips. PMID:25465760

  17. Airflows after inhalation of terbutaline sulphate aerosol from a 750-ml spacer for four weeks.

    PubMed

    Eriksson, N E; Hidinger, K G; Rosenhall, L; Hagstad, H; Löfgren, L; Perk, J; Stiksa, G; Ström, K

    1986-01-01

    Terbutaline sulphate was administered to 40 adult asthmatic patients via an ordinary metered-dose inhaler (MDI) or one connected to a 750-ml spacer in an open, randomized, crossover study. Spirometry was obtained before the start of the study and again after four weeks of treatment with each inhaler. The patients recorded on a diary card the severity of their asthma symptoms and the peak expiratory flow rate (PEFR) in the morning before and after drug administration and in the evening. Preinhalation spirometric values were higher after four weeks with the 750-ml spacer than at the start of the study (P less than or equal to 0.05). Daily morning and evening PEFR values were higher after use of the 750-ml spacer than after use of the ordinary MDI (P less than 0.05). Daily symptom scores were generally low. A significantly better effect (P less than or equal to 0.05) with the 750-ml spacer was achieved only in daytime dyspnea. The investigators conclude that the attachment of a 750-ml spacer to an ordinary metered-dose inhaler can improve the efficacy of terbutaline sulphate in the long-term treatment of asthma. PMID:3698068

  18. Engineering damping in insulating magnet-metal bilayers using ultrathin spacer layers

    NASA Astrophysics Data System (ADS)

    Aradhya, Sriharsha V.; Jermain, Colin L.; Paik, Hanjong; Heron, John T.; Schlom, Darrell G.; Ralph, Daniel C.; Buhrman, Robert A.

    2015-03-01

    Insulating magnetic materials, particularly yttrium iron garnet (YIG), are of significant interest for fundamental research as well as technological applications. Thus far copper spacer layers of ~10 nm - 1 μm thickness sandwiched between YIG and heavy metal films have been shown to modulate the damping of the magnetic layer either higher or lower. We report on the effect of ultrathin nonmagnetic spacer layers on the damping of YIG with different heavy metal overlayers. We start with YIG films grown by oxide molecular beam epitaxy with thicknesses below 20 nm and Gilbert damping as low as 0.0005. We observe that a spacer layer can increase the damping by 50% in YIG/spacer/Ta samples compared to YIG/Ta, and the increase can be as large 500% for YIG/spacer/Pt compared to YIG/Pt. These observations suggest a significant increase in the effective spin mixing conductance at the YIG-heavy metal interface that might be used to improve the efficiency of the spin torque produced by the spin Hall effect.

  19. The CRISPR RNA-guided surveillance complex in Escherichia coli accommodates extended RNA spacers

    PubMed Central

    Luo, Michelle L.; Jackson, Ryan N.; Denny, Steven R.; Tokmina-Lukaszewska, Monika; Maksimchuk, Kenneth R.; Lin, Wayne; Bothner, Brian; Wiedenheft, Blake; Beisel, Chase L.

    2016-01-01

    Bacteria and archaea acquire resistance to foreign genetic elements by integrating fragments of foreign DNA into CRISPR (clustered regularly interspaced short palindromic repeats) loci. In Escherichia coli, CRISPR-derived RNAs (crRNAs) assemble with Cas proteins into a multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade recognizes DNA targets via protein-mediated recognition of a protospacer adjacent motif and complementary base pairing between the crRNA spacer and the DNA target. Previously determined structures of Cascade showed that the crRNA is stretched along an oligomeric protein assembly, leading us to ask how crRNA length impacts the assembly and function of this complex. We found that extending the spacer portion of the crRNA resulted in larger Cascade complexes with altered stoichiometry and preserved in vitro binding affinity for target DNA. Longer spacers also preserved the in vivo ability of Cascade to repress target gene expression and to recruit the Cas3 endonuclease for target degradation. Finally, longer spacers exhibited enhanced silencing at particular target locations and were sensitive to mismatches within the extended region. These findings demonstrate the flexibility of the Type I-E CRISPR machinery and suggest that spacer length can be modified to fine-tune Cascade activity. PMID:27174938

  20. New titanium spacer for cervical laminoplasty: initial clinical experience. Technical note.

    PubMed

    Tani, Satoshi; Suetsua, Futoshi; Mizuno, Junichi; Uchikado, Hisaaki; Nagashima, Hiroyasu; Akiyama, Masahiko; Isoshima, Akira; Ohashi, Hiroki; Hirano, Yoshitaka; Abe, Toshiaki

    2010-01-01

    Many commercially available hydroxyapatite (HA) spacers for cervical laminoplasty have been introduced but have disadvantages such as lack of plasticity, easy cracking, and occasional difficulty in fixation by sutures. Here we present the short-term results of a newly designed titanium spacer (Laminoplasty Basket) in open-door cervical laminoplasty, and evaluated clinically and radiologically. The titanium box-shaped spacer with two arms for fixation was easily inserted and fixed into the laminoplasty space with 4-mm or 5-mm length screws after the posterior cervical arch was repositioned for the canal expansion. Twenty-one patients with cervical myelopathy due to spondylosis or ossification of the longitudinal ligament or developmental narrow canal observed for more than 6 months postoperatively were enrolled in this study. The neurological condition of these patients improved from 9.4 points on the Japanese Orthopaedic Association scale preoperatively to 13.5 points at 6 months after surgery. Postoperative radiological evaluation showed no laminar closure or implant failure and cervical spine curvature was maintained. These results seemed to have no significant difference compared with those using HA spacers. This titanium spacer is a potential substitute for conventional HA or other similar devices in cervical laminoplasty. PMID:21206196

  1. Adverse impact of feed channel spacers on the performance of pressure retarded osmosis.

    PubMed

    Kim, Yu Chang; Elimelech, Menachem

    2012-04-17

    This article analyzes the influence of feed channel spacers on the performance of pressure retarded osmosis (PRO). Unlike forward osmosis (FO), an important feature of PRO is the application of hydraulic pressure on the high salinity (draw solution) side to retard the permeating flow for energy conversion. We report the first observation of membrane deformation under the action of the high hydraulic pressure on the feed channel spacer and the resulting impact on membrane performance. Because of this observation, reverse osmosis and FO tests that are commonly used for measuring membrane transport properties (water and salt permeability coefficients, A and B, respectively) and the structural parameter (S) can no longer be considered appropriate for use in PRO analysis. To accurately predict the water flux as a function of applied hydraulic pressure difference and the resulting power density in PRO, we introduced a new experimental protocol that accounts for membrane deformation in a spacer-filled channel to determine the membrane properties (A, B, and S). PRO performance model predictions based on these determined A, B, and S values closely matched experimental data over a range of draw solution concentrations (0.5 to 2 M NaCl). We also showed that at high pressures feed spacers block the permeation of water through the membrane area in contact with the spacer, a phenomenon that we term the shadow effect, thereby reducing overall water flux. The implications of the results for power generation by PRO are evaluated and discussed. PMID:22420537

  2. CFD study of isothermal water flow in rod bundle with split-type spacer grid

    NASA Astrophysics Data System (ADS)

    Batta, A.; Class, A. G.

    2014-06-01

    The design of rod bundles in nuclear application nowadays is assessed by CFD (computational fluid dynamics). The accuracy of CFD models need validation. Within the OECD/NEA benchmark MATiS-H (Measurement and Analysis of Turbulent Mixing in Sub-channels - Horizontal) a single-phase water flow in a 5x5 rod bundle is studied. In the benchmark, two types of spacer grids are tested, the swirl type and the split type, where the current study focuses on the split type spacer grid. Comparison of CFD results obtained at Karlsruhe Institut of Technology (KIT) with experimental results of KAERI (Korea Atomic Energy Research Institute) are presented. In the benchmark velocities components along selected lines downstream of the spacer grid are measured and compared to CFD results. The CFD code STAR CCM+ with the Realized k-ɛ model is used. Comparisons with experimental results show quantitative and qualitative agreement for the averaged values of velocity components. Comparisons of results to other benchmark partners using different modeling show that the selected mesh size and models for the analysis of the current case gives relatively accurate results. However, the used turbulent model (Realized k-ɛ does not capture the turbulent intensity correctly. Computation shows that the flow has very high mixing due to the spacer grid, which does not decay within the measurements domain (z/ DH =0-10 downstream of spacer grid). The same conclusion can be drawn from experimental data.

  3. Monobenzoporphyrins as Sensitizers for Dye-Sensitized Solar Cells: Observation of Significant Spacer-Group Effect.

    PubMed

    Jinadasa, R G Waruna; Li, Bihong; Schmitz, Benjamin; Kumar, Siddhartha; Hu, Yi; Kerr, Lei; Wang, Hong

    2016-08-23

    A series of monobenzoporphyrins (WH1-WH4) bearing different conjugated spacer groups were designed and synthesized as sensitizers for dye-sensitized solar cells. Although a phenyl spacer only has a minimal impact on the absorption bands of the monobenzoporphyrin, an ethynylphenyl (WH3) or a vinyl (WH4) spacer redshifts and broadens the absorption bands of the dyes to result in much enhanced light-harvesting ability. Dye-sensitized solar cells based on these monobenzoporphyrin dyes displayed remarkable differences in power conversion efficiencies (PCEs). The monobenzoporphyrin bearing no spacer (WH1) resulted in a PCE of only 0.5 %; in contrast, the monobenzoporphyrin bearing vinyl spacers (WH4) achieved a PCE of 5.2 %. The high efficiency of the WH4 cell is attributed to the higher light-harvesting ability, the lesser extent of aggregation on the TiO2 surface, and the more favorable electron-density distributions of the HOMO and LUMO for electron injection and collection. This work demonstrates the exceptional tunability of benzoporphyrins as sensitizers for dye-sensitized solar cells. PMID:27469616

  4. High-throughput analysis of type I-E CRISPR/Cas spacer acquisition in E. coli

    PubMed Central

    Savitskaya, Ekaterina; Semenova, Ekaterina; Dedkov, Vladimir; Metlitskaya, Anastasia; Severinov, Konstantin

    2013-01-01

    In Escherichia coli, the acquisition of new CRISPR spacers is strongly stimulated by a priming interaction between a spacer in CRISPR RNA and a protospacer in foreign DNA. Priming also leads to a pronounced bias in DNA strand from which new spacers are selected. Here, ca. 200,000 spacers acquired during E. coli type I-E CRISPR/Cas-driven plasmid elimination were analyzed. Analysis of positions of plasmid protospacers from which newly acquired spacers have been derived is inconsistent with spacer acquisition machinery sliding along the target DNA as the primary mechanism responsible for strand bias during primed spacer acquisition. Most protospacers that served as donors of newly acquired spacers during primed spacer acquisition had an AAG protospacer adjacent motif, PAM. Yet, the introduction of multiple AAG sequences in the target DNA had no effect on the choice of protospacers used for adaptation, which again is inconsistent with the sliding mechanism. Despite a strong preference for an AAG PAM during CRISPR adaptation, the AAG (and CTT) triplets do not appear to be avoided in known E. coli phages. Likewise, PAM sequences are not avoided in Streptococcus thermophilus phages, indicating that CRISPR/Cas systems may not have been a strong factor in shaping host-virus interactions. PMID:23619643

  5. Long Intergenic Noncoding RNAs Mediate the Human Chondrocyte Inflammatory Response and Are Differentially Expressed in Osteoarthritis Cartilage

    PubMed Central

    Pearson, Mark J.; Philp, Ashleigh M.; Heward, James A.; Roux, Benoit T.; Walsh, David A.; Davis, Edward T.; Lindsay, Mark A.

    2016-01-01

    Objective To identify long noncoding RNAs (lncRNAs), including long intergenic noncoding RNAs (lincRNAs), antisense RNAs, and pseudogenes, associated with the inflammatory response in human primary osteoarthritis (OA) chondrocytes and to explore their expression and function in OA. Methods OA cartilage was obtained from patients with hip or knee OA following joint replacement surgery. Non‐OA cartilage was obtained from postmortem donors and patients with fracture of the neck of the femur. Primary OA chondrocytes were isolated by collagenase digestion. LncRNA expression analysis was performed by RNA sequencing (RNAseq) and quantitative reverse transcriptase–polymerase chain reaction. Modulation of lncRNA chondrocyte expression was achieved using LNA longRNA GapmeRs (Exiqon). Cytokine production was measured with Luminex. Results RNAseq identified 983 lncRNAs in primary human hip OA chondrocytes, 183 of which had not previously been identified. Following interleukin‐1β (IL‐1β) stimulation, we identified 125 lincRNAs that were differentially expressed. The lincRNA p50‐associated cyclooxygenase 2–extragenic RNA (PACER) and 2 novel chondrocyte inflammation–associated lincRNAs (CILinc01 and CILinc02) were differentially expressed in both knee and hip OA cartilage compared to non‐OA cartilage. In primary OA chondrocytes, these lincRNAs were rapidly and transiently induced in response to multiple proinflammatory cytokines. Knockdown of CILinc01 and CILinc02 expression in human chondrocytes significantly enhanced the IL‐1–stimulated secretion of proinflammatory cytokines. Conclusion The inflammatory response in human OA chondrocytes is associated with widespread changes in the profile of lncRNAs, including PACER, CILinc01, and CILinc02. Differential expression of CILinc01 and CIinc02 in hip and knee OA cartilage, and their role in modulating cytokine production during the chondrocyte inflammatory response, suggest that they may play an important role

  6. LincSNP: a database of linking disease-associated SNPs to human large intergenic non-coding RNAs

    PubMed Central

    2014-01-01

    Background Genome-wide association studies (GWAS) have successfully identified a large number of single nucleotide polymorphisms (SNPs) that are associated with a wide range of human diseases. However, many of these disease-associated SNPs are located in non-coding regions and have remained largely unexplained. Recent findings indicate that disease-associated SNPs in human large intergenic non-coding RNA (lincRNA) may lead to susceptibility to diseases through their effects on lincRNA expression. There is, therefore, a need to specifically record these SNPs and annotate them as potential candidates for disease. Description We have built LincSNP, an integrated database, to identify and annotate disease-associated SNPs in human lincRNAs. The current release of LincSNP contains approximately 140,000 disease-associated SNPs (or linkage disequilibrium SNPs), which can be mapped to around 5,000 human lincRNAs, together with their comprehensive functional annotations. The database also contains annotated, experimentally supported SNP-lincRNA-disease associations and disease-associated lincRNAs. It provides flexible search options for data extraction and searches can be performed by disease/phenotype name, SNP ID, lincRNA name and chromosome region. In addition, we provide users with a link to download all the data from LincSNP and have developed a web interface for the submission of novel identified SNP-lincRNA-disease associations. Conclusions The LincSNP database aims to integrate disease-associated SNPs and human lincRNAs, which will be an important resource for the investigation of the functions and mechanisms of lincRNAs in human disease. The database is available at http://bioinfo.hrbmu.edu.cn/LincSNP. PMID:24885522

  7. The Golden Ratio of Gait Harmony: Repetitive Proportions of Repetitive Gait Phases

    PubMed Central

    Iosa, Marco; Marchetti, Fabio; Morone, Giovanni; Caltagirone, Carlo; Paolucci, Stefano; Peppe, Antonella

    2013-01-01

    In nature, many physical and biological systems have structures showing harmonic properties. Some of them were found related to the irrational number ϕ known as the golden ratio that has important symmetric and harmonic properties. In this study, the spatiotemporal gait parameters of 25 healthy subjects were analyzed using a stereophotogrammetric system with 25 retroreflective markers located on their skin. The proportions of gait phases were compared with ϕ, the value of which is about 1.6180. The ratio between the entire gait cycle and stance phase resulted in 1.620 ± 0.058, that between stance and the swing phase was 1.629 ± 0.173, and that between swing and the double support phase was 1.684 ± 0.357. All these ratios did not differ significantly from each other (F = 0.870, P = 0.422, repeated measure analysis of variance) or from ϕ (P = 0.670, 0.820, 0.422, resp., t-tests). The repetitive gait phases of physiological walking were found in turn in repetitive proportions with each other, revealing an intrinsic harmonic structure. Harmony could be the key for facilitating the control of repetitive walking. Harmony is a powerful unifying factor between seemingly disparate fields of nature, including human gait. PMID:23862161

  8. Custom Anatomical 3D Spacer for Temporomandibular Joint Resection and Reconstruction.

    PubMed

    Green, John Marshall; Lawson, Sarah T; Liacouras, Peter C; Wise, Edward M; Gentile, Michael A; Grant, Gerald Thomas

    2016-03-01

    Two cases are presented using a two-stage approach and a custom antibiotic spacer placement. Temporomandibular reconstruction can be very demanding and accomplished with a variety of methods in preparation of a total joint and ramus reconstruction with total joint prostheses (TMJ Concepts, Ventura, CA). Three-dimensional reconstructions from diagnostic computed tomography were used to establish a virtually planned resection which included the entire condyle-ramus complex. From these data, digital designs were used to manufacture molds to facilitate intraoperative fabrication of precise custom anatomic spacers from rapidly setting antibiotic-impregnated polymethyl methacrylate. Molds were manufactured using vat polymerization (stereolithography) with a photopolymer in the first case and powder bed fusion (electron beam melting) with Ti6AL4V for the second. Surgical methodology and the use of molds for intraoperative spacer fabrication for each case are discussed. PMID:26889353

  9. Rotor bore and turbine rotor wheel/spacer heat exchange flow circuit

    DOEpatents

    Caruso, Philip M.; Eldrid, Sacheverel Quentin; Ladhani, Azad A.; DeMania, Alan Richard; Palmer, Gene David; Wilson, Ian David; Rathbun, Lisa Shirley; Akin, Robert Craig

    2002-01-01

    In a turbine having closed-circuit steam-cooling passages about the rim of the rotor during steady-state operation, compressor discharge air is supplied to the rotor bore for passage radially outwardly into the wheel space cavities between the wheels and spacers. Communicating slots and channels in the spacers and wheels at circumferentially spaced positions enable egress of the compressor discharge air into the hot gas flow path. At turbine startup, cooling air flows through the closed-circuit steam passages to cool the outer rim of the rotor while compressor discharge air pre-warms the wheels and spacers. At steady-state, cooling steam is supplied in the closed-circuit steam-cooling passages and compressor discharge air is supplied through the bore and into the wheel space cavities to cool the rotor.

  10. Stable inverted small molecular organic solar cells using a p-doped optical spacer.

    PubMed

    Lee, Sang-Hoon; Seo, Ji-Won; Lee, Jung-Yong

    2015-01-01

    We report inverted small molecular organic solar cells using a doped window layer as an optical spacer. The optical spacer was used to shift the optical field distribution inside the active layers, generating more charge carriers from sunlight. In this report, N,N,N',N'-tetrakis(4-methoxyphenyl)-benzidine (MeO-TPD) was doped with 2,2-(perfluoronaphthalene-2,6-diylidene)dimalononitrile (F6-TCNNQ), a p-type dopant material. P-doped MeO-TPD was adopted as an optical spacer because it has a large energy band gap, and its conductivity can be increased by several orders of magnitude through a doping process. As a result, a power conversion efficiency of 4.15% was achieved with the doped window layer of optimized thickness. Lastly, we present significantly improved stability of the inverted devices with the MeO-TPD layer. PMID:25407588

  11. Building a Better Halide Receptor: Optimum Choice of Spacer, Binding Unit, and Halosubstitution.

    PubMed

    Nepal, Binod; Scheiner, Steve

    2016-03-16

    Quantum calculations are used to measure the binding of halides to a number of bipodal dicationic receptors, constructed as a pair of binding units separated by a spacer group. A number of variations are studied. A H atom on each binding unit (imidazolium or triazolium) is replaced by Br or I. Benzene, thiophene, carbazole, and dimethylnaphthalene are considered as spacer groups. Each receptor is paired with halides F(-) , Cl(-) , Br(-) , and I(-) . Substitution with I on the binding unit yields a large enhancement of binding, as much as 13 orders of magnitude; a much smaller increase occurs for substitution with Br. Imidazolium is a more effective binding agent than is triazolium. Benzene and dimethylnaphthalene represent the best spacers, followed by thiophene and carbazole. F(-) binds much more strongly than do the other halides, which obey the order Cl(-) >Br(-) >I(-) . PMID:26676206

  12. Flunisolide hydrofluoroalkane with integrated spacer for treating asthma: an updated review.

    PubMed

    Berger, William E; Tashkin, Donald P

    2015-01-01

    Flunisolide hydrofluoroalkane (HFA) with integrated spacer is the most recent reformulated inhaled corticosteroid (ICS) for asthma available in the United States. It is the only product that combines a corticosteroid extrafine aerosol with a built-in spacer. The potential clinical benefit of the flunisolide HFA formulation and its integrated spacer for treating persistent asthma was assessed through a comprehensive review of the published literature and data from the past 10 years focusing on (1) flunisolide, the molecule, and the impact of the HFA reformulation; (2) updated information on the anti-inflammatory response to flunisolide HFA, particularly in the distal airways; and (3) the usefulness of an integrated spacer. Flunisolide HFA was found effective and safe in clinical studies and comparable with the chlorofluorocarbon (CFC) formulation, but at about one-third the dose of flunisolide CFC, likely reflecting both the device and the particle size of the reformulated product. Compared with the CFC formulation, the extrafine aerosol and smaller particle size of flunisolide HFA substantially increased pulmonary deposition and decreased oropharyngeal deposition. The integrated spacer further enhanced the pulmonary/oropharyngeal deposition ratio. Examination of lung biopsy specimens indicated a favorable anti-inflammatory response to flunisolide HFA in peripheral airways. Pediatric studies showed no significant effects on growth. The data indicate that flunisolide HFA is a safe and effective maintenance therapy for asthma patients. The integrated spacer may provide an added advantage for patients, especially those who may be more likely to experience adverse effects of ICSs, both local and systemic, including children susceptible to adverse effects on growth. PMID:25635610

  13. Smooth Pins Reinforcing Static Cement Spacers for Infected Total Knee Arthroplasty Are Not Safe.

    PubMed

    Llado, Roald J; Banerjee, Samik; Khanuja, Harpal S

    2016-05-01

    Prosthetic joint infection is one of the most dreaded complications following elective lower extremity primary total joint arthroplasty, resulting in substantial pain, disability, and health care costs. Both static and articulating antibiotic-impregnated spacers have been used in the management of 2-stage revision for infected total knee arthroplasty, which remains the gold standard for treatment of these infections. Articulating spacers may provide theoretical benefits with regard to improved range of motion after reimplantation secondary to less scar formations and soft tissue contractures. However, static spacers may be necessary to overcome instability associated with substantial bone defects, incompetent extensor mechanisms, and collateral ligament insufficiencies. In these scenarios, static spacers are often reinforced with intramedullary rods or Steinmann pins to provide additional knee stability, improve construct strength, maintain extension, and avoid flexion contractures. This case report describes an extremely rare case of migration of smooth pins through the posterior tibia into the calf following static spacer use in a 48-year-old man. Various mechanical and systemic complications have been reported in up to 50% of patients with the use of polymethyl methacrylate spacer devices, such as acute renal failure, allergic reactions from antibiotic use, stiffness, bone loss, fractures, and dislocations. However, to the best of the authors' knowledge, this complication of hardware migration has not been reported previously in the literature. The authors believe that orthopedic surgeons should consider the use of threaded pin dowels or intramedullary rods to avoid this potential untoward complication. [Orthopedics. 2016; 39(3):e553-e557.]. PMID:27045481

  14. Varieties of Repetitive Behavior in Autism: Comparisons to Mental Retardation.

    ERIC Educational Resources Information Center

    Bodfish, James W.; Symons, Frank J.; Parker, Dawn E.; Lewis, Mark H.

    2000-01-01

    A study compared specific repetitive behaviors in 32 adults with autism with 34 controls with mental retardation. The occurrence of each behavior category, except dyskinesias, was higher in individuals with autism and they showed a greater number of topographies of stereotypy and compulsions. Repetitive behavior severity also predicated autism…

  15. Repetitive and Stereotyped Behaviours in Pervasive Developmental Disorders

    ERIC Educational Resources Information Center

    Carcani-Rathwell, Iris; Rabe-Hasketh, Sophia; Santosh, Paramala J.

    2006-01-01

    Background: Repetitive and stereotyped behaviours are a heterogeneous group of behaviours present in many neuropsychiatric disorders. Despite their core significance in PDD, it is not clear whether there are distinct groups of these behaviours with different specificity to autism. Methods: A two-factor model of the repetitive behaviours, namely…

  16. 10 CFR 52.8 - Combining licenses; elimination of repetition.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Combining licenses; elimination of repetition. 52.8... NUCLEAR POWER PLANTS General Provisions § 52.8 Combining licenses; elimination of repetition. (a) An applicant for a license under this part may combine in its application several applications for...

  17. Longitudinal Patterns of Repetitive Behavior in Toddlers with Autism

    PubMed Central

    Wolff, Jason J.; Botteron, Kelly N.; Dager, Stephen R.; Elison, Jed T.; Estes, Annette M.; Gu, Hongbin; Hazlett, Heather C.; Pandey, Juhi; Paterson, Sarah J.; Schultz, Robert T.; Zwaigenbaum, Lonnie; Piven, Joseph

    2014-01-01

    Background Recent evidence suggests that restricted and repetitive behaviors may differentiate children who develop autism spectrum disorder (ASD) by late infancy. How these core symptoms manifest early in life, particularly among infants at high-risk for the disorder, is not well characterized. Methods Prospective, longitudinal parent-report data (Repetitive Behavior Scales-Revised) were collected for 190 high-risk toddlers and 60 low-risk controls from 12 to 24 months age. Forty-one high-risk children were classified with ASD at age 2. Profiles of repetitive behavior were compared between groups using generalized estimating equations. Results Longitudinal profiles for children diagnosed with ASD differed significantly from high- and low-risk children without the disorder on all measures of repetitive behavior. High-risk toddlers without ASD were intermediate to low-risk and ASD positive counterparts. Toddlers with ASD showed significantly higher rates of repetitive behavior across subtypes at the 12 month time point. Repetitive behaviors were significantly correlated with adaptive behavior and socialization scores among children with ASD at 24 months-age but were largely unrelated to measures of general cognitive ability. Conclusions These findings suggest that as early as 12 months age, a broad range of repetitive behaviors are highly elevated in children who go on to develop ASD. While some degree of repetitive behavior is elemental to typical early development, the extent of these behaviors among children who develop ASD appears highly atypical. PMID:24552513

  18. Evidence-Based Behavioral Interventions for Repetitive Behaviors in Autism

    ERIC Educational Resources Information Center

    Boyd, Brian A.; McDonough, Stephen G.; Bodfish, James W.

    2012-01-01

    Restricted and repetitive behaviors (RRBs) are a core symptom of autism spectrum disorders (ASD). There has been an increased research emphasis on repetitive behaviors; however, this research primarily has focused on phenomenology and mechanisms. Thus, the knowledge base on interventions is lagging behind other areas of research. The literature…

  19. Pre-Lexical Disorders in Repetition Conduction Aphasia

    ERIC Educational Resources Information Center

    Sidiropoulos, Kyriakos; de Bleser, Ria; Ackermann, Hermann; Preilowski, Bruno

    2008-01-01

    At the level of clinical speech/language evaluation, the repetition type of conduction aphasia is characterized by repetition difficulties concomitant with reduced short-term memory capacities, in the presence of fluent spontaneous speech as well as unimpaired naming and reading abilities. It is still unsettled which dysfunctions of the…

  20. A Negative Effect of Repetition in Episodic Memory

    ERIC Educational Resources Information Center

    Peterson, Daniel J.; Mulligan, Neil W.

    2012-01-01

    One of the foundational principles of human memory is that repetition (i.e., being presented with a stimulus multiple times) improves recall. In the current study a group of participants who studied a list of cue-target pairs twice recalled fewer targets than a group who studied the pairs only once, a negative repetition effect. Such a…

  1. 10 CFR 63.23 - Elimination of repetition.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 2 2013-01-01 2013-01-01 false Elimination of repetition. 63.23 Section 63.23 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses License Application § 63.23 Elimination of repetition. In...

  2. 10 CFR 63.23 - Elimination of repetition.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Elimination of repetition. 63.23 Section 63.23 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses License Application § 63.23 Elimination of repetition. In...

  3. 10 CFR 63.23 - Elimination of repetition.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 2 2014-01-01 2014-01-01 false Elimination of repetition. 63.23 Section 63.23 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses License Application § 63.23 Elimination of repetition. In...

  4. 10 CFR 63.23 - Elimination of repetition.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 2 2012-01-01 2012-01-01 false Elimination of repetition. 63.23 Section 63.23 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses License Application § 63.23 Elimination of repetition. In...

  5. 10 CFR 63.23 - Elimination of repetition.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 2 2011-01-01 2011-01-01 false Elimination of repetition. 63.23 Section 63.23 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN A GEOLOGIC REPOSITORY AT YUCCA MOUNTAIN, NEVADA Licenses License Application § 63.23 Elimination of repetition. In...

  6. Selecting appropriate designs and comparison conditions in repetition paradigms.

    PubMed

    Feuerriegel, Daniel

    2016-07-01

    The studies described by Vogels (this issue) demonstrate the complexity of repetition effects in the visual processing stream. In addition to signal suppression, findings of inherited effects from earlier processing, and discrepancies between the stimulus selectivity of cells before and after repetition, have informed the inferences that can be drawn from measures over larger scales such as functional magnetic resonance imaging (fMRI) or electroencephalography (EEG). This work also demonstrates that integration of evidence across recording methods is vital for understanding repetition effects in the brain. It is however difficult to integrate evidence across different recording methods and repetition paradigms. At the crux of this difficulty is the selection of comparison or unrepeated stimulus conditions within paradigms, which influence the observed strength, selectivity and even direction of repetition effects. This viewpoint highlights prevalent methodological issues with regard to repeated-unrepeated stimulus comparisons: inherited adaptation, stimulus specific expectations, concurrent memory retrieval, stimulus novelty and familiarity, attention, and changes in neuronal selectivity with repetition. The extent to which current conflicting and uncertain findings are due to selection of unrepeated stimulus conditions is unknown, but needs to be addressed to develop models of repetition spanning recording methods and repetition paradigms. PMID:26654854

  7. Conversational Characteristics of Children with Fragile X Syndrome: Repetitive Speech.

    ERIC Educational Resources Information Center

    Belser, Richard C.; Sudhalter, Vicki

    2001-01-01

    Comparison of the production of repetitive speech during conversations in 30 people with either fragile X syndrome, autistic disorder, or mental retardation not caused by fragile X found repetitive speech more prevalent among those with fragile X. Results support the hypothesis that such speech dysfluency reflects the effects of physiological…

  8. 10 CFR 60.23 - Elimination of repetition.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 2 2013-01-01 2013-01-01 false Elimination of repetition. 60.23 Section 60.23 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES Licenses License Applications § 60.23 Elimination of repetition. In its application,...

  9. 10 CFR 60.23 - Elimination of repetition.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 2 2014-01-01 2014-01-01 false Elimination of repetition. 60.23 Section 60.23 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES Licenses License Applications § 60.23 Elimination of repetition. In its application,...

  10. 10 CFR 60.23 - Elimination of repetition.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 2 2012-01-01 2012-01-01 false Elimination of repetition. 60.23 Section 60.23 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES Licenses License Applications § 60.23 Elimination of repetition. In its application,...

  11. 10 CFR 60.23 - Elimination of repetition.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 2 2011-01-01 2011-01-01 false Elimination of repetition. 60.23 Section 60.23 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES Licenses License Applications § 60.23 Elimination of repetition. In its application,...

  12. 10 CFR 60.23 - Elimination of repetition.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 2 2010-01-01 2010-01-01 false Elimination of repetition. 60.23 Section 60.23 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES Licenses License Applications § 60.23 Elimination of repetition. In its application,...

  13. 10 CFR 52.8 - Combining licenses; elimination of repetition.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 2 2011-01-01 2011-01-01 false Combining licenses; elimination of repetition. 52.8 Section 52.8 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS General Provisions § 52.8 Combining licenses; elimination of repetition. (a)...

  14. 10 CFR 52.8 - Combining licenses; elimination of repetition.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 2 2014-01-01 2014-01-01 false Combining licenses; elimination of repetition. 52.8 Section 52.8 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS General Provisions § 52.8 Combining licenses; elimination of repetition. (a)...

  15. 10 CFR 52.8 - Combining licenses; elimination of repetition.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 2 2012-01-01 2012-01-01 false Combining licenses; elimination of repetition. 52.8 Section 52.8 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS General Provisions § 52.8 Combining licenses; elimination of repetition. (a)...

  16. 10 CFR 52.8 - Combining licenses; elimination of repetition.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 2 2013-01-01 2013-01-01 false Combining licenses; elimination of repetition. 52.8 Section 52.8 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSES, CERTIFICATIONS, AND APPROVALS FOR NUCLEAR POWER PLANTS General Provisions § 52.8 Combining licenses; elimination of repetition. (a)...

  17. Early Grade Repetition and Inattention Associated with Neurofibromatosis Type 1

    ERIC Educational Resources Information Center

    Coude, Francois X.; Mignot, Claire; Lyonnet, Stanislas; Munnich, Arnold

    2007-01-01

    Objective: The authors analyze the occurrence of grade repetition and inattention in children diagnosed with neurofibromatosis type 1 (NF1). Method: The participant group consisted of 310 patients with NF1 and a control group of 242 individuals. The number of grade repetitions for each participant during his or her time in elementary, middle, and…

  18. Phylogeny of Trypanosoma brucei and Trypanosoma evansi in naturally infected cattle in Nigeria by analysis of repetitive and ribosomal DNA sequences.

    PubMed

    Takeet, Michael I; Peters, Sunday O; Fagbemi, Benjamin O; De Donato, Marcos; Takeet, Vivian O; Wheto, Mathew; Imumorin, Ikhide G

    2016-08-01

    In continuing efforts to better understand the genetics of bovine trypanosomosis, we assessed genetic diversity of Trypanosoma brucei and Trypanosoma evansi in naturally infected Nigerian cattle using repetitive DNA and internal transcribed spacer 1 of rDNA sequences and compared these sequences to species from other countries. The length of repetitive DNA sequences in both species ranged from 161 to 244 bp and 239 to 240 bp for T. brucei and T. evansi, respectively, while the ITS1 rDNA sequences length range from 299 to 364 bp. The mean GC content of ITS1 rDNA sequences was 33.57 %, and that of repetitive sequences were 39.9 and 31.1 % for T. brucei and T. evansi, respectively. Result from sequence alignment revealed both T. brucei and T. evansi repetitive DNA sequences to be more polymorphic than ITS1 rDNA sequences, with moderate points of deletion and insertions. T. brucei separated into two clades when subjected to phylogenetic analysis. T. evansi repetitive DNA sequences clustered tightly within the T. brucei clade while the ITS1 rDNA sequences of T. brucei were clearly separated from T. theileri and T. vivax individually used as outgroups. This study suggest that ITS1 rDNA sequences may not be suitable for phylogenetic differentiation of the Trypanozoon group and also suggest that T. evansi may be a phenotypic variant of T. brucei which may have potential implications in designing prevention and therapeutic strategies. PMID:27174432

  19. Self-structuring of lamellar bridged silsesquioxanes with long side spacers.

    PubMed

    Fernandes, Mariana; Nobre, Sónia S; Xu, Qinghong; Carcel, Carole; Cachia, Jean Nicolas; Cattoën, Xavier; Sousa, José M; Ferreira, Rute A S; Carlos, Luís D; Santilli, Celso V; Wong Chi Man, Michel; Bermudez, Verónica de Zea

    2011-09-22

    Diurea cross-linked bridged silsesquioxanes (BSs) C(10)C(n)C(10) derived from organosilane precursors, including decylene chains as side spacers and alkylene chains with variable length as central spacers (EtO)(3)Si-(CH(2))(10)-Y-(CH(2))(n)-Y-(CH(2))(10)-Si(OEt)(3) (n = 7, 9-12; Y = urea group and Et = ethyl), have been synthesized through the combination of self-directed assembly and an acid-catalyzed sol-gel route involving the addition of dimethylsulfoxide (DMSO) and a large excess of water. This new family of hybrids has enabled us to conclude that the length of the side spacers plays a unique role in the structuring of alkylene-based BSs, although their morphology remains unaffected. All the samples adopt a lamellar structure. While the alkylene chains are totally disordered in the case of the C(10)C(7)C(10) sample, a variable proportion of all-trans and gauche conformers exists in the materials with longer central spacers. The highest degree of structuring occurs for n = 9. The inclusion of decylene instead of propylene chains as side spacers leads to the formation of a stronger hydrogen-bonded urea-urea array as evidenced by two dimensional correlation Fourier transform infrared spectroscopic analysis. The emission spectra and emission quantum yields of the C(10)C(n)C(10) materials are similar to those reported for diurea cross-linked alkylene-based BSs incorporating propylene chains as side spacers and prepared under different experimental conditions. The emission of the C(10)C(n)C(10) hybrids is ascribed to the overlap of two distinct components that occur within the urea cross-linkages and within the siliceous nanodomains. Time-resolved photoluminescence spectroscopy has provided evidence that the average distance between the siliceous domains and the urea cross-links is similar in the C(10)C(n)C(10) BSs and in oxyethylene-based hybrid analogues incorporating propylene chains as side spacers (diureasils), an indication that the longer side chains in the

  20. Production Principles and Technological Development of Novel Woven Spacer Preforms and Integrated Stiffener Structures

    NASA Astrophysics Data System (ADS)

    Torun, Ahmet R.; Mountasir, Adil; Hoffmann, Gerald; Cherif, Chokri

    2013-06-01

    3D textile preforms offer a high potential to increase mechanical properties of composites and/or decrease manufacturing costs. Within the scope of this study, production principles were developed for complex spacer preforms and integrated stiffeners. These principles were applied through technological further development of the well-known face-to-face and terry weaving techniques. Various woven preforms were produced with Glass fibre/Polypropylene (GF/PP) Commingled yarns, however, the technology is suitable for any type of reinforcement yarns. U-shaped woven spacer preform was consolidated into a sandwich composite component for lightweight applications.

  1. Heterogeneous Diversity of Spacers within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)

    NASA Astrophysics Data System (ADS)

    He, Jiankui; Deem, Michael W.

    2010-09-01

    Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of antiviral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face.

  2. Molecular analysis of 16S-23S spacer regions of Acetobacter species.

    PubMed

    Kretová, M; Grones, J

    2005-01-01

    16S-23S rDNA internal transcribed spacer regions (ITS) similarities were determined in 8 Acetobacter and 1 Gluconacetobacter strains. ITS-PCR amplification of the 16S-23S spacers showed 2 products of similar size in 7 strains; only 1 product of similar size was found in the 2 remaining strains. Analysis of the PCR products using restriction endonucleases HaeIII, HpaII and AluI revealed 3 different restriction groups of A. pasteurianus for AluI and HaeIII, and 4 restriction groups for HpaII. ITS nucleotide sequences of all studied strains exhibited a 52-98% similarity. PMID:16408846

  3. Multilayer barrier films comprising nitrogen spacers between free-standing barrier layers

    NASA Astrophysics Data System (ADS)

    Granstrom, Jimmy Erik

    The air sensitivity of organic electronic devices has delayed the broad commercialization of the printed "plastics" electronics technology. The vacuum deposition methods used to fabricate multi-layers which fulfill the encapsulation requirements for plastic electronic devices are complex and expensive. Fully printed "plastic" electronics requires the development of encapsulation architectures which comprise solution deposited barriers and/or low-cost free-standing barrier films based on polymers, e.g. poly ethylene terephthalate (PET). One way to reach this goal is the insertion of contaminant-free (e.g. pure N2) gas-phase spacers between free-standing barrier films in a multilayer structure. The spacers themselves do not exhibit any barrier properties (diffusion of gas permeants in a gas phase is orders of magnitude faster than in a solid), but they delay the attainment of steady state. The spacer also reduces the chemical potential gradient across downstream barrier layers during the transient regime, reducing permeation rate to the device. Furthermore, if sorption is not fully equilibrated and introduces a kinetic barrier to transport, the additional sorption and desorption steps needed for permeant to reach the device may also slow the steady-state permeation rate. Encapsulation architectures utilizing both single-matrix (without nitrogen spacers) and multiple-matrix structures (with nitrogen spacers) were fabricated in this study, including Russian Doll structures utilizing pairs of free-standing barrier films and epoxy seals separated by nitrogen spacers. This structure enables the use of low-cost epoxy to attach two or more free-standing barrier films to a substrate with improved barrier performance. The performance of various Russian Doll encapsulations was evaluated with the calcium thin film optical transmission test, showing improved performance of the Russian doll configuration relative to a non-nested barrier/spacer architecture, and demonstrating that

  4. Nonword Repetition and Speech Motor Control in Children

    PubMed Central

    Reuterskiöld, Christina; Grigos, Maria I.

    2015-01-01

    This study examined how familiarity of word structures influenced articulatory control in children and adolescents during repetition of real words (RWs) and nonwords (NWs). A passive reflective marker system was used to track articulator movement. Measures of accuracy were obtained during repetition of RWs and NWs, and kinematic analysis of movement duration and variability was conducted. Participants showed greater consonant and vowel accuracy during RW than NW repetition. Jaw movement duration was longer in NWs compared to RWs across age groups, and younger children produced utterances with longer jaw movement duration compared to older children. Jaw movement variability was consistently greater during repetition of NWs than RWs in both groups of participants. The results indicate that increases in phonological short-term memory demands affect articulator movement. This effect is most pronounced in younger children. A range of skills may develop during childhood, which supports NW repetition skills. PMID:26557688

  5. Repetition priming of nonwords in young and older adults.

    PubMed

    Light, L L; La Voie, D; Kennison, R

    1995-03-01

    In 3 experiments, a pronunciation task was used to examine repetition priming of novel nonwords in young and older adults. The contributions of item and associative priming to the total repetition priming effect were assessed. In Experiment 1, age consistency was found in both components of repetition priming after 9 repetitions of nonwords. Experiment 2 established that young and older adults were similar in item and associative priming after as few as 2 repetitions of nonwords. Finally, Experiment 3 demonstrated that associative priming persists for at least 3 min and that it is dissociable from cued recall. The overall pattern of results strongly argues that elaborative processing is not necessary to obtain associative priming in indirect memory tasks and that young and older adults show similar magnitudes of associative priming. PMID:7738504

  6. Repetition suppression and its contextual determinants in predictive coding.

    PubMed

    Auksztulewicz, Ryszard; Friston, Karl

    2016-07-01

    This paper presents a review of theoretical and empirical work on repetition suppression in the context of predictive coding. Predictive coding is a neurobiologically plausible scheme explaining how biological systems might perform perceptual inference and learning. From this perspective, repetition suppression is a manifestation of minimising prediction error through adaptive changes in predictions about the content and precision of sensory inputs. Simulations of artificial neural hierarchies provide a principled way of understanding how repetition suppression - at different time scales - can be explained in terms of inference and learning implemented under predictive coding. This formulation of repetition suppression is supported by results of numerous empirical studies of repetition suppression and its contextual determinants. PMID:26861557

  7. Repetition and Emotive Communication in Music Versus Speech

    PubMed Central

    Margulis, Elizabeth Hellmuth

    2013-01-01

    Music and speech are often placed alongside one another as comparative cases. Their relative overlaps and disassociations have been well explored (e.g., Patel, 2008). But one key attribute distinguishing these two domains has often been overlooked: the greater preponderance of repetition in music in comparison to speech. Recent fMRI studies have shown that familiarity – achieved through repetition – is a critical component of emotional engagement with music (Pereira et al., 2011). If repetition is fundamental to emotional responses to music, and repetition is a key distinguisher between the domains of music and speech, then close examination of the phenomenon of repetition might help clarify the ways that music elicits emotion differently than speech. PMID:23576998

  8. Repetition is easy: Why repeated referents have reduced prominence

    PubMed Central

    Lam, Tuan Q.; Watson, Duane G.

    2011-01-01

    The repetition and predictability of a word in a conversation are two factors that are believed to affect whether or not it is emphasized: predictable, repeated words are less acoustically prominent than unpredictable, new words. However, because predictability and repetition are correlated, it is unclear whether speakers lengthen unpredictable words to facilitate comprehension or whether this lengthening is the result of difficulties in accessing a new (non-repeated) lexical item. In this paper, we investigate the relationship between acoustic prominence, repetition, and predictability in a description task. In Experiment 1, we find that repeated referents are produced with reduced prominence, even when these referents are unexpected. In Experiment 2, we find that predictability and repetition both have independent effects on duration and intensity. However, word duration was primarily determined by repetition, and intensity was primarily determined by predictability. The data are most consistent with an account in which multiple cognitive factors influence the acoustic prominence of a word. PMID:21156876

  9. Transgenerational effects of environmental enrichment on repetitive motor behavior development.

    PubMed

    Bechard, Allison R; Lewis, Mark H

    2016-07-01

    The favorable consequences of environmental enrichment (EE) on brain and behavior development are well documented. Much less is known, however, about transgenerational benefits of EE on non-enriched offspring. We explored whether transgenerational effects of EE might extend to the development of repetitive motor behaviors in deer mice. Repetitive motor behaviors are invariant patterns of movement that, across species, can be reduced by EE. We found that EE not only attenuated the development of repetitive behavior in dams, but also in their non-enriched offspring. Moreover, maternal behavior did not seem to mediate the transgenerational effect we found, although repetitive behavior was affected by reproductive experience. These data support a beneficial transgenerational effect of EE on repetitive behavior development and suggest a novel benefit of reproductive experience. PMID:27059336

  10. Hole-transfer induced energy transfer in perylene diimide dyads with a donor-spacer-acceptor motif.

    PubMed

    Kölle, Patrick; Pugliesi, Igor; Langhals, Heinz; Wilcken, Roland; Esterbauer, Andreas J; de Vivie-Riedle, Regina; Riedle, Eberhard

    2015-10-14

    We investigate the photoinduced dynamics of perylene diimide dyads based on a donor-spacer-acceptor motif with polyyne spacers of varying length by pump-probe spectroscopy, time resolved fluorescence, chemical variation and quantum chemistry. While the dyads with pyridine based polyyne spacers undergo energy transfer with near-unity quantum efficiency, in the dyads with phenyl based polyyne spacers the energy transfer efficiency drops below 50%. This suggests the presence of a competing electron transfer process from the spacer to the energy donor as the excitation sink. Transient absorption spectra, however, reveal that the spacer actually mediates the energy transfer dynamics. The ground state bleach features of the polyyne spacers appear due to the electron transfer decay with the same time constant present in the rise of the ground state bleach and stimulated emission of the perylene energy acceptor. Although the electron transfer process initially quenches the fluorescence of the donor it does not inhibit energy transfer to the perylene energy acceptor. The transient signatures reveal that electron and energy transfer processes are sequential and indicate that the donor-spacer electron transfer state itself is responsible for the energy transfer. Through the introduction of a Dexter blocker unit into the spacer we can clearly exclude any through bond Dexter-type energy transfer. Ab initio calculations on the donor-spacer and the donor-spacer-acceptor systems reveal the existence of a bright charge transfer state that is close in energy to the locally excited state of the acceptor. Multipole-multipole interactions between the bright charge transfer state and the acceptor state enable the energy transfer. We term this mechanism coupled hole-transfer FRET. These dyads represent a first example that shows how electron transfer can be connected to energy transfer for use in novel photovoltaic and optoelectronic devices. PMID:26347443

  11. Large repetitively Q-switched oscillators

    NASA Astrophysics Data System (ADS)

    Epstein, H. M.; Dulaney, J. L.; O'Loughlin, J. F.; Altman, W. P.

    A versatile waveform laser which can operate in bursts from 5 to 160 ms long and deliver up to 30 kJ power burst has been constructed. This Nd:glass laser system consists of four oscillators in parallel. Each oscillator can be varied in length from about 3 to 10 m, and contains two pump heads 670 mm long by 64 mm in diameter phosphate glass laser rods. When trains of Q-switched pulses are required, 70 mm diameter Pockels cells and dielectric polarizers are added to the oscillator cavity. The basic burst duration of 5 ms can be stretched to 10, 20, 40, 80,and 160 ms by sequencing the firing of flashlamps, with the longest pulse length attained by sequentially firing 1/4 heads. Trains of Q-switched pulses up to 10 kHz in repetition rate and 50 to 900 ns wide can be obtained by varying the cavity configuration and Pockels cell firing rate. Spatial distributions are flat-topped within about 10 percent. Overall efficiency for the oscillator with a CW waveform can exceed 4.8 percent.

  12. The repetition of large-earthquake ruptures.

    PubMed Central

    Sieh, K

    1996-01-01

    This survey of well-documented repeated fault rupture confirms that some faults have exhibited a "characteristic" behavior during repeated large earthquakes--that is, the magnitude, distribution, and style of slip on the fault has repeated during two or more consecutive events. In two cases faults exhibit slip functions that vary little from earthquake to earthquake. In one other well-documented case, however, fault lengths contrast markedly for two consecutive ruptures, but the amount of offset at individual sites was similar. Adjacent individual patches, 10 km or more in length, failed singly during one event and in tandem during the other. More complex cases of repetition may also represent the failure of several distinct patches. The faults of the 1992 Landers earthquake provide an instructive example of such complexity. Together, these examples suggest that large earthquakes commonly result from the failure of one or more patches, each characterized by a slip function that is roughly invariant through consecutive earthquake cycles. The persistence of these slip-patches through two or more large earthquakes indicates that some quasi-invariant physical property controls the pattern and magnitude of slip. These data seem incompatible with theoretical models that produce slip distributions that are highly variable in consecutive large events. Images Fig. 3 Fig. 7 Fig. 9 PMID:11607662

  13. Repetitive Interrogation of 2-Level Quantum Systems

    NASA Technical Reports Server (NTRS)

    Prestage, John D.; Chung, Sang K.

    2010-01-01

    Trapped ion clocks derive information from a reference atomic transition by repetitive interrogations of the same quantum system, either a single ion or ionized gas of many millions of ions. Atomic beam frequency standards, by contrast, measure reference atomic transitions in a continuously replenished "flow through" configuration where initial ensemble atomic coherence is zero. We will describe some issues and problems that can arise when atomic state selection and preparation of the quantum atomic system is not completed, that is, optical pumping has not fully relaxed the coherence and also not fully transferred atoms to the initial state. We present a simple two-level density matrix analysis showing how frequency shifts during the state-selection process can cause frequency shifts of the measured clock transition. Such considerations are very important when a low intensity lamp light source is used for state selection, where there is relatively weak relaxation and re-pumping of ions to an initial state and much weaker 'environmental' relaxation of the atomic coherence set-up in the atomic sample.

  14. Repetitive elements regulate circular RNA biogenesis

    PubMed Central

    Wilusz, Jeremy E

    2015-01-01

    It was long assumed that eukaryotic precursor mRNAs (pre-mRNAs) are almost always spliced to generate a linear mRNA that is subsequently translated to produce a protein. However, it is now clear that thousands of protein-coding genes can be non-canonically spliced to produce circular noncoding RNAs, some of which are expressed at much higher levels than their associated linear mRNAs. How then does the splicing machinery decide whether to generate a linear mRNA or a circular RNA? Recent work has revealed that intronic repetitive elements, including sequences derived from transposons, are critical regulators of this decision. In most cases, circular RNA biogenesis appears to be initiated when complementary sequences from 2 different introns base pair to one another. This brings the splice sites from the intervening exon(s) into close proximity and facilitates the backsplicing event that generates the circular RNA. As many pre-mRNAs contain multiple intronic repeats, distinct circular transcripts can be produced depending on which repeats base pair to one another. Intronic repeats are thus critical regulatory sequences that control the functional output of their host genes, and potentially cause the functions of protein-coding genes to be highly divergent across species. PMID:26442181

  15. SI Engine with repetitive NS spark plug

    NASA Astrophysics Data System (ADS)

    Pancheshniy, Sergey; Nikipelov, Andrey; Anokhin, Eugeny; Starikovskiy, Andrey; Laplase Team; Mipt Team; Pu Team

    2013-09-01

    Now de-facto the only technology for fuel-air mixtures ignition in IC engines exists. It is a spark discharge of millisecond duration in a short discharge gap. The reason for such a small variety of methods of ignition initiation is very specific conditions of the engine operation. First, it is very high-pressure of fuel-air mixture - from 5-7 atmospheres in old-type engines and up to 40-50 atmospheres on the operating mode of HCCI. Second, it is a very wide range of variation of the oxidizer/fuel ratio in the mixture - from almost stoichiometric (0.8-0.9) at full load to very lean (φ = 0.3-0.5) mixtures at idle and/or economical cruising mode. Third, the high velocity of the gas in the combustion chamber (up to 30-50 m/s) resulting in a rapid compression of swirling inlet flow. The paper presents the results of tests of distributed spark ignition system powered by repetitive pulse nanosecond discharge. Dynamic pressure measurements show the increased pressure and frequency stability for nanosecond excitation in comparison with the standard spark plug. Excitation by single nanosecond high-voltage pulse and short train of pulses was examined. In all regimes the nanosecond pulsed excitation demonstrate a better performance.

  16. A chenopod extensin lacks repetitive tetrahydroxyproline blocks

    SciTech Connect

    Li, Xiongbiao; Kieliszewski, M.; Lamport, D.T.A. )

    1990-02-01

    An extensin isolated from sugar beet (Beta vulgaris) cell suspension cultures fulfills all criteria for membership of the extensin family save one, notably, lack of the diagnostic pentamer Ser-Hyp-Hyp-Hyp-Hyp. However, sequence analysis of the major tryptic peptides shows that sugar beet extensin shares a motif in common with tomato extensin P1 but differs by the position of an insertion sequence (X) or (Y) which, in sugar beet, splits the tetrahydroxyproline block: Ser-Hyp-Hyp-(X)-Hyp-Hyp-Thr-Hyp-Val-Tyr-Lys, where (X) is (Val-His-Glu/Lys-Tyr-Pro), while in tomato the insertion sequence (Y) = (Val-Lys-Pro-Tyr-His-Pro) and, when it occurs, immediately follows the tetrahydroxyproline block: Ser-Hyp-Hyp-Hyp-Hyp-(Y)-Thr-Hyp-Val-Tyr-Lys. Based on these data were reinterpret three highly repetitive cDNA sequences, including nodulin N75 from soybean and wound-induced P33 of carrot, as extensins with split tetra(hydroxy)proline blocks.

  17. Understanding communicative actions: a repetitive TMS study.

    PubMed

    Stolk, Arjen; Noordzij, Matthijs L; Volman, Inge; Verhagen, Lennart; Overeem, Sebastiaan; van Elswijk, Gijs; Bloem, Bas; Hagoort, Peter; Toni, Ivan

    2014-02-01

    Despite the ambiguity inherent in human communication, people are remarkably efficient in establishing mutual understanding. Studying how people communicate in novel settings provides a window into the mechanisms supporting the human competence to rapidly generate and understand novel shared symbols, a fundamental property of human communication. Previous work indicates that the right posterior superior temporal sulcus (pSTS) is involved when people understand the intended meaning of novel communicative actions. Here, we set out to test whether normal functioning of this cerebral structure is required for understanding novel communicative actions using inhibitory low-frequency repetitive transcranial magnetic stimulation (rTMS). A factorial experimental design contrasted two tightly matched stimulation sites (right pSTS vs left MT+, i.e., a contiguous homotopic task-relevant region) and tasks (a communicative task vs a visual tracking task that used the same sequences of stimuli). Overall task performance was not affected by rTMS, whereas changes in task performance over time were disrupted according to TMS site and task combinations. Namely, rTMS over pSTS led to a diminished ability to improve action understanding on the basis of recent communicative history, while rTMS over MT+ perturbed improvement in visual tracking over trials. These findings qualify the contributions of the right pSTS to human communicative abilities, showing that this region might be necessary for incorporating previous knowledge, accumulated during interactions with a communicative partner, to constrain the inferential process that leads to action understanding. PMID:24268321

  18. Development of a repetitive compact torus injector

    NASA Astrophysics Data System (ADS)

    Onchi, Takumi; McColl, David; Dreval, Mykola; Rohollahi, Akbar; Xiao, Chijin; Hirose, Akira; Zushi, Hideki

    2013-10-01

    A system for Repetitive Compact Torus Injection (RCTI) has been developed at the University of Saskatchewan. CTI is a promising fuelling technology to directly fuel the core region of tokamak reactors. In addition to fuelling, CTI has also the potential for (a) optimization of density profile and thus bootstrap current and (b) momentum injection. For steady-state reactor operation, RCTI is necessary. The approach to RCTI is to charge a storage capacitor bank with a large capacitance and quickly charge the CT capacitor bank through a stack of integrated-gate bipolar transistors (IGBTs). When the CT bank is fully charged, the IGBT stack will be turned off to isolate banks, and CT formation/acceleration sequence will start. After formation of each CT, the fast bank will be replenished and a new CT will be formed and accelerated. Circuits for the formation and the acceleration in University of Saskatchewan CT Injector (USCTI) have been modified. Three CT shots at 10 Hz or eight shots at 1.7 Hz have been achieved. This work has been sponsored by the CRC and NSERC, Canada.

  19. Can the Edinburgh Risk of Repetition Scale Predict Repetition of Deliberate Self-Poisoning in an Australian Clinical Setting?

    ERIC Educational Resources Information Center

    Carter, Gregory Leigh; Clover, Kerrie Ann; Bryant, Jennifer Lynn; Whyte, Ian MacGregor

    2002-01-01

    Tests the ability of the Edinburgh Risk of Repetition Scale (ERRS) to identify patients at high risk for repeat deliberate self-poisoning (DSP). A statistically significant relationship between ERRS scores and repetition was observed; however, sensitivity and specificity were low. The ERRS had limited value in identifying patients at high risk of…

  20. An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli.

    PubMed

    Zhi, Shuai; Li, Qiaozhi; Yasui, Yutaka; Banting, Graham; Edge, Thomas A; Topp, Edward; McAllister, Tim A; Neumann, Norman F

    2016-10-01

    Several studies have demonstrated that E. coli appears to display some level of host adaptation and specificity. Recent studies in our laboratory support these findings as determined by logic regression modeling of single nucleotide polymorphisms (SNP) in intergenic regions (ITGRs). We sought to determine the degree of host-specific information encoded in various ITGRs across a library of animal E. coli isolates using both whole genome analysis and a targeted ITGR sequencing approach. Our findings demonstrated that ITGRs across the genome encode various degrees of host-specific information. Incorporating multiple ITGRs (i.e., concatenation) into logic regression model building resulted in greater host-specificity and sensitivity outcomes in biomarkers, but the overall level of polymorphism in an ITGR did not correlate with the degree of host-specificity encoded in the ITGR. This suggests that distinct SNPs in ITGRs may be more important in defining host-specificity than overall sequence variation, explaining why traditional unsupervised learning phylogenetic approaches may be less informative in terms of revealing host-specific information encoded in DNA sequence. In silico analysis of 80 candidate ITGRs from publically available E. coli genomes was performed as a tool for discovering highly host-specific ITGRs. In one ITGR (ydeR-yedS) we identified a SNP biomarker that was 98% specific for cattle and for which 92% of all E. coli isolates originating from cattle carried this unique biomarker. In the case of humans, a host-specific biomarker (98% specificity) was identified in the concatenated ITGR sequences of rcsD-ompC, ydeR-yedS, and rclR-ykgE, and for which 78% of E. coli originating from humans carried this biomarker. Interestingly, human-specific biomarkers were dominant in ITGRs regulating antibiotic resistance, whereas in cattle host-specific biomarkers were found in ITGRs involved in stress regulation. These data suggest that evolution towards host

  1. Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone.

    PubMed

    Melia, Tisha; Hao, Pengying; Yilmaz, Feyza; Waxman, David J

    2016-01-01

    Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as key chromatin regulators, yet few studies have characterized lincRNAs in a single tissue under diverse conditions. Here, we analyzed 45 mouse liver RNA sequencing (RNA-Seq) data sets collected under diverse conditions to systematically characterize 4,961 liver lincRNAs, 59% of them novel, with regard to gene structures, species conservation, chromatin accessibility, transcription factor binding, and epigenetic states. To investigate the potential for functionality, we focused on the responses of the liver lincRNAs to growth hormone stimulation, which imparts clinically relevant sex differences to hepatic metabolism and liver disease susceptibility. Sex-biased expression characterized 247 liver lincRNAs, with many being nuclear RNA enriched and regulated by growth hormone. The sex-biased lincRNA genes are enriched for nearby and correspondingly sex-biased accessible chromatin regions, as well as sex-biased binding sites for growth hormone-regulated transcriptional activators (STAT5, hepatocyte nuclear factor 6 [HNF6], FOXA1, and FOXA2) and transcriptional repressors (CUX2 and BCL6). Repression of female-specific lincRNAs in male liver, but not that of male-specific lincRNAs in female liver, was associated with enrichment of H3K27me3-associated inactive states and poised (bivalent) enhancer states. Strikingly, we found that liver-specific lincRNA gene promoters are more highly species conserved and have a significantly higher frequency of proximal binding by liver transcription factors than liver-specific protein-coding gene promoters. Orthologs for many liver lincRNAs were identified in one or more supraprimates, including two rat lincRNAs showing the same growth hormone-regulated, sex-biased expression as their mouse counterparts. This integrative analysis of liver lincRNA chromatin states, transcription factor occupancy, and growth hormone regulation provides novel insights into the

  2. Genetic diversity, inter-gene pool introgression and nutritional quality of common beans (Phaseolus vulgaris L.) from Central Africa.

    PubMed

    Blair, Matthew W; González, Laura F; Kimani, Paul M; Butare, Louis

    2010-07-01

    The Great Lakes region of Central Africa is a major producer of common beans in Africa. The region is known for high population density and small average farm size. The common bean represents the most important legume crop of the region, grown on over a third of the cultivated land area, and the per capita consumption is among the highest in the world for the food crop. The objective of this study was to evaluate the genetic diversity in a collection of 365 genotypes from the Great Lakes region of Central Africa, including a large group of landraces from Rwanda as well as varieties from primary centers of diversity and from neighboring countries of Central Africa, such as the Democratic Republic of Congo and Uganda, using 30 fluorescently labeled microsatellite markers and automated allele detection. In addition, the landraces were evaluated for their seed iron and zinc concentration to determine if genetic diversity influenced nutritional quality. Principal coordinate and neighbor-joining analyses allowed the separation of the landraces into 132 Andean and 195 Mesoamerican (or Middle American) genotypes with 32 landraces and 6 varieties intermediate between the gene pools and representing inter-gene pool introgression in terms of seed characteristics and alleles. Genetic diversity and the number of alleles were high for the collection, reflecting the preference for a wide range of seed types in the region and no strong commercial class preference, although red, red mottled and brown seeded beans were common. Observed heterozygosity was also high and may be explained by the common practice of maintaining seed and plant mixtures, a coping strategy practiced by Central African farmers to reduce the effects of abiotic and biotic stresses. Finally, nutritional quality differed between the gene pools with respect to seed iron and zinc concentration, while genotypes from the intermediate group were notably high in both minerals. In conclusion, this study has shown that

  3. Hepatic Long Intergenic Noncoding RNAs: High Promoter Conservation and Dynamic, Sex-Dependent Transcriptional Regulation by Growth Hormone

    PubMed Central

    Melia, Tisha; Hao, Pengying; Yilmaz, Feyza

    2015-01-01

    Long intergenic noncoding RNAs (lincRNAs) are increasingly recognized as key chromatin regulators, yet few studies have characterized lincRNAs in a single tissue under diverse conditions. Here, we analyzed 45 mouse liver RNA sequencing (RNA-Seq) data sets collected under diverse conditions to systematically characterize 4,961 liver lincRNAs, 59% of them novel, with regard to gene structures, species conservation, chromatin accessibility, transcription factor binding, and epigenetic states. To investigate the potential for functionality, we focused on the responses of the liver lincRNAs to growth hormone stimulation, which imparts clinically relevant sex differences to hepatic metabolism and liver disease susceptibility. Sex-biased expression characterized 247 liver lincRNAs, with many being nuclear RNA enriched and regulated by growth hormone. The sex-biased lincRNA genes are enriched for nearby and correspondingly sex-biased accessible chromatin regions, as well as sex-biased binding sites for growth hormone-regulated transcriptional activators (STAT5, hepatocyte nuclear factor 6 [HNF6], FOXA1, and FOXA2) and transcriptional repressors (CUX2 and BCL6). Repression of female-specific lincRNAs in male liver, but not that of male-specific lincRNAs in female liver, was associated with enrichment of H3K27me3-associated inactive states and poised (bivalent) enhancer states. Strikingly, we found that liver-specific lincRNA gene promoters are more highly species conserved and have a significantly higher frequency of proximal binding by liver transcription factors than liver-specific protein-coding gene promoters. Orthologs for many liver lincRNAs were identified in one or more supraprimates, including two rat lincRNAs showing the same growth hormone-regulated, sex-biased expression as their mouse counterparts. This integrative analysis of liver lincRNA chromatin states, transcription factor occupancy, and growth hormone regulation provides novel insights into the

  4. 3D laser inspection of fuel assembly grid spacers for nuclear reactors based on diffractive optical elements

    NASA Astrophysics Data System (ADS)

    Finogenov, L. V.; Lemeshko, Yu A.; Zav'yalov, P. S.; Chugui, Yu V.

    2007-06-01

    Ensuring the safety and high operation reliability of nuclear reactors takes 100% inspection of geometrical parameters of fuel assemblies, which include the grid spacers performed as a cellular structure with fuel elements. The required grid spacer geometry of assembly in the transverse and longitudinal cross sections is extremely important for maintaining the necessary heat regime. A universal method for 3D grid spacer inspection using a diffractive optical element (DOE), which generates as the structural illumination a multiple-ring pattern on the inner surface of a grid spacer cell, is investigated. Using some DOEs one can inspect the nomenclature of all produced grids. A special objective has been developed for forming the inner surface cell image. The problems of diffractive elements synthesis, projecting optics calculation, adjusting methods as well as calibration of the experimental measuring system are considered. The algorithms for image processing for different constructive elements of grids (cell, channel hole, outer grid spacer rim) and the experimental results are presented.

  5. Repetition suppression of faces is modulated by emotion

    NASA Astrophysics Data System (ADS)

    Ishai, Alumit; Pessoa, Luiz; Bikle, Philip C.; Ungerleider, Leslie G.

    2004-06-01

    Single-unit recordings and functional brain imaging studies have shown reduced neural responses to repeated stimuli in the visual cortex. By using event-related functional MRI, we compared the activation evoked by repetitions of neutral and fearful faces, which were either task relevant (targets) or irrelevant (distracters). We found that within the inferior occipital gyri, lateral fusiform gyri, superior temporal sulci, amygdala, and the inferior frontal gyri/insula, targets evoked stronger responses than distracters and their repetition was associated with significantly reduced responses. Repetition suppression, as manifested by the difference in response amplitude between the first and third repetitions of a target, was stronger for fearful than neutral faces. Distracter faces, regardless of their repetition or valence, evoked negligible activation, indicating top-down attenuation of behaviorally irrelevant stimuli. Our findings demonstrate a three-way interaction between emotional valence, repetition, and task relevance and suggest that repetition suppression is influenced by high-level cognitive processes in the human brain. face perception | functional MRI

  6. Differences in output from corticosteroid inhalers used with a volumatic spacer.

    PubMed

    Miller, M R; Bright, P

    1995-10-01

    Corticosteroid inhaler therapy using a spacer device is commonly used as an important part of asthma management. Increasingly, generic corticosteroid inhalers are being used with spacer devices. We have therefore tested whether these generic inhalers yield equivalence in dose when compared to the established inhalers. We measured the in vitro output, discharged into a Volumatic spacer from beclomethasone dipropionate inhalers (250 micrograms.puff-1) made by three manufacturers, Allen & Hanburys, 3M and Baker Norton. The output from 20 of each type of inhaler was sampled, in random order, by a computer driven pump system. Beclomethasone was absorbed onto a coded filter, which was analysed independently for drug content. The output per puff differed significantly between the inhalers of each manufacturer, with a 36% difference between the highest output from the Allen & Hanburys device and the lowest output device. We conclude that there are important differences in output from these inhalers when used with a spacer, and that substitution of one device with another will not necessarily give equivalent therapy to the patient. PMID:8586114

  7. Archaeal Viruses of the Sulfolobales: Isolation, Infection, and CRISPR Spacer Acquisition.

    PubMed

    Erdmann, Susanne; Garrett, Roger A

    2015-01-01

    Infection of archaea with phylogenetically diverse single viruses, performed in different laboratories, has failed to activate spacer acquisition into host CRISPR loci. The first successful uptake of archaeal de novo spacers was observed on infection of Sulfolobus solfataricus P2 with an environmental virus mixture isolated from Yellowstone National Park (Erdmann and Garrett, Mol Microbiol 85:1044-1056, 2012). Experimental studies of isolated genetic elements from this mixture revealed that SMV1 (S ulfolobus Monocauda Virus 1), a tailed spindle-shaped virus, can induce spacer acquisition in CRISPR loci of Sulfolobus species from a second coinfecting conjugative plasmid or virus (Erdmann and Garrett, Mol Microbiol 85:1044-1056, 2012; Erdmann et al. Mol Microbiol 91:900-917, 2014). Here we describe, firstly, the isolation of archaeal virus mixtures from terrestrial hot springs and the techniques used both to infect laboratory strains with these virus mixtures and to obtain purified virus particles. Secondly, we present the experimental conditions required for activating SMV1-induced spacer acquisition in two different Sulfolobus species. PMID:25981476

  8. Joint perpendicular anisotropy and strong interlayer exchange coupling in systems with thin vanadium spacers

    SciTech Connect

    Devolder, T. Le Goff, A.; Eimer, S.; Adam, J.-P.

    2015-04-28

    We study the influence of the insertion of a vanadium spacer layer between an FeCoB layer and a [Co/Ni] multilayer in an MgO substrate-based system mimicking the reference system of a perpendicular anisotropy magnetic tunnel junction. The anisotropy of the [Co/Ni] multilayer gradually improves with the vanadium thicknesses t, up to an optimized state for t = 8 Å, with little influence of the thermal annealing. The interlayer exchange coupling is ferromagnetic and very strong for t≤6 Å. It can be adjusted by thermal treatment at t = 8 Å from no coupling in the as-grown state to more than 2 mJ/m{sup 2} after 250 °C annealing. For this spacer thickness, the magnetic properties are consistent with the occurrence of a bcc (001) to an fcc (111) crystalline structure transition at the vanadium spacer. The remaining interlayer exchange coupling at t = 8 Å is still substantially higher than the one formerly obtained with a Tantalum spacer, which holds promise for further optimization of the reference layers of tunnel junctions meant for magnetic random access memories.

  9. Joint perpendicular anisotropy and strong interlayer exchange coupling in systems with thin vanadium spacers

    NASA Astrophysics Data System (ADS)

    Devolder, T.; Le Goff, A.; Eimer, S.; Adam, J.-P.

    2015-04-01

    We study the influence of the insertion of a vanadium spacer layer between an FeCoB layer and a [Co/Ni] multilayer in an MgO substrate-based system mimicking the reference system of a perpendicular anisotropy magnetic tunnel junction. The anisotropy of the [Co/Ni] multilayer gradually improves with the vanadium thicknesses t, up to an optimized state for t = 8 Å, with little influence of the thermal annealing. The interlayer exchange coupling is ferromagnetic and very strong for t ≤6 Å. It can be adjusted by thermal treatment at t = 8 Å from no coupling in the as-grown state to more than 2 mJ/m2 after 250 °C annealing. For this spacer thickness, the magnetic properties are consistent with the occurrence of a bcc (001) to an fcc (111) crystalline structure transition at the vanadium spacer. The remaining interlayer exchange coupling at t = 8 Å is still substantially higher than the one formerly obtained with a Tantalum spacer, which holds promise for further optimization of the reference layers of tunnel junctions meant for magnetic random access memories.

  10. Novel mutation in spacer region of POLG associated with ataxia neuropathy spectrum and gastroparesis.

    PubMed

    Bostan, Alionka; Glibert, Gerald; Dachy, Bernard; Dan, Bernard

    2012-09-25

    Clinical expression of POLG mutations is largely variable. We present a patient with a new mutation in spacer region of mitochondrial polymerase gamma protein (P765T). The clinical picture is characterized by the presence of sensory-ataxic neuropathy, ophthalmoplegia, dysarthria and gastroparesis, which had not been previously observed in ataxia neuropathy spectrum. PMID:22805437

  11. Investigations in Number, Data, and Space[R]. WWC Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2009

    2009-01-01

    Investigations in Number, Data, and Space[R], published by Pearson Scott Foresman, is an activity-based K-5 mathematics curriculum designed to help students understand the fundamental ideas of number and operations, geometry, data, measurement, and early algebra. The curriculum encourages students to use prior knowledge to develop an understanding…

  12. Investigations in Number, Data, and Space[R]. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2013

    2013-01-01

    "Investigations in Number, Data, and Space"[R], published by Pearson Scott Foresman, is an activity-based K-5 mathematics curriculum designed to help students understand number and operations, geometry, data, measurement, and early algebra. Each instructional unit focuses on a particular content area and lasts from two to five-and-a-half weeks.…

  13. Repetition enhancement and memory effects for duration.

    PubMed

    Wiener, Martin; Thompson, James C

    2015-06-01

    A remarkable aspect of conscious perception is that moments carryover from one to the next, also known as temporal continuity. This ability is thus crucial for detecting regularities, such as in speech and music, and may rely on an accurate perception of time. Investigations of human time perception have detailed two electroencephalographic (EEG) components associated with timing, the contingent negative variation (CNV) and late positive component of timing (LPCt); however, the precise roles of these components in timing remain elusive. Recently, we demonstrated that the perception of duration is influenced by durations presented on prior trials, which we explained by the creation of an implicit memory standard that adapts to local changes in sequence presentation. Here, we turn to the neural basis of this effect. Human participants performed a temporal bisection task in which they were required to classify the duration of auditory stimuli into short and long duration categories; crucially, the presentation order was first-order counterbalanced, allowing us to measure the effect of each presented duration on the next. EEG recordings revealed that the CNV and LPCt signals both covaried with the duration presented on the current trial, with CNV predicting reaction time and LPCt predicting choice. Additionally, both signals covaried with the duration presented in the prior trial but in different ways, with the CNV amplitude reflecting the change in the memory standard and the LPCt reflecting decision uncertainty. Furthermore, we observed a repetition enhancement effect of duration only for the CNV, suggesting that this signal additionally indexes the similarity of successive durations. These findings demonstrate dissociable roles for the CNV and LPCt, and demonstrate that both signals are continuously updated on a trial-by-trial basis that reflects shifts in temporal decisions. PMID:25818689

  14. Epithelial topography for repetitive tooth formation

    PubMed Central

    Gaete, Marcia; Fons, Juan Manuel; Popa, Elena Mădălina; Chatzeli, Lemonia; Tucker, Abigail S.

    2015-01-01

    ABSTRACT During the formation of repetitive ectodermally derived organs such as mammary glands, lateral line and teeth, the tissue primordium iteratively initiates new structures. In the case of successional molar development, new teeth appear sequentially in the posterior region of the jaw from Sox2+ cells in association with the posterior aspect of a pre-existing tooth. The sequence of molar development is well known, however, the epithelial topography involved in the formation of a new tooth is unclear. Here, we have examined the morphology of the molar dental epithelium and its development at different stages in the mouse in vivo and in molar explants. Using regional lineage tracing we show that within the posterior tail of the first molar the primordium for the second and third molar are organized in a row, with the tail remaining in connection with the surface, where a furrow is observed. The morphology and Sox2 expression of the tail retains characteristics reminiscent of the earlier stages of tooth development, such that position along the A-P axes of the tail correlates with different temporal stages. Sox9, a stem/progenitor cell marker in other organs, is expressed mainly in the suprabasal epithelium complementary with Sox2 expression. This Sox2 and Sox9 expressing molar tail contains actively proliferating cells with mitosis following an apico-basal direction. Snail2, a transcription factor implicated in cell migration, is expressed at high levels in the tip of the molar tail while E-cadherin and laminin are decreased. In conclusion, our studies propose a model in which the epithelium of the molar tail can grow by posterior movement of epithelial cells followed by infolding and stratification involving a population of Sox2+/Sox9+ cells. PMID:26538639

  15. Epithelial topography for repetitive tooth formation.

    PubMed

    Gaete, Marcia; Fons, Juan Manuel; Popa, Elena Mădălina; Chatzeli, Lemonia; Tucker, Abigail S

    2015-01-01

    During the formation of repetitive ectodermally derived organs such as mammary glands, lateral line and teeth, the tissue primordium iteratively initiates new structures. In the case of successional molar development, new teeth appear sequentially in the posterior region of the jaw from Sox2(+) cells in association with the posterior aspect of a pre-existing tooth. The sequence of molar development is well known, however, the epithelial topography involved in the formation of a new tooth is unclear. Here, we have examined the morphology of the molar dental epithelium and its development at different stages in the mouse in vivo and in molar explants. Using regional lineage tracing we show that within the posterior tail of the first molar the primordium for the second and third molar are organized in a row, with the tail remaining in connection with the surface, where a furrow is observed. The morphology and Sox2 expression of the tail retains characteristics reminiscent of the earlier stages of tooth development, such that position along the A-P axes of the tail correlates with different temporal stages. Sox9, a stem/progenitor cell marker in other organs, is expressed mainly in the suprabasal epithelium complementary with Sox2 expression. This Sox2 and Sox9 expressing molar tail contains actively proliferating cells with mitosis following an apico-basal direction. Snail2, a transcription factor implicated in cell migration, is expressed at high levels in the tip of the molar tail while E-cadherin and laminin are decreased. In conclusion, our studies propose a model in which the epithelium of the molar tail can grow by posterior movement of epithelial cells followed by infolding and stratification involving a population of Sox2(+)/Sox9(+) cells. PMID:26538639

  16. Hydrogel Spacer Prospective Multicenter Randomized Controlled Pivotal Trial: Dosimetric and Clinical Effects of Perirectal Spacer Application in Men Undergoing Prostate Image Guided Intensity Modulated Radiation Therapy

    SciTech Connect

    Mariados, Neil; Sylvester, John; Shah, Dhiren; Karsh, Lawrence; Hudes, Richard; Beyer, David; Kurtzman, Steven; Bogart, Jeffrey; Hsi, R. Alex; Kos, Michael; Ellis, Rodney; Logsdon, Mark; Zimberg, Shawn; Forsythe, Kevin; Zhang, Hong; Soffen, Edward; Francke, Patrick; Mantz, Constantine; Rossi, Peter; DeWeese, Theodore; and others

    2015-08-01

    Purpose: Perirectal spacing, whereby biomaterials are placed between the prostate and rectum, shows promise in reducing rectal dose during prostate cancer radiation therapy. A prospective multicenter randomized controlled pivotal trial was performed to assess outcomes following absorbable spacer (SpaceOAR system) implantation. Methods and Materials: Overall, 222 patients with clinical stage T1 or T2 prostate cancer underwent computed tomography (CT) and magnetic resonance imaging (MRI) scans for treatment planning, followed with fiducial marker placement, and were randomized to receive spacer injection or no injection (control). Patients received postprocedure CT and MRI planning scans and underwent image guided intensity modulated radiation therapy (79.2 Gy in 1.8-Gy fractions). Spacer safety and impact on rectal irradiation, toxicity, and quality of life were assessed throughout 15 months. Results: Spacer application was rated as “easy” or “very easy” 98.7% of the time, with a 99% hydrogel placement success rate. Perirectal spaces were 12.6 ± 3.9 mm and 1.6 ± 2.0 mm in the spacer and control groups, respectively. There were no device-related adverse events, rectal perforations, serious bleeding, or infections within either group. Pre-to postspacer plans had a significant reduction in mean rectal V70 (12.4% to 3.3%, P<.0001). Overall acute rectal adverse event rates were similar between groups, with fewer spacer patients experiencing rectal pain (P=.02). A significant reduction in late (3-15 months) rectal toxicity severity in the spacer group was observed (P=.04), with a 2.0% and 7.0% late rectal toxicity incidence in the spacer and control groups, respectively. There was no late rectal toxicity greater than grade 1 in the spacer group. At 15 months 11.6% and 21.4% of spacer and control patients, respectively, experienced 10-point declines in bowel quality of life. MRI scans at 12 months verified spacer absorption. Conclusions: Spacer

  17. Repetitive XUV laser based on the fast capillary discharge

    NASA Astrophysics Data System (ADS)

    Schmidt, Jiri; Kolacek, Karel; Frolov, Oleksandr; Prukner, Vaclav; Straus, Jaroslav

    2011-09-01

    For testing and application purposes we have built a new small Marx generator capable to run in a repetitive regime. Its repeating frequency is currently up to 1 Hz. The generator is covered by metal sheets and feeds the CAPEX facility and ensures its full independence on the CAPEX-U machine (using another Marx generator). This paper reports on the first experimental results of a new experimental set-up of the CAPEX apparatus (repetitive lasing at 46.9 nm), mainly on set-up description, electrical parameters, and laser pulse stability in the repetitive regime.

  18. Assessing host-specificity of Escherichia coli using a supervised learning logic-regression-based analysis of single nucleotide polymorphisms in intergenic regions.

    PubMed

    Zhi, Shuai; Li, Qiaozhi; Yasui, Yutaka; Edge, Thomas; Topp, Edward; Neumann, Norman F

    2015-11-01

    Host specificity in E. coli is widely debated. Herein, we used supervised learning logic-regression-based analysis of intergenic DNA sequence variability in E. coli in an attempt to identify single nucleotide polymorphism (SNP) biomarkers of E. coli that are associated with natural selection and evolution toward host specificity. Seven-hundred and eighty strains of E. coli were isolated from 15 different animal hosts. We utilized logic regression for analyzing DNA sequence data of three intergenic regions (flanked by the genes uspC-flhDC, csgBAC-csgDEFG, and asnS-ompF) to identify genetic biomarkers that could potentially discriminate E. coli based on host sources. Across 15 different animal hosts, logic regression successfully discriminated E. coli based on animal host source with relatively high specificity (i.e., among the samples of the non-target animal host, the proportion that correctly did not have the host-specific marker pattern) and sensitivity (i.e., among the samples from a given animal host, the proportion that correctly had the host-specific marker pattern), even after fivefold cross validation. Permutation tests confirmed that for most animals, host specific intergenic biomarkers identified by logic regression in E. coli were significantly associated with animal host source. The highest level of biomarker sensitivity was observed in deer isolates, with 82% of all deer E. coli isolates displaying a unique SNP pattern that was 98% specific to deer. Fifty-three percent of human isolates displayed a unique biomarker pattern that was 98% specific to humans. Twenty-nine percent of cattle isolates displayed a unique biomarker that was 97% specific to cattle. Interestingly, even within a related host group (i.e., Family: Canidae [domestic dogs and coyotes]), highly specific SNP biomarkers (98% and 99% specificity for dog and coyotes, respectively) were observed, with 21% of dog E. coli isolates displaying a unique dog biomarker and 61% of coyote isolates

  19. BIODEGRADABLE BRANCHED POLYCATIONIC POLYMERS WITH VARYING HYDROPHILIC SPACERS FOR NON-VIRAL GENE DELIVERY

    PubMed Central

    Chew, Sue Anne; Hacker, Michael C.; Saraf, Anita; Raphael, Robert M.; Kasper, F. Kurtis; Mikos, Antonios G.

    2009-01-01

    Biodegradable branched polycationic polymers with varying hydrophilic spacer lengths were synthesized from different triacrylate monomers and the amine monomer 1-(2-aminoethyl)piperazine by Michael addition polymerization. The hydrophilic spacers were varied by the number of ethyleneoxy groups in the triacrylate monomer (E/M) that ranged from 0 to 14. The polymer degradation depended on the spacer length and pH; the amount of ester degraded as determined by 1H-NMR after 14 days was 43.4 ± 2.1% (pH 5.0) and 89.7 ± 1.3% (pH 7.4) for the polymer with 0 E/M compared to 55.7 ± 2.6% (pH 5.0) and 98.5 ± 1.6% (pH 7.4) for the polymer with 14 E/M. Cell viability of rat fibroblasts after exposure to polymer solutions of concentrations up to 1000 μg/mL remained high (above 66.9 ± 12.1% compared to below 7.6 ± 1.1% for polyethylenimine at a concentration of 50 μg/mL or higher) and increased with the spacer length. The polyplexes made with all the synthesized polymers showed higher transfection efficiency (4.5 ± 1.7% to 9.4 ± 2.0%, dependent on the polymer/pDNA weight ratio) with an enhanced green fluorescent protein reporter gene compared to naked pDNA (0.8 ± 0.4%) as quantified by flow cytometry. This study demonstrates that hydrophilic spacers can be incorporated into polycationic polymers to reduce their cytotoxicity and enhance their degradability for non-viral gene delivery. PMID:19678696

  20. Distractibility during infants' examining and repetitive rhythmic activity.

    PubMed

    Doolittle, E J; Ruff, H A

    1998-05-01

    The goal of this study was to assess the role of examining and repetitive rhythmic activity in infants' exploration of novel objects. Sixteen 8-month-old infants played with novel toys as auditory-visual slide distractors occurred on one side at random intervals. The results showed that examining, but not repetitive activities, declined with exposure to the objects. They also showed that infants had different patterns of distractibility during examining and repetitive rhythmic activities. The infants were slower to turn to the distractor if they were examining the toy than if they were engaged in other activity, but the probability of a response did not differ. In contrast, when engaged in repetitive rhythmic activity, infants were less likely to respond to the distractor than when engaged in other activities, including examining; the speed with which they responded, however, did not differ. The results suggest that, during these two activities, the mechanisms for resisting distraction are quite different. PMID:9589216

  1. Fixture tests bellows reliability through repetitive pressure/temperature cycling

    NASA Technical Reports Server (NTRS)

    Levinson, C.

    1967-01-01

    Fixture explores the reliability of bellows used in precision in inertial systems. The fixture establishes the ability of the bellows to withstand repetitive over-stress pressure cycling at elevated temperatures. It is applicable in quality control and reliability programs.

  2. The Effect of Repetition on Tempo Preferences of Elementary Children.

    ERIC Educational Resources Information Center

    Moskovitz, Elisa M.

    1992-01-01

    Reports on a study of children's preferences between slow and fast tempo classical music excerpts. Finds that students preferred music with a slow tempo. Concludes that repetition had a positive effect on children's preferences. (CFR)

  3. Repetition in visual word identification: benefits and costs.

    PubMed

    Burt, Jennifer S; Kipps, Tahli J; Matthews, Julian R

    2014-10-01

    University students performed lexical tasks with visually presented target words after the presentation of an identical or unrelated prime, at short (80-120 ms) or longer (410-710 ms) prime-target stimulus onset asynchronies (SOAs). Experiment 1 showed perceptual identification benefits in vocal responding at a short SOA that were reduced (accuracy) or reversed (latency) at a longer SOA. Experiment 2 showed a transition from a repetition benefit to a cost over 3 SOAs in a target-masked version of the lexical decision task (LDT; target displayed for only 141 ms). In Experiment 3 the repetition cost was replicated at a 530-ms SOA in the LDT with masked targets, but a repetition benefit was observed in the conventional LDT (target displayed until response). The dependence of repetition costs on target masking is more consistent with biases based on episodic confusions than refractoriness of lexical representations. PMID:25248100

  4. Neural dynamics during repetitive visual stimulation

    NASA Astrophysics Data System (ADS)

    Tsoneva, Tsvetomira; Garcia-Molina, Gary; Desain, Peter

    2015-12-01

    Objective. Steady-state visual evoked potentials (SSVEPs), the brain responses to repetitive visual stimulation (RVS), are widely utilized in neuroscience. Their high signal-to-noise ratio and ability to entrain oscillatory brain activity are beneficial for their applications in brain-computer interfaces, investigation of neural processes underlying brain rhythmic activity (steady-state topography) and probing the causal role of brain rhythms in cognition and emotion. This paper aims at analyzing the space and time EEG dynamics in response to RVS at the frequency of stimulation and ongoing rhythms in the delta, theta, alpha, beta, and gamma bands. Approach.We used electroencephalography (EEG) to study the oscillatory brain dynamics during RVS at 10 frequencies in the gamma band (40-60 Hz). We collected an extensive EEG data set from 32 participants and analyzed the RVS evoked and induced responses in the time-frequency domain. Main results. Stable SSVEP over parieto-occipital sites was observed at each of the fundamental frequencies and their harmonics and sub-harmonics. Both the strength and the spatial propagation of the SSVEP response seem sensitive to stimulus frequency. The SSVEP was more localized around the parieto-occipital sites for higher frequencies (>54 Hz) and spread to fronto-central locations for lower frequencies. We observed a strong negative correlation between stimulation frequency and relative power change at that frequency, the first harmonic and the sub-harmonic components over occipital sites. Interestingly, over parietal sites for sub-harmonics a positive correlation of relative power change and stimulation frequency was found. A number of distinct patterns in delta (1-4 Hz), theta (4-8 Hz), alpha (8-12 Hz) and beta (15-30 Hz) bands were also observed. The transient response, from 0 to about 300 ms after stimulation onset, was accompanied by increase in delta and theta power over fronto-central and occipital sites, which returned to baseline

  5. The Influences of Number of Syllables and Wordlikeness on Children's Repetition of Nonwords.

    ERIC Educational Resources Information Center

    Gathercole, Susan E; And Others

    1991-01-01

    Investigates developmental association between nonword repetition performance and vocabulary knowledge by evaluating the role of phonological memory and linguistic factors in nonword repetition. (29 references) (GLR)

  6. Short palindromic repetitive DNA elements in enterobacteria: a survey.

    PubMed

    Bachellier, S; Clément, J M; Hofnung, M

    1999-01-01

    We present a survey of short palindromic repetitive elements in enterobacteria. Seven families are presented. Five were already known (RSA, IRU, 29-bp repeats, BIMEs and boxC), and their properties are updated; in particular, a new composite element is shown to include the formerly identified boxC repeats. Two repetitions, YPAL1 and YPAL2, found primarily in Yersinia, are described here for the first time. PMID:10673002

  7. Repetition of Attempted Suicide Among Immigrants in Europe

    PubMed Central

    Lipsicas, Cendrine Bursztein; Mäkinen, Ilkka Henrik; Wasserman, Danuta; Apter, Alan; Kerkhof, Ad; Michel, Konrad; Renberg, Ellinor Salander; van Heeringen, Kees; Värnik, Airi; Schmidtke, Armin

    2014-01-01

    Objectives To compare frequencies of suicide attempt repetition in immigrants and local European populations, and the timing of repetition in these groups. Method: Data from 7 European countries, comprising 10 574 local and 3032 immigrant subjects, were taken from the World Health Organization European Multicentre Study on Suicidal Behaviour and the ensuing Monitoring Suicidal Behaviour in Europe (commonly referred to as MONSUE) project. The relation between immigrant status and repetition of suicide attempt within 12-months following first registered attempt was analyzed with binary logistic regression, controlling for sex, age, and method of attempt. Timing of repetition was controlled for sex, age, and the recommended type of aftercare. Results: Lower odds of repeating a suicide attempt were found in Eastern European (OR 0.50; 95% CI 0.41 to 0.61, P < 0.001) and non-European immigrants (OR 0.68; 95% CI 0.51 to 0.90, P < 0.05), compared with the locals. Similar patterns were identified in the sex-specific analysis. Eastern European immigrants tended to repeat their attempt much later than locals (OR 0.58; 95% CI 0.35 to 0.93, P < 0.05). In general, 32% of all repetition occurred within 30 days. Repetition tended to decrease with age and was more likely in females using harder methods in their index attempt (OR 1.29; 95% CI 1.08 to 1.54, P < 0.01). Large variations in the general repetition frequency were identified between the collecting centres, thus influencing the results. Conclusions: The lower repetition frequencies in non-Western immigrants, compared with locals, in Europe stands in contrast to their markedly higher tendency to attempt suicide in general, possibly pointing to situational stress factors related to their suicidal crisis that are less persistent over time. Our findings also raise the possibility that suicide attempters and repeaters constitute only partially overlapping populations. PMID:25565687

  8. Negative effects of item repetition on source memory

    PubMed Central

    Yi, Do-Joon; Raye, Carol L.; Johnson, Marcia K.

    2013-01-01

    In the present study, we explored how item repetition affects source memory for new item–feature associations (picture–location or picture–color). We presented line drawings varying numbers of times in Phase 1. In Phase 2, each drawing was presented once with a critical new feature. In Phase 3, we tested memory for the new source feature of each item from Phase 2. Experiments 1 and 2 demonstrated and replicated the negative effects of item repetition on incidental source memory. Prior item repetition also had a negative effect on source memory when different source dimensions were used in Phases 1 and 2 (Experiment 3) and when participants were explicitly instructed to learn source information in Phase 2 (Experiments 4 and 5). Importantly, when the order between Phases 1 and 2 was reversed, such that item repetition occurred after the encoding of critical item–source combinations, item repetition no longer affected source memory (Experiment 6). Overall, our findings did not support predictions based on item predifferentiation, within-dimension source interference, or general interference from multiple traces of an item. Rather, the findings were consistent with the idea that prior item repetition reduces attention to subsequent presentations of the item, decreasing the likelihood that critical item–source associations will be encoded. PMID:22411165

  9. Naming and repetition in aphasia: Steps, routes, and frequency effects

    PubMed Central

    Nozari, Nazbanou; Kittredge, Audrey K.; Dell, Gary S.; Schwartz, Myrna F.

    2010-01-01

    This paper investigates the cognitive processes underlying picture naming and auditory word repetition. In the 2-step model of lexical access, both the semantic and phonological steps are involved in naming, but the former has no role in repetition. Assuming recognition of the to-be-repeated word, repetition could consist of retrieving the word’s output phonemes from the lexicon (the lexical-route model), retrieving the output phonology directly from input phonology (the nonlexical-route model) or employing both routes together (the summation dual-route model). We tested these accounts by comparing the size of the word frequency effect (an index of lexical retrieval) in naming and repetition data from 59 aphasic patients with simulations of naming and repetition models. The magnitude of the frequency effect (and the influence of other lexical variables) was found to be comparable in naming and repetition, and equally large for both the lexical and summation dual-route models. However, only the dual-route model was fully consistent with data from patients, suggesting that nonlexical input is added on top of a fully-utilized lexical route. PMID:21076661

  10. Properties of water surface discharge at different pulse repetition rates

    NASA Astrophysics Data System (ADS)

    Ruma, Hosseini, S. H. R.; Yoshihara, K.; Akiyama, M.; Sakugawa, T.; Lukeš, P.; Akiyama, H.

    2014-09-01

    The properties of water surface discharge plasma for variety of pulse repetition rates are investigated. A magnetic pulse compression (MPC) pulsed power modulator able to deliver pulse repetition rates up to 1000 Hz, with 0.5 J per pulse energy output at 25 kV, was used as the pulsed power source. Positive pulse with a point-to-plane electrode configuration was used for the experiments. The concentration and production yield of hydrogen peroxide (H2O2) were quantitatively measured and orange II organic dye was treated, to evaluate the chemical properties of the discharge reactor. Experimental results show that the physical and chemical properties of water surface discharge are not influenced by pulse repetition rate, very different from those observed for under water discharge. The production yield of H2O2 and degradation rate per pulse of the dye did not significantly vary at different pulse repetition rates under a constant discharge mode on water surface. In addition, the solution temperature, pH, and conductivity for both water surface and underwater discharge reactors were measured to compare their plasma properties for different pulse repetition rates. The results confirm that surface discharge can be employed at high pulse repetition rates as a reliable and advantageous method for industrial and environmental decontamination applications.

  11. Properties of water surface discharge at different pulse repetition rates

    SciTech Connect

    Ruma,; Yoshihara, K.; Hosseini, S. H. R. Sakugawa, T.; Akiyama, H.; Akiyama, M.; Lukeš, P.

    2014-09-28

    The properties of water surface discharge plasma for variety of pulse repetition rates are investigated. A magnetic pulse compression (MPC) pulsed power modulator able to deliver pulse repetition rates up to 1000 Hz, with 0.5 J per pulse energy output at 25 kV, was used as the pulsed power source. Positive pulse with a point-to-plane electrode configuration was used for the experiments. The concentration and production yield of hydrogen peroxide (H₂O₂) were quantitatively measured and orange II organic dye was treated, to evaluate the chemical properties of the discharge reactor. Experimental results show that the physical and chemical properties of water surface discharge are not influenced by pulse repetition rate, very different from those observed for under water discharge. The production yield of H₂O₂ and degradation rate per pulse of the dye did not significantly vary at different pulse repetition rates under a constant discharge mode on water surface. In addition, the solution temperature, pH, and conductivity for both water surface and underwater discharge reactors were measured to compare their plasma properties for different pulse repetition rates. The results confirm that surface discharge can be employed at high pulse repetition rates as a reliable and advantageous method for industrial and environmental decontamination applications.

  12. FMRI repetition suppression for voices is modulated by stimulus expectations.

    PubMed

    Andics, Attila; Gál, Viktor; Vicsi, Klára; Rudas, Gábor; Vidnyánszky, Zoltán

    2013-04-01

    According to predictive coding models of sensory processing, stimulus expectations have a profound effect on sensory cortical responses. This was supported by experimental results, showing that fMRI repetition suppression (fMRI RS) for face stimuli is strongly modulated by the probability of stimulus repetitions throughout the visual cortical processing hierarchy. To test whether processing of voices is also affected by stimulus expectations, here we investigated the effect of repetition probability on fMRI RS in voice-selective cortical areas. Changing ('alt') and identical ('rep') voice stimulus pairs were presented to the listeners in blocks, with a varying probability of alt and rep trials across blocks. We found auditory fMRI RS in the nonprimary voice-selective cortical regions, including the bilateral posterior STS, the right anterior STG and the right IFC, as well as in the IPL. Importantly, fMRI RS effects in all of these areas were strongly modulated by the probability of stimulus repetition: auditory fMRI RS was reduced or not present in blocks with low repetition probability. Our results revealed that auditory fMRI RS in higher-level voice-selective cortical regions is modulated by repetition probabilities and thus suggest that in audition, similarly to the visual modality, processing of sensory information is shaped by stimulus expectation processes. PMID:23268783

  13. Fundamental Oscillation up to 1.42 THz in Resonant Tunneling Diodes by Optimized Collector Spacer Thickness

    NASA Astrophysics Data System (ADS)

    Kanaya, Hidetoshi; Sogabe, Riku; Maekawa, Takeru; Suzuki, Safumi; Asada, Masahiro

    2014-05-01

    We report an increase in the oscillation frequency of terahertz oscillators using AlAs/InGaAs double-barrier resonant tunneling diodes (RTDs) by optimizing the collector spacer thickness. For high-frequency oscillation of RTDs, the electron delay time, which is composed of the dwell time in the resonance region and the transit time in the collector depletion region, must be reduced. Although the transit time is reduced by a thin collector spacer, the capacitance increases. Thus, an optimum thickness of collector spacer layer exists. In this report, we investigate the dependence of oscillation frequency on the collector spacer thickness. The RTDs were integrated with 20-μm-long slot antennas, and oscillations up to 1.1, 1.42, and 1.29 THz were obtained for spacer thicknesses of 25, 12, and 6 nm, respectively. The optimum spacer thickness for high-frequency oscillation was around 12 nm. The highest frequency in this experiment was 1.42 THz oscillation, with an output power of ~1 μW. We also extracted the electron velocity in the collector depletion region and the dwell time from the dependence of the delay time on the collector spacer thickness.

  14. An experimental study on the effect of spacer on concentration polarization in a long channel reverse osmosis membrane cell.

    PubMed

    Mo, H; Ng, H Y

    2010-01-01

    This study was to experimentally investigate the performance and organic fouling behaviour in a 1-m long RO membrane channel with or without spacer for desalting. It was found that local permeate flux distributed heterogeneously along the long membrane channel without a spacer inserted due to exponential growth of concentration polarization, which also resulted in decreasing salt rejection and increasing organic fouling along the membrane channel in the downstream direction. This heterogeneity could be lessened by inserting a spacer into the channel, which mitigated concentration polarization due to the enhanced turbulence caused by a spacer, especially at the downstream portion of the channel. However, in the upstream of the channel, inserting a spacer exerted an additional vertical resistance which might counteract the effect of concentration polarization mitigation by a spacer and caused a lower permeate flux. This suggests that it is necessary to consider the integral effect of spacer for designing an RO membrane module and an overall RO system in order to prevent extra resistance, reduce concentration polarization and membrane fouling. PMID:20389001

  15. Intergenic Variable-Number Tandem-Repeat Polymorphism Upstream of rocA Alters Toxin Production and Enhances Virulence in Streptococcus pyogenes.

    PubMed

    Zhu, Luchang; Olsen, Randall J; Horstmann, Nicola; Shelburne, Samuel A; Fan, Jia; Hu, Ye; Musser, James M

    2016-07-01

    Variable-number tandem-repeat (VNTR) polymorphisms are ubiquitous in bacteria. However, only a small fraction of them has been functionally studied. Here, we report an intergenic VNTR polymorphism that confers an altered level of toxin production and increased virulence in Streptococcus pyogenes The nature of the polymorphism is a one-unit deletion in a three-tandem-repeat locus upstream of the rocA gene encoding a sensor kinase. S. pyogenes strains with this type of polymorphism cause human infection and produce significantly larger amounts of the secreted cytotoxins S. pyogenes NADase (SPN) and streptolysin O (SLO). Using isogenic mutant strains, we demonstrate that deleting one or more units of the tandem repeats abolished RocA production, reduced CovR phosphorylation, derepressed multiple CovR-regulated virulence factors (such as SPN and SLO), and increased virulence in a mouse model of necrotizing fasciitis. The phenotypic effect of the VNTR polymorphism was nearly the same as that of inactivating the rocA gene. In summary, we identified and characterized an intergenic VNTR polymorphism in S. pyogenes that affects toxin production and virulence. These new findings enhance understanding of rocA biology and the function of VNTR polymorphisms in S. pyogenes. PMID:27141081

  16. Bacterial interspersed mosaic elements (BIMEs) are a major source of sequence polymorphism in Escherichia coli intergenic regions including specific associations with a new insertion sequence.

    PubMed

    Bachellier, S; Clément, J M; Hofnung, M; Gilson, E

    1997-03-01

    A significant fraction of Escherichia coli intergenic DNA sequences is composed of two families of repeated bacterial interspersed mosaic elements (BIME-1 and BIME-2). In this study, we determined the sequence organization of six intergenic regions in 51 E. coli and Shigella natural isolates. Each region contains a BIME in E. coli K-12. We found that multiple sequence variations are located within or near these BIMEs in the different bacteria. Events included excisions of a whole BIME-1, expansion/deletion within a BIME-2 and insertions of non-BIME sequences like the boxC repeat or a new IS element, named IS 1397. Remarkably, 14 out of IS 1397 integration sites correspond to a BIME sequence, strongly suggesting that this IS element is specifically associated with BIMEs, and thus inserts only in extragenic regions. Unlike BIMEs, IS 1397 is not detected in all E. coli isolates. Possible relationships between the presence of this IS element and the evolution of BIMEs are discussed. PMID:9055066

  17. Replication origins and a sequence involved in coordinate induction of the immediate-early gene family are conserved in an intergenic region of herpes simplex virus.

    PubMed Central

    Whitton, J L; Clements, J B

    1984-01-01

    We have determined the structure of the 5' portion of herpes simplex virus type 2 (HSF-2) immediate-early (IE) mRNA-3 and have obtained the DNA sequence specifying the N terminus of its encoded polypeptide, Vmw182, its untranslated leader and the intergenic region between IEmRNAs-3 & 4/5. Comparison of the HSV-2 intergenic sequences with the HSV-1 equivalent region identifies several conserved regions: (1) an AT-rich element with core consensus TAATGARAT which is likely to be the 'activator' sequence through which coordinate induction of the IE gene family is mediated. (2) GC-rich and GA-rich tracts, found in a wide variety of eukaryotic promoters, which vary in position and orientation between HSV-2 and HSV-1 and which represent modulators of transcription. (3) TATA homologies present 15-25 base pairs (bp) upstream of mRNA 5' termini. (4) a 137bp direct repeat in HSV-2 which contains sequence almost identical to the HSV-1 replication origin. Images PMID:6322134

  18. Specific binding of Thiobacillus ferrooxidans RbcR to the intergenic sequence between the rbc operon and the rbcR gene.

    PubMed Central

    Kusano, T; Sugawara, K

    1993-01-01

    The presence of two sets (rbcL1-rbcS1 and rbcL2-rbcS2) of rbc operons has been demonstrated in Thiobacillus ferrooxidans Fe1 (T. Kusano, T. Takeshima, C. Inoue, and K. Sugawara, J. Bacteriol. 173:7313-7323, 1991). A possible regulatory gene, rbcR, 930 bp long and possibly translated into a 309-amino-acid protein, was found upstream from the rbcL1 gene as a single copy. The gene is located divergently to rbcL1 with a 144-bp intergenic sequence. As in the cases of the Chromatium vinosum RbcR and Alcaligenes eutrophus CfxR, T. ferrooxidans RbcR is thought to be a new member of the LysR family, and these proteins share 46.5 and 42.8% identity, respectively. Gel mobility shift assays showed that T. ferrooxidans RbcR, produced in Escherichia coli, binds specifically to the intergenic sequence between rbcL1 and rbcR. Footprinting and site-directed mutagenesis experiments further demonstrated that RbcR binds to overlapping promoter elements of the rbcR and rbcL1 genes. The above data strongly support the participation of RbcR in regulation of the rbcL1-rbcS1 operon and the rbcR gene in T. ferrooxidans. Images PMID:8432695

  19. Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED).

    PubMed

    Bose, Michael; Slick, David; Sarto, Mickey J; Murphy, Patrick; Roberts, David; Roberts, Jacqueline; Barber, Robert D

    2006-08-01

    Microbial genome sequencing projects have revealed an apparently wide distribution of SmtB/ArsR metal-responsive transcriptional regulators among prokaryotes. Using a position-dependent weight matrix approach, prokaryotic genome sequences were screened for SmtB/ArsR DNA binding sites using data derived from intergenic sequences upstream of orthologous genes encoding these regulators. Sixty SmtB/ArsR operators linked to metal detoxification genes, including nine among various archaeal species, are predicted among 230 annotated and draft prokaryotic genome sequences. Independent multiple sequence alignments of putative operator sites and corresponding winged helix-turn-helix motifs define sequence signatures for the DNA binding activity of this SmtB/ArsR subfamily. Prediction of an archaeal SmtB/ArsR based upon these signature sequences is confirmed using purified Methanosarcina acetivorans C2A protein and electrophoretic mobility shift assays. Tools used in this study have been incorporated into a web application, the Prokaryotic InterGenic Exploration Database (PIGED; http://bioinformatics.uwp.edu/~PIGED/home.htm), facilitating comparable studies. Use of this tool and establishment of orthology based on DNA binding signatures holds promise for deciphering potential cellular roles of various archaeal winged helix-turn-helix transcriptional regulators. PMID:16877320

  20. Similar Results in Children with Asthma for Steady State Pharmacokinetic Parameters of Ciclesonide Inhaled with or without Spacer

    PubMed Central

    Boss, H.; Minic, P.; Nave, R.

    2010-01-01

    Background: Ciclesonide is an inhaled corticosteroid administered by a metered dose inhaler (MDI) to treat bronchial asthma. After inhalation, the inactive ciclesonide is converted by esterases in the airways to active metabolite desisobutyryl-ciclesonide (des-CIC). Aim: To compare the pharmacokinetic (PK) parameters of des-CIC in children after administration of therapeutic dose of ciclesonide with and without spacer (AeroChamber Plus™). Methods: Open-label, 3 period, cross over, repeated dose, PK study in 37 children with mild to moderate stable asthma (age: 6–11 y; body weight: 20–53 kg). During each 7-day treatment period, ciclesonide was inhaled once in the morning: A) 160 μg MDI with spacer, B) 80 μg MDI with spacer, and C) 160 μg MDI without spacer. Serum PK parameters of ciclesonide and des-CIC were determined on Day 7 of each period. The primary PK parameters were the AUCτ and Cmax for des-CIC. Results: Inhaling ciclesonide with spacer led to a dose proportional systemic exposure (AUCτ) of des-CIC (0.316 μg*h/L for 80 μg and 0.663 μg*h/L for 160 μg). The dose-normalized systemic exposure for des-CIC (based on AUCτ) was 27% higher after inhalation of ciclesonide 80 μg or 160 μg with spacer than without spacer; the corresponding Cmax values for des-CIC were, respectively, 63% and 55% higher with spacer. No clinically relevant abnormalities or adverse drug reactions were observed. Conclusions: Inhalation of therapeutic ciclesonide dose with spacer led to a slight increase in the systemic exposure of des-CIC, which does not warrant dose adjustment. PMID:23761990

  1. Finite element modeling of stress distribution in intervertebral spacers of different surface geometries.

    PubMed

    Lee, Jae Hyup; Baek, Myong-Hyun; Kim, Young Eun; Seo, Jun-Hyuk; Song, Dong Ryul; Ryu, Hyun-Seung; Lee, Choon-Ki; Chang, Bong-Soon

    2013-11-01

    Intervertebral disc spacers using bioactive ceramics have been used to treat degenerative spinal disease. Tooth-shaped spacers are commonly used to prevent migration, but there is a possibility of fracture when inserted or after insertion. Intervertebral disc spacers with either an isosceles triangle-shaped tooth (T1) or a right triangle-shaped tooth (T2) were used as a control group. The design factors for the experimental group were modified to prevent fractures induced by stress concentration, and the surfaces of the spacers were designed as either an isosceles triangle-shaped valley (V1) or a right triangle-shaped valley (V2). Linear analysis using finite element model (FEM) was performed, and Von Mises stress distribution was calculated by applying 1000 N of uniformly distributed load. Samples of the V2 design were made with bioactive glass-ceramics (BGS-7) and evaluated for compressive strength, fatigue degree, and impact strength. Von Mises stress was highest at the first tooth from the posterior side for the control group and at the center for the experimental group. Compared with the control group, the experimental group showed 18.4% and 82.5% reduction (V1 vs. T1 and V2 vs. T2, respectively) in the maximum stress at the bottom of the valleys. The FEM analysis revealed that the V2 design had the most even load distribution. The V2 samples with bioactive glass-ceramics were evaluated for compressive strength, and all six samples were not fractured up to 24 000 N. However, the average impact strength was 19.42 kN, suggesting that momentary force caused damage at a lower load than compression with a steady speed. The BGS-7 intervertebral disc spacer with V2 design was not fractured during the fatigue test at maximum pressure of 8000 N, R ≥10, 5 Hz, and 5 million cycles. These data confirm that the BGS-7 spacer with the V2 design may be clinically applicable. Collectively, the modified surface geometry of the experimental group significantly lowered Von

  2. Influence of spacer length on heparin coupling efficiency and fibrinogen adsorption of modified titanium surfaces

    PubMed Central

    Tebbe, David; Thull, Roger; Gbureck, Uwe

    2007-01-01

    Background Chemical bonding of the drug onto surfaces by means of spacer molecules is accompanied with a reduction of the biological activity of the drug due to a constricted mobility since normally only short spacer molecule like aminopropyltrimethoxysilane (APMS) are used for drug coupling. This work aimed to study covalent attachment of heparin to titanium(oxide) surfaces by varying the length of the silane coupling agent, which should affect the biological potency of the drug due to a higher mobility with longer spacer chains. Methods Covalent attachment of heparin to titanium metal and TiO2 powder was carried out using the coupling agents 3-(Trimethoxysilyl)-propylamine (APMS), N- [3-(Trimethoxysilyl)propyl]ethylenediamine (Diamino-APMS) and N1- [3-(Trimethoxy-silyl)-propyl]diethylenetriamine (Triamino-APMS). The amount of bound coupling agent and heparin was quantified photometrically by the ninhydrin reaction and the tolidine-blue test. The biological potency of heparin was determined photometrically by the chromogenic substrate Chromozym TH and fibrinogen adsorption to the modified surfaces was researched using the QCM-D (Quartz Crystal Microbalance with Dissipation Monitoring) technique. Results Zeta-potential measurements confirmed the successful coupling reaction; the potential of the unmodified anatase surface (approx. -26 mV) shifted into the positive range (> + 40 mV) after silanisation. Binding of heparin results in a strongly negatively charged surface with zeta-potentials of approx. -39 mV. The retaining biological activity of heparin was highest for the spacer molecule Triamino-APMS. QCM-D measurements showed a lower viscosity for adsorbed fibrinogen films on heparinised surfaces by means of Triamino-APMS. Conclusion The remaining activity of heparin was found to be highest for the covalent attachment with Triamino-APMS as coupling agent due to the long chain of this spacer molecule and therefore the highest mobility of the drug. Furthermore, the

  3. Controlled current matching in small molecule organic tandem solar cells using doped spacer layers

    NASA Astrophysics Data System (ADS)

    Schueppel, Rico; Timmreck, Ronny; Allinger, Nikola; Mueller, Toni; Furno, Mauro; Uhrich, Christian; Leo, Karl; Riede, Moritz

    2010-02-01

    Current matching of the subcells is crucial to optimize the performance of tandem solar cells. Due to the thin film optics of organic solar cells, the position of the two subcells relative to the reflecting electrode becomes a very important issue. This is demonstrated for an indium tin oxide (ITO)/pin/pii/Al structure with thin intrinsic absorbing layers consisting of zinc-phthalocyanine and fullerene C60 and a metal-free lossless recombination contact between the subcells. By keeping the thickness of the absorbing layers constant and changing only the thickness of the inner p-doped transparent layer in 16 steps from 0to186nm, the distance of the ITO-sided subcell from the reflecting electrode (Al) is systematically varied. Thus, the p-doped layer works as an optical spacer between both subcells. The influence of its thickness on the thin film optics is shown in optical simulations and confirmed with current-voltage measurements. If both subcells are separated only by the recombination contact, they are positioned in the first interference maximum of the incident light and the currents of the individual subcells nearly matches. By increasing the spacer layer thickness, the ITO-sided subcell is moved to the first interference minimum, limiting the measured short circuit current density jsc of the tandem solar cell to about 1/2 of its initial value without spacer. At a spacer thickness of about 140nm, jsc recovers in the second interference maximum to nearly its original value. Within this series, an almost constant high fill factor of about 59% as well as a constant open circuit voltage of 1.06V is observed, showing that the Ohmic losses in the spacer are negligible. The power conversion efficiency of these devices reaches nearly 4% in the first and approximately 3.6% in the second interference maximum, respectively, in an outdoor test at 1sun. Furthermore, it is shown that for thicker absorber layers, an optimized current density cannot be reached in the first

  4. Dual routes for verbal repetition: articulation-based and acoustic-phonetic codes for pseudoword and word repetition, respectively.

    PubMed

    Yoo, Sejin; Chung, Jun-Young; Jeon, Hyeon-Ae; Lee, Kyoung-Min; Kim, Young-Bo; Cho, Zang-Hee

    2012-07-01

    Speech production is inextricably linked to speech perception, yet they are usually investigated in isolation. In this study, we employed a verbal-repetition task to identify the neural substrates of speech processing with two ends active simultaneously using functional MRI. Subjects verbally repeated auditory stimuli containing an ambiguous vowel sound that could be perceived as either a word or a pseudoword depending on the interpretation of the vowel. We found verbal repetition commonly activated the audition-articulation interface bilaterally at Sylvian fissures and superior temporal sulci. Contrasting word-versus-pseudoword trials revealed neural activities unique to word repetition in the left posterior middle temporal areas and activities unique to pseudoword repetition in the left inferior frontal gyrus. These findings imply that the tasks are carried out using different speech codes: an articulation-based code of pseudowords and an acoustic-phonetic code of words. It also supports the dual-stream model and imitative learning of vocabulary. PMID:22632812

  5. Experimental and clinical studies on dose reduction effects of spacers in interstitial brachytherapy for carcinoma of the mobile tongue.

    PubMed

    Fujita, M; Tamamoto, M; Hirokawa, Y; Kashiwado, K; Akagi, Y; Kashimoto, K; Wada, T

    1993-12-01

    The difference of radiation dose reduction effect with spacers of different materials, a heat-curing denture base resin and a silicon impression material, was examined experimentally and clinically. Radium needles and iridium hairpins were used as radioactive sources. In both studies, it was revealed that a dose reduction effect of silicon impression material was greater than that of denture base resin. Silicon impression material was thought to be a better material for spacers because of its larger radiation dose reduction effect and the time saving to produce the spacer. PMID:8284088

  6. Comparison of conventional paint-on die spacers and those used with the all-ceramic restorations.

    PubMed

    Campbell, S D

    1990-02-01

    The study compared the thickness of conventional (Tru-Fit and Belle de St. Claire) and all-ceramic (Dicor and Cerestore) die spacers. Three coats of Tru-Fit, two coats of Belle de St. Claire, and two coats of Cerestore die spacers provided a 25 microns thickness. A single coat of the Dicor spacer resulted in a 37 microns layer. A significantly thinner layer occurred at the convex occlusal line angles for all of the materials tested. This could impede the flow of the luting agent at the time of cementation. PMID:2406424

  7. Effect of spacer layer on the magnetization dynamics of permalloy/rare-earth/permalloy trilayers

    SciTech Connect

    Luo, Chen Yin, Yuli; Zhang, Dong; Jiang, Sheng; Yue, Jinjin; Zhai, Ya; Du, Jun; Zhai, Hongru

    2015-05-07

    The permalloy/rare-earth/permalloy trilayers with different types (Gd and Nd) and thicknesses of spacer layer are investigated using frequency dependence of ferromagnetic resonance (FMR) measurements at room temperature, which shows different behaviors with different rare earth spacer layers. By fitting the frequency dependence of the FMR resonance field and linewidth, we find that the in-plane uniaxial anisotropy retains its value for all samples, the perpendicular anisotropy remains almost unchanged for different thickness of Gd layer but the values are tailored by different thicknesses of Nd layer. The Gilbert damping is almost unchanged with different thicknesses of Gd; however, the Gilbert damping is significantly enhanced from 8.4×10{sup −3} to 20.1×10{sup −3} with 6 nm of Nd and then flatten out when the Nd thickness rises above 6 nm.

  8. Effect of GFRP spacer on local deformation of large superconductor in coil pack

    NASA Astrophysics Data System (ADS)

    Nishimura, Arata; Tamura, Hitoshi; Mito, Toshiyuki; Yamamoto, Junya

    1994-07-01

    Local deformation in a large superconductor caused by GFRP (glass fiber reinforced plastic) spacers and epoxy adhesives was investigated after compressive rigidity testing. The epoxy adhesive used for attaching the GFRP spacers to the superconductor changed shape from an almost square sheet into a lens-like sheet during deformation, and a dent appeared on the surface of the superconductor. Three-dimensional FEM (finite element method) analysis showed that a compressive stress in the vertical direction of the loading axis existed in the adhesive plane. This stress component makes the adhesive lens-like and it results in the dent created during the compressive testing. This local deformation should yield a part of the permanent deformation observed after the compressive load cycle at 4.2 K.

  9. Metagenomic data of fungal internal transcribed spacer from serofluid dish, a traditional Chinese fermented food

    PubMed Central

    Chen, Peng; Zhao, Yang; Wu, Zhengrong; Liu, Ronghui; Xu, Ruixiang; Yan, Lei; Li, Hongyu

    2015-01-01

    Serofluid dish (or Jiangshui, in Chinese), a traditional food in the Chinese culture for thousands of years, is made from vegetables by fermentation. In this work, microorganism community of the fermented serofluid dish was investigated by the culture-independent method. The metagenomic data in this article contains the sequences of fungal internal transcribed spacer (ITS) regions of rRNA genes from 12 different serofluid dish samples. The metagenome comprised of 50,865 average raw reads with an average of 8,958,220 bp and G + C content is 45.62%. This is the first report on metagenomic data of fungal ITS from serofluid dish employing Illumina platform to profile the fungal communities of this little known fermented food from Gansu Province, China. The Metagenomic data of fungal internal transcribed spacer can be accessed at NCBI, SRA database accession no. SRP067411. PMID:26981389

  10. An embedded nonvolatile memory cell with spacer floating gate for power management integrated circuit applications

    NASA Astrophysics Data System (ADS)

    Na, Kee-Yeol; Baek, Ki-Ju; Lee, Gun-Woong; Kim, Yeong-Seuk

    2013-08-01

    This paper describes a simple nonvolatile memory cell with a poly-Si spacer floating gate for power management integrated circuit applications. The proposed memory cell is fabricated using a 0.35 μm double-poly high-voltage CMOS process which includes PIP capacitor, LV (5 V), and HV (20 V) CMOS devices. The floating gates of the proposed cell are buried under a LDD spacer oxide; thus the unit cell can be scaled easily in the channel length direction. In addition, any extra photo masking step is not required for the proposed cell in the applied fabrication process. The proposed cell shows an acceptable threshold voltage window of up to 104 cycles and less than 2% threshold voltage shifts in an 85 °C retention test.

  11. Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein.

    PubMed

    Silas, Sukrit; Mohr, Georg; Sidote, David J; Markham, Laura M; Sanchez-Amat, Antonio; Bhaya, Devaki; Lambowitz, Alan M; Fire, Andrew Z

    2016-02-26

    CRISPR systems mediate adaptive immunity in diverse prokaryotes. CRISPR-associated Cas1 and Cas2 proteins have been shown to enable adaptation to new threats in type I and II CRISPR systems by the acquisition of short segments of DNA (spacers) from invasive elements. In several type III CRISPR systems, Cas1 is naturally fused to a reverse transcriptase (RT). In the marine bacterium Marinomonas mediterranea (MMB-1), we showed that a RT-Cas1 fusion protein enables the acquisition of RNA spacers in vivo in a RT-dependent manner. In vitro, the MMB-1 RT-Cas1 and Cas2 proteins catalyze the ligation of RNA segments into the CRISPR array, which is followed by reverse transcription. These observations outline a host-mediated mechanism for reverse information flow from RNA to DNA. PMID:26917774

  12. Synthesis of photoresponsive cholesterol-based azobenzene organogels: dependence on different spacer lengths.

    PubMed

    Ren, Yuchun; Wang, Bin; Zhang, Xiuqing

    2015-01-01

    A series of azobenzene-cholesterol organogel compounds (M 0 -M 12 ) with different spacers were designed and synthesized. The molecular structures were confirmed by (1)H NMR and (13)C NMR spectroscopy. The rapid and reversible photoresponsive properties of the compounds were investigated by UV-vis spectroscopy. Their thermal phase behaviors were studied by DSC. The length of the spacer plays a crucial role in the gelation. Compound M 6 is the only one that can gelate in ethanol, isopropanol and 1-butanol and the reversible gel-sol transitions are also investigated. To obtain visual insight into the microstructure of the gels, the typical structures of the xerogels were studied by SEM. Morphologies of the aggregates change from flower-like, network and rod with different sizes. By using IR and XRD characterization, it is found that intermolecular H-bonding, the solvents and van der Waals interaction are the main contributions to the specific superstructure. PMID:26199664

  13. Novel Capacitor Structure Using Sidewall Spacer for Highly Reliable Ferroelectric Random Access Memory Device

    NASA Astrophysics Data System (ADS)

    Kim, Hyun-Ho; Park, Jung-Hoon; Song, Yoon-Jong; Jang, Nak-Won; Joo, Heung-Jin; Kang, Seung-Kuk; Joo, Seok-Ho; Lee, Sung-Young; Kim, Kinam

    2004-04-01

    Since ferroelectric capacitors prepared by 1-mask etching are degraded after the etching, we systematically investigated the origin of the degradation. It was found that the major degradation originates from the formation of the nonstoichiometric and amorphorized Pb(ZrxTi1-x)O3 (PZT) layer on the sidewall of the PZT film during etching of the bottom electrode (BE). Therefore, to eliminate the undesired etch-damaged layer, we developed a novel etching technology using a ferroelectric (FE) sidewall spacer, which results in the enhancement of the remnant polarization after completing the capacitor etching process. Using the novel FE sidewall spacer, the sensing margin of bit-line-developed voltage was improved to 400 mV, which can guarantee highy reliable high-density ferroelectric random access memory (FRAM) devices.

  14. Synthesis, Characterization and Biological Studies of New Linear Thermally Stable Schiff Base Polymers with Flexible Spacers.

    PubMed

    Qureshi, Farah; Khuhawar, Muhammad Yar; Jahangir, Taj Muhammad; Channar, Abdul Hamid

    2016-01-01

    Five new linear Schiff base polymers having azomethine structures, ether linkages and extended aliphatic chain lengths with flexible spacers were synthesized by polycondensation of dialdehyde (monomer) with aliphatic and aromatic diamines. The formation yields of monomer and polymers were obtained within 75-92%. The polymers with flexible spacers of n-hexane were somewhat soluble in acetone, chloroform, THF, DMF and DMSO on heating. The monomer and polymers were characterized by melting point, elemental microanalysis, FT-IR, (1)HNMR, UV-Vis spectroscopy, thermogravimetry (TG), differential thermal analysis (DTA), fluorescence emission, scanning electron microscopy (SEM) and viscosities and thermodynamic parameters measurements of their dilute solutions. The studies supported formation of the monomer and polymers and on the basis of these studies their structures have been assigned. The synthesized polymers were tested for their antibacterial and antifungal activities. PMID:26970795

  15. Metagenomic data of fungal internal transcribed spacer from serofluid dish, a traditional Chinese fermented food.

    PubMed

    Chen, Peng; Zhao, Yang; Wu, Zhengrong; Liu, Ronghui; Xu, Ruixiang; Yan, Lei; Li, Hongyu

    2016-03-01

    Serofluid dish (or Jiangshui, in Chinese), a traditional food in the Chinese culture for thousands of years, is made from vegetables by fermentation. In this work, microorganism community of the fermented serofluid dish was investigated by the culture-independent method. The metagenomic data in this article contains the sequences of fungal internal transcribed spacer (ITS) regions of rRNA genes from 12 different serofluid dish samples. The metagenome comprised of 50,865 average raw reads with an average of 8,958,220 bp and G + C content is 45.62%. This is the first report on metagenomic data of fungal ITS from serofluid dish employing Illumina platform to profile the fungal communities of this little known fermented food from Gansu Province, China. The Metagenomic data of fungal internal transcribed spacer can be accessed at NCBI, SRA database accession no. SRP067411. PMID:26981389

  16. Enhanced spin-torque in double tunnel junctions using a nonmagnetic-metal spacer

    SciTech Connect

    Chen, C. H.; Cheng, Y. H.; Ko, C. W.; Hsueh, W. J.

    2015-10-12

    This study proposes an enhancement in the spin-transfer torque of a magnetic tunnel junction (MTJ) designed with double-barrier layer structure using a nonmagnetic metal spacer, as a replacement for the ferromagnetic material, which is traditionally used in these double-barrier stacks. Our calculation results show that the spin-transfer torque and charge current density of the proposed double-barrier MTJ can be as much as two orders of magnitude larger than the traditional double-barrier one. In other words, the proposed double-barrier MTJ has a spin-transfer torque that is three orders larger than that of the single-barrier stack. This improvement may be attributed to the quantum-well states that are formed in the nonmagnetic metal spacer and the resonant tunneling mechanism that exists throughout the system.

  17. Place field repetition and spatial learning in a multicompartment environment

    PubMed Central

    Grieves, Roddy M.; Jenkins, Bryan W.; Harland, Bruce C.

    2015-01-01

    Abstract Recent studies have shown that place cells in the hippocampus possess firing fields that repeat in physically similar, parallel environments. These results imply that it should be difficult for animals to distinguish parallel environments at a behavioral level. To test this, we trained rats on a novel odor‐location task in an environment with four parallel compartments which had previously been shown to yield place field repetition. A second group of animals was trained on the same task, but with the compartments arranged in different directions, an arrangement we hypothesised would yield less place field repetition. Learning of the odor‐location task in the parallel compartments was significantly impaired relative to learning in the radially arranged compartments. Fewer animals acquired the full discrimination in the parallel compartments compared to those trained in the radial compartments, and the former also required many more sessions to reach criterion compared to the latter. To confirm that the arrangement of compartments yielded differences in place cell repetition, in a separate group of animals we recorded from CA1 place cells in both environments. We found that CA1 place cells exhibited repeated fields across four parallel local compartments, but did not do so when the same compartments were arranged radially. To confirm that the differences in place field repetition across the parallel and radial compartments depended on their angular arrangement, and not incidental differences in access to an extra‐maze visual landmark, we repeated the recordings in a second set of rats in the absence of the orientation landmark. We found, once again, that place fields showed repetition in parallel compartments, and did not do so in radially arranged compartments. Thus place field repetition, or lack thereof, in these compartments was not dependent on extra‐maze cues. Together, these results imply that place field repetition constrains spatial learning

  18. Similarity Grouping and Repetition Blindness are Both Influenced by Attention

    PubMed Central

    de Haan, Bianca; Rorden, Chris

    2009-01-01

    Previous studies have reported seemingly conflicting results regarding how the amount of stimulus similarity between two simultaneously presented target stimuli impacts perceptual performance. There are many reports of ‘repetition blindness’, where individuals do worse when shown two similar stimuli relative to two different stimuli. On the other hand, there are reports of ‘similarity grouping’, where participants perform better when identifying two similar objects relative to two different objects. This manuscript posits that repetition blindness and similarity grouping coexist and can be elicited in the same subjects in a single task. This not only explains the previous opposite effects of stimulus similarity on task performance, but also provides a unique opportunity to directly compare these opposite effects of stimulus similarity with respect to susceptibility to a modulating factor. Since previous studies have provided inconclusive results on whether attentional relevance can modulate the effect of stimulus similarity on task performance, the current manuscript aims to compare repetition blindness and similarity grouping with respect to their susceptibility to attentional relevance. The results of the first experiment confirmed that both repetition blindness and similarity grouping can be elicited in the same experiment, suggesting that repetition blindness and similarity grouping coexist. The results of the second experiment suggest that both repetition blindness and similarity grouping can be modulated by attentional relevance. These results support the explanation of repetition blindness as a token individuation failure. Furthermore, these results suggest that supposedly pre-attentional grouping mechanisms might not operate as independently from top-down attentional modulations as traditionally thought. PMID:20300466

  19. Repetitive sequences: the hidden diversity of heterochromatin in prochilodontid fish

    PubMed Central

    Terencio, Maria L.; Schneider, Carlos H.; Gross, Maria C.; do Carmo, Edson Junior; Nogaroto, Viviane; de Almeida, Mara Cristina; Artoni, Roberto Ferreira; Vicari, Marcelo R.; Feldberg, Eliana

    2015-01-01

    Abstract The structure and organization of repetitive elements in fish genomes are still relatively poorly understood, although most of these elements are believed to be located in heterochromatic regions. Repetitive elements are considered essential in evolutionary processes as hotspots for mutations and chromosomal rearrangements, among other functions – thus providing new genomic alternatives and regulatory sites for gene expression. The present study sought to characterize repetitive DNA sequences in the genomes of Semaprochilodus insignis (Jardine & Schomburgk, 1841) and Semaprochilodus taeniurus (Valenciennes, 1817) and identify regions of conserved syntenic blocks in this genome fraction of three species of Prochilodontidae (Semaprochilodus insignis, Semaprochilodus taeniurus, and Prochilodus lineatus (Valenciennes, 1836) by cross-FISH using Cot-1 DNA (renaturation kinetics) probes. We found that the repetitive fractions of the genomes of Semaprochilodus insignis and Semaprochilodus taeniurus have significant amounts of conserved syntenic blocks in hybridization sites, but with low degrees of similarity between them and the genome of Prochilodus lineatus, especially in relation to B chromosomes. The cloning and sequencing of the repetitive genomic elements of Semaprochilodus insignis and Semaprochilodus taeniurus using Cot-1 DNA identified 48 fragments that displayed high similarity with repetitive sequences deposited in public DNA databases and classified as microsatellites, transposons, and retrotransposons. The repetitive fractions of the Semaprochilodus insignis and Semaprochilodus taeniurus genomes exhibited high degrees of conserved syntenic blocks in terms of both the structures and locations of hybridization sites, but a low degree of similarity with the syntenic blocks of the Prochilodus lineatus genome. Future comparative analyses of other prochilodontidae species will be needed to advance our understanding of the organization and evolution of

  20. Molecular phylogenetic studies on filarial parasites based on 5S ribosomal spacer sequences.

    PubMed

    Xie, H; Bain, O; Williams, S A

    1994-06-01

    This paper is the first large-scale molecular phylogenetic study on filarial parasites (family Onchocercidae) which includes 16 species of 6 genera: Brugia beaveri Ash et Little, 1962, B. buckleyi Dissanaike et Paramananthan, 1961; B. malayi (Brug, 1927) Buckley, 1960; B. pahangi (Buckley et Edeson, 1956) Buckley, 1960; B. patei (Buckley, Nelson et Heisch, 1958) Buckley, 1960; B. timori Partono et al, 1977; Wuchereria bancrofti (Cobbold, 1877) Seurat, 1921: W. kalimantani Palmieri. Purnomo, Dennis and Marwoto, 1980: Mansonella perstans (Manson, 1891) Eberhard et Orihel, 1984; loa loc, Stiles, 1905; Onchocerca volvulus (Leuckart, 1983) Railliet er Henry, 1910; O. ochengi Bwangamoi, 1969; O. gutturosa Neumann, 1910; Dirofilaria immitis (Leidy, 1856) Railliet e Henry, 1911; Acanthocheilonema viteae (Krepkogorskaya, 1933) Bain, Baker et Chabaud, 1982 and Litomosoides sigmodontis Chandler, 1931. 5S rRNA gene spacer region sequence data were collected by PCR, cloning and dideoxy sequencing. The 5S rRNA gene spacer region sequences were aligned and analyzed by maximum parsimony algorithms, distance methods and maximum likelihood methods to construct phylogenetic trees. Bootstrap analysis was used to test the robustness of the different phylogenetic reconstructions. The data indicated that 5S spacer region sequences are highly conserved within species yet differ significantly between species. Spliced leader sequences were observed in all of the 5S rDNA spacers with no sequence variation, although flanking region sequence and length heterogeneity was observed even within species. All of the various tree-building methods gave very similar results. This study identified four clades which are strongly supported by bootstrap analysis the Brugia clade; the Wuchereria clade; the Brugia-Wuchereria clade and the Onchocerca clade. The analyses indicated that L. sigmodontis and A. viteae may be the most primitive among the 16 species studied. The data did not show any close

  1. Modified Open-Door Laminoplasty Using a Ceramic Spacer and Suture Fixation for Cervical Myelopathy

    PubMed Central

    Toyone, Tomoaki; Shiboi, Ryutaro; Inada, Kunimasa; Oikawa, Yasuhiro; Takahashi, Kazuhisa; Ohtori, Seiji; Inoue, Gen; Miyagi, Masayuki; Ishikawa, Tetsuhiro; Shirahata, Toshiyuki; Kudo, Yoshifumi; Inagaki, Katsunori

    2015-01-01

    Purpose To introduce a new simple technique using suture anchors and ceramic spacers to stabilize the elevated laminae in open-door cervical laminoplasty. Although ceramic spacers were placed in the opened laminae and fixed with nylon threads in this series, it was occasionally difficult to fix the nylon threads to the lateral mass. Materials and Methods Study 1: A preliminary study was conducted using a suture anchor system. Sixteen consecutive patients who underwent surgery for cervical myelopathy were prospectively examined. Study 2: The second study was performed prospectively to evaluate the feasibility of this new technique based on the result of the preliminary study. Clinical outcomes were examined in 45 consecutive patients [cervical spondylotic myelopathy (CSM)] and 43 consecutive patients (OPLL). The Japanese Orthopedic Association scoring system (JOA score), axial neck pain, and radiological findings were analyzed. Results 1) In one case, re-operation was necessary due to dislodgement of the ceramic spacer following rupture of the thread. 2) In all patients, postoperative CT scans showed that the anchors were securely inserted into the bone. In the CSM group, the average JOA score improved from 9.5 points preoperatively to 13.3 at follow-up (recovery 51%). In the OPLL group, the average JOA score improved from 10.1 (5-14) points preoperatively to 14.4 (11-16) at follow-up (recovery 62%). There were no serious complications. Conclusion The use of the suture anchor system made it unnecessary to create a hole in the lateral mass and enabled reliable and faster fixation of the HA spacers in open-door laminoplasty. PMID:26446650

  2. A new class of pseudopeptide antagonists of the kinin B1 receptor containing alkyl spacers.

    PubMed

    Galoppini, C; Meini, S; Tancredi, M; Di Fenza, A; Triolo, A; Quartara, L; Maggi, C A; Formaggio, F; Toniolo, C; Mazzucco, S; Papini, A; Rovero, P

    1999-02-11

    Four previously reported kinin receptor peptide antagonists, including the B1 receptor-selective peptides desArg10-HOE 140 (H-D-Arg-Arg-Pro-Hyp-Gly-Thi-Ser-D-Tic-Oic-OH) and B-9858 (H-Lys-Lys-Arg-Pro-Hyp-Gly-Igl-Ser-D-Igl-Oic-OH), have been modified by replacement of the central tetrapeptide Pro-Hyp-Gly-Xaa with linear alkyl spacers of variable length. The analogue of desArg10-HOE 140 containing the 11-aminoundecanoic acid as spacer, MEN 11575 [H-D-Arg-Arg-NH-(CH2)10-CO-Ser-D-Tic-Oic-OH], was found to be slightly more potent than the unmodified peptide (pA2 = 7.1) as a kinin B1 receptor antagonist in the rat ileum longitudinal smooth muscle assay. Moreover, MEN 11575 is devoid of residual agonist activity at the kinin B1 receptor (rat ileum) and antagonist activity at the kinin B2 receptor (guinea pig ileum longitudinal smooth muscle). Both these activities are displayed by the parent peptide desArg10-HOE 140. Therefore, despite its greatly simplified chemical structure, MEN 11575 shows an improved pharmacological profile in terms of both potency and selectivity, and it represents a good template for the development of new peptidomimetic kinin B1 receptor antagonists. We also report an attempt to investigate the conformational role of the flexible, linear spacer of MEN 11575 and to design more constrained analogues, possibly locked in the bioactive conformation, using semirigid spacers based on Calpha-tetrasubstituted alpha-amino acids of the family of 1-aminocycloalkane-1-carboxylic acids (Acnc). PMID:9986712

  3. Effect of siloxane spacer length on organosilicon bi-quaternary ammonium amphiphiles.

    PubMed

    Hao, Chuanming; Cui, Yuezhi; Yang, Pengfei; Zhang, Huayong; Mao, Dejiang; Cui, Xiao; Li, Junying

    2015-04-01

    A series of organosilicon Bola-form bi-quaternary ammonium amphiphiles, [OH5C3(C2H5)2N+-(CH2)3-Si(CH2)3-O-(Si(CH3)2O)n-Si(CH2)3⋯(CH2)3-N+(C2H5)2C3H5O]Cl2- (SinN2Cl2, n=0, 4, 6, 8), with the same headgroups and different length of hydrophobic linkage has been synthesized. The critical micelle concentration (CMC) of each amphiphiles was determined by equilibrium surface tension. With the increased length of hydrophobic siloxane spacer, the CMC values follow the order of Si8N2Cl2spacer and its internal oxygen atom, which make the molecular stretch free. The antimicrobial property of Si4N2Cl2 is more effective than others below the concentration of CMC, while the antimicrobial property of Si8N2Cl2 is more effective above the concentration of CMC, which indicated that both the adsorbability in formation of micellar and the hydrophobicity arising from the different length of siloxane spacer are important to inhibit microbe. Moreover, their wetting ability has been characterized by contact angles on various material surfaces. It shows that the higher weight of lipophilic siloxane spacer leads to lower contact angels. PMID:25794442

  4. Accuracy of Different Putty-Wash Impression Techniques with Various Spacer Thickness

    PubMed Central

    Arora, Aman; Singh, Vijay Pratap

    2012-01-01

    ABSTRACT One of the most important steps is accurate impression making for fabrication of fixed partial denture. The two different putty-wash techniques that are commonly used are: (1) Putty-wash one-step technique, (2) putty-wash two-step technique. A uniform wash space is needed for an accurate impression. Nissan et al recommended the use of two-step technique for accurate impression making as there is uniform wash space for the light body material to polymerize. The aim of the present study was to compare the accuracy of stone casts obtained from different putty-wash impression techniques using various spacer thickness. The critical factor that influences the accuracy of putty-wash impression techniques is the controlled wash bulk which is absent in one-step putty-wash impression technique and with polyethylene spacer was used. How to cite this article: Chugh A, Arora A, Singh VP. Accuracy of Different Putty-Wash Impression Techniques with Various Spacer Thickness. Int J Clin Pediatr Dent 2012;5(1):33-38. PMID:25206132

  5. PEG as a spacer arm markedly increases the immunogenicity of meningococcal group Y polysaccharide conjugate vaccine.

    PubMed

    Huang, Qingrui; Li, Dongxia; Kang, Aijun; An, Wenqi; Fan, Bei; Ma, Xiaowei; Ma, Guanghui; Su, Zhiguo; Hu, Tao

    2013-11-28

    Neisseria meningitidis is a life-threatening pathogen that causes meningitis and other clinical manifestations. As a key virulence determinant, meningococcal capsular polysaccharide (PS) can be used to prevent meningococcal diseases. Conjugation of PS to carrier protein can significantly improve the immunogenicity of PS and induce memory response in infants and young children. However, the conjugate vaccine may suffer from steric shielding of antigenic PS epitopes by carrier protein. Here, a heterobifunctional polyethylene glycol (PEG) was used as a spacer arm to conjugate meningococcal group Y capsular PS with tetanus toxoid (TT). PEG can avoid self-crosslink of PS and increase the PS/TT ratio of the vaccine. Significant structural change in TT and PS was not observed upon conjugation. As compared to the vaccine without PEG, immunization with the vaccine using PEG as the spacer arm led to a 3.0-fold increase in the PS-specific IgG titers and a prolonged immune persistence. Paradoxically, PEG, a non-immunogenic hydrophilic polymer has been widely used to couple therapeutic protein for increasing its circulatory time and decreasing its immunogenicity. Presumably, PEG can fully decrease the steric shielding effect of TT on antigenic epitopes of PS and suppress the immunogenicity of TT. In addition, PEG can prolong the immune persistence of the conjugate vaccine and improve its ability to elicit cellular immunity. Thus, PEG can be used as a spacer arm to develop more effective PS conjugate vaccine for prevention of bacterial infection. PMID:23511718

  6. Plane wave scattering from a plasmonic nanowire array spacer-separated from a plasmonic film

    NASA Astrophysics Data System (ADS)

    Thomas, Arun; Trivedi, Rahul; Dhawan, Anuj

    2016-06-01

    In this paper, we present a theoretical analysis of the electromagnetic response of a plasmonic nanowire–spacer–plasmonic film system. The analytical solution presented in this paper is a full-wave solution, which is used to compute the fields scattered by the plasmonic nanostructure system on illumination by a plane electromagnetic wave. The physical structure comprises of an array of plasmonic nanowires made of a plasmonic metal such as gold or silver placed over a plasmonic film of the same material and separated from it by a dielectric spacer such as silica or alumina. Such a nanostructure exhibits a spectrum that is extremely sensitive to various geometric and electromagnetic parameters such as spacer thickness and spacer refractive index, which makes it favourable for various sensing applications such as chemical and biological sensing, strain sensing, position sensing, vibration sensing, and thickness sensing. We report a comparison of our analytical solution with a numerical rigorous coupled wave analysis of the same structure with the plasmonic medium being treated as local in nature.

  7. Production of high resistivity water by electrodialysis. Influence of ion-exchange textiles as conducting spacers

    SciTech Connect

    Laktionov, E.; Dejean, E.; Sandeaux, J.; Sandeaux, R.; Gavach, C.; Pourcelly, G.

    1999-01-01

    Production of high resistivity water was investigated by electrodialysis (ED) using either inert or conducting spacers. Ion-exchange textiles were used as conducting spacers. Experiments were performed on a preindustrial scale with a pilot consisting of nine two-compartment cells, each membrane having an effective area of 176 cm{sup 2}. Three configurations of the ED stack were investigated for the dilution compartment: EDIT-(2) with a 2-mm thick ion-exchange textile, and ED-(2) or ED-(0.4), with a 0.4-mm thick inert spacer inserted between 2 or 0.4 mm thick dilution compartments, respectively. The textile induces a moderate increase in the pressure drop between the inlet and outlet of the stack. The performances of the different processes were compared under various experimental conditions of pH, nitrogen bubbling throughout the feed solution, flow rate, and current density. The results show that for an inlet conductivity of 10--15 {micro}S/cm, a flow rate of 2.2 {times} 10{sup {minus}5} m{sup 3}/s, and an applied voltage of 80 V, an outlet conductivity of 0.4 {micro}S/cm was obtained with the EDIT process, while no value lower than 5 {micro}S/cm was obtained with the ED process using both stacks.

  8. Effects of water-soluble spacers on the hydrophobic association of fluorocarbon modified polyacrylamide

    SciTech Connect

    Hwang, F.S.; Hogen-Esch, T.E.

    1993-12-31

    A number of acrylamide-acrylate copolymers were synthesized in which the acrylate (CH{sub 2}=CHCOO(CH{sub 2}CH{sub 2}O){sub n}R{sub t}) is hydrophobic on account of the presence of a 1,1-dihydroperfluorooctyl group (R{sub F}) connected to the acrylate via a-(CH{sub 2}CH{sub 2}O){sub n} hydrophobic spacer (n=0-3). Copolymerization of the two comonomers was carried out in aqueous media in the presence of potassium perfluoro octanoate and acetone (10 vol%) and was initiated by sodium metabisufite and ammonium persulfate at 50{degrees}C. The Brookfield viscosities measured at 0.4 sec{sup {minus}1} as a function of comonomer molar content gave bell-shaped curves having maxima at .10-.15 mole% comonomer except for the comonomer without hydrophilic spacer (n=0) where the maximum is at .60 mole%. The viscosity maxima of the copolymers are quite dependent on the value of n giving the highest viscosities at n=3 (45,000 cp) that decreases value of n. The increased effectiveness of the longer spacers is attributed to decreased intermolecular excluded volume effects in the formation of the polymer assemblies.

  9. Spacer multi-patterning control strategy with optical CD metrology on device structures

    NASA Astrophysics Data System (ADS)

    Lee, Jongsu; Lee, Byoung-Hoon; Ma, Won-Kwang; Han, Sang-Jun; Kim, Young-Sik; Kwak, Noh-Jung; Theeuwes, Thomas; Guo, Wei; Song, Yi; Wisse, Baukje; Kruijswijk, Stefan; Cramer, Hugo; Welch, Steven; Verma, Alok; Zhang, Rui; Chai, Yvon; Hsu, Sharon; Miceli, Giacomo; Sun, Kyu-Tae; Byun, Jin-Moo

    2016-03-01

    Spacer multi patterning process continues to be a key enabler of future design shrinks in DRAM and NAND process flows. Improving Critical Dimension Uniformity (CDU) for main features remains high priority for multi patterning technology and requires improved metrology and control solutions. In this paper Spacer Patterning Technology is evaluated using an angle resolved scatterometry tool for both intra field control of the core CD after partition etch (S1) and interfield pitch-walking control after final etch (S1-S2). The intrafield measurements were done directly on device using dense sampling. The inter-field corrections were based on sparse full wafer measurements on biased OCD targets. The CDU improvement after partition-etch was verified by direct scatterometer and CD-SEM measurement on device. The final etch performance across wafer was verified with scatterometer on OCD target. The scatterometer metrology in combination with the control strategy demonstrated a consistent CDU improvement of core (S1) intrafield CD after partition etch between 23-39% and 47-53% on interfield pitch-walking (S1-S2) after final etch. To confirm these improvements with CD-SEM, oversampling of more than 16 times is needed compared to scatterometer. Based on the results it is concluded that scatterometry in combination with the evaluated metrology and control strategy in principle qualifies for a spacer process CDU control loop in a manufacturing environment.

  10. Design, synthesis and hydrolytic behavior of mutual prodrugs of NSAIDs with gabapentin using glycol spacers.

    PubMed

    Mahdi, Monther Faisal; Alsaad, Hiba Najeh

    2012-01-01

    The free –COOH present in NSAIDs is thought to be responsible for the GI irritation associated with all traditional NSAIDs. Exploitation of mutual prodrugs is an approach wherein the NSAID is covalently bounded to a second pharmacologically active carrier/drug with the ultimate aim of reducing the gastric irritation. In this study some NSAIDs were conjugated with gabapentin via ester bonds using glycol spacers with the expectation of reducing gastric adverse effects and obtaining synergistic analgesic effects. The kinetics of ester hydrolysis were studied in two different non enzymatic buffer solutions at pH 1.2 and 7.4, as well as in 80% human plasma using HPLC with chloroform -methanol as mobile phase. Compounds 9a–c with ethylene glycol spacers showed significant stability at buffer solutions with half lives ranging from about 8–25 h, while the underwent a reasonable plasma hydrolysis (49%–88%) in 2 h. Compound 9d with a propylene glycol spacer shows a higher rate of enzymatic hydrolysis than the corresponding ethylene glycol compound 9c. The result of compounds 9a-c indicate that these compounds may be stable during their passage through the GIT until reaching the blood circulation. PMID:24281258

  11. Adsorption studies of divalent, dinuclear coordination complexes as molecular spacers on SWCNTs.

    PubMed

    Alston, Jeffrey R; Banks, David J; McNeill, Chauncey X; Mitchell, James B; Popov, Leonid D; Shcherbakov, Igor N; Poler, J C

    2015-11-28

    In order to enhance the electrical energy storage capabilities of nanostructured carbon materials, inter-particle spacer strategies are needed to maintain ion-accessible surface area between the nanoparticles. This paper presents a comparison between different classes of divalent, dinuclear coordination complexes which both show strong adsorption to SWCNTs and have molecular spacer properties that maintain electrochemical activity. We find that a novel, dinuclear zinc hydrazone complex binds as an ion-pair at very high loading while not inducing significant aggregation as compared to our previously studies of dinuclear ruthenium complexes. These conclusions are supported by conductivity and dispersion stability data. Moreover, since zinc is an earth abundant metal, these complexes can be used as components in sustainable energy storage materials. Binding kinetics and binding equilibrium data are presented. Modeling of the adsorption isotherm is best fit with the BET model. Kinetics data support an independent binding model. Preliminary capacitance and membrane resistance data are consistent with the complexes acting as molecular spacers between the SWCNTs in a condensed thin film. PMID:26457656

  12. Design, Synthesis and Hydrolytic Behavior of Mutual Prodrugs of NSAIDs with Gabapentin Using Glycol Spacers

    PubMed Central

    Mahdi, Monther Faisal; Alsaad, Hiba Najeh

    2012-01-01

    The free –COOH present in NSAIDs is thought to be responsible for the GI irritation associated with all traditional NSAIDs. Exploitation of mutual prodrugs is an approach wherein the NSAID is covalently bounded to a second pharmacologically active carrier/drug with the ultimate aim of reducing the gastric irritation. In this study some NSAIDs were conjugated with gabapentin via ester bonds using glycol spacers with the expectation of reducing gastric adverse effects and obtaining synergistic analgesic effects. The kinetics of ester hydrolysis were studied in two different non enzymatic buffer solutions at pH 1.2 and 7.4, as well as in 80% human plasma using HPLC with chloroform -methanol as mobile phase. Compounds 9a–c with ethylene glycol spacers showed significant stability at buffer solutions with half lives ranging from about 8–25 h, while the underwent a reasonable plasma hydrolysis (49%–88%) in 2 h. Compound 9d with a propylene glycol spacer shows a higher rate of enzymatic hydrolysis than the corresponding ethylene glycol compound 9c. The result of compounds 9a-c indicate that these compounds may be stable during their passage through the GIT until reaching the blood circulation. PMID:24281258

  13. Binding of 12-s-12 dimeric surfactants to calf thymus DNA: Evaluation of the spacer length influence.

    PubMed

    Sarrión, Beatriz; Bernal, Eva; Martín, Victoria Isabel; López-López, Manuel; López-Cornejo, Pilar; García-Calderón, Margarita; Moyá, María Luisa

    2016-08-01

    Several cationic dimeric surfactants have shown high affinity towards DNA. Bis-quaternary ammonium salts (m-s-m) have been the most common type of dimeric surfactants investigated and it is generally admitted that those that posses a short spacer (s≤3) show better efficiency to bind or compact DNA. However, experimental results in this work show that 12-s-12 surfactants with long spacers make the surfactant/ctDNA complexation more favorable than those with short spacers. A larger contribution of the hydrophobic interactions, which control the binding Gibbs energy, as well as a higher average charge of the surfactant molecules bound to the nucleic acid, which favors the electrostatic attractions, could explain the experimental observations. Dimeric surfactants with intermediate spacer length seem to be the less efficient for DNA binding. PMID:27108208

  14. The relationship between fMRI adaptation and repetition priming.

    PubMed

    Ganel, Tzvi; Gonzalez, Claudia L R; Valyear, Kenneth F; Culham, Jody C; Goodale, Melvyn A; Köhler, Stefan

    2006-09-01

    Neuroimaging investigations of the cortically defined fMRI adaptation effect and of the behaviorally defined repetition priming effect have provided useful insights into how visual information is perceived and stored in the brain. Yet, although both phenomena are typically associated with reduced activation in visually responsive brain regions as a result of stimulus repetition, it is presently unknown whether they rely on common or dissociable neural mechanisms. In an event-related fMRI experiment, we manipulated fMRI adaptation and repetition priming orthogonally. Subjects made comparative size judgments for pairs of stimuli that depicted either the same or different objects; some of the pairs presented during scanning had been shown previously and others were new. This design allowed us to examine whether object-selective regions in occipital and temporal cortex were sensitive to adaptation, priming, or both. Critically, it also allowed us to test whether any region showing sensitivity to both manipulations displayed interactive or additive effects. Only a partial overlap was found between areas that were sensitive to fMRI adaptation and those sensitive to repetition priming. Moreover, in most of the object-selective regions that showed both effects, the reduced activation associated with the two phenomena were additive rather than interactive. Together, these findings suggest that fMRI adaptation and repetition priming can be dissociated from one another in terms of their neural mechanisms. PMID:16854597

  15. Flexible high-repetition-rate ultrafast fiber laser

    PubMed Central

    Mao, Dong; Liu, Xueming; Sun, Zhipei; Lu, Hua; Han, Dongdong; Wang, Guoxi; Wang, Fengqiu

    2013-01-01

    High-repetition-rate pulses have widespread applications in the fields of fiber communications, frequency comb, and optical sensing. Here, we have demonstrated high-repetition-rate ultrashort pulses in an all-fiber laser by exploiting an intracavity Mach-Zehnder interferometer (MZI) as a comb filter. The repetition rate of the laser can be tuned flexibly from about 7 to 1100 GHz by controlling the optical path difference between the two arms of the MZI. The pulse duration can be reduced continuously from about 10.1 to 0.55 ps with the spectral width tunable from about 0.35 to 5.7 nm by manipulating the intracavity polarization controller. Numerical simulations well confirm the experimental observations and show that filter-driven four-wave mixing effect, induced by the MZI, is the main mechanism that governs the formation of the high-repetition-rate pulses. This all-fiber-based laser is a simple and low-cost source for various applications where high-repetition-rate pulses are necessary. PMID:24226153

  16. Selective scanpath repetition during memory-guided visual search

    PubMed Central

    Wynn, Jordana S.; Bone, Michael B.; Dragan, Michelle C.; Hoffman, Kari L.; Buchsbaum, Bradley R.; Ryan, Jennifer D.

    2016-01-01

    ABSTRACT Visual search efficiency improves with repetition of a search display, yet the mechanisms behind these processing gains remain unclear. According to Scanpath Theory, memory retrieval is mediated by repetition of the pattern of eye movements or “scanpath” elicited during stimulus encoding. Using this framework, we tested the prediction that scanpath recapitulation reflects relational memory guidance during repeated search events. Younger and older subjects were instructed to find changing targets within flickering naturalistic scenes. Search efficiency (search time, number of fixations, fixation duration) and scanpath similarity (repetition) were compared across age groups for novel (V1) and repeated (V2) search events. Younger adults outperformed older adults on all efficiency measures at both V1 and V2, while the search time benefit for repeated viewing (V1–V2) did not differ by age. Fixation-binned scanpath similarity analyses revealed repetition of initial and final (but not middle) V1 fixations at V2, with older adults repeating more initial V1 fixations than young adults. In young adults only, early scanpath similarity correlated negatively with search time at test, indicating increased efficiency, whereas the similarity of V2 fixations to middle V1 fixations predicted poor search performance. We conclude that scanpath compression mediates increased search efficiency by selectively recapitulating encoding fixations that provide goal-relevant input. Extending Scanpath Theory, results suggest that scanpath repetition varies as a function of time and memory integrity. PMID:27570471

  17. Repetitively Q-switched Nd:BeL lasers

    NASA Technical Reports Server (NTRS)

    Degnan, J.; Birnbaum, M.; Deshazer, L. G.

    1979-01-01

    The thermal and mechanical characteristics which will ultimately limit the performance of Nd:BeL at high average power levels were investigated. The output beam characteristics (pulse width, peak power, beam dimensions and collimation) were determined at high repetition rates for both Nd:BeL and Nd:YAG. The output of Nd:BeL was shown to exceed that of Nd:YAG by a factor of 2.7 at low Q-switched repetition rates (1 Hz). This result follows from the smaller stimulated emission cross section of x-axis Nb:BeL compared to that of NdYAG by the same factor. At high repetition rates (10 Hz) the output of Nd:Bel falls to a level of three-fifths of its low repetition rate value while under similar tests the output of Nd:YAG remains essentially constant. A comparison of the measured values of the elasto-optic coefficients, the dn/dT values and the linear expansion coefficients for BeL and YAG failed to provide an explanation for the performance of BeL; however, thermal lensing was observed in Nd:BeL. Results imply that the output of a high repetition rate Q-switched Nd:BeL laser (high thermal loading) could be dramatically increased by utilization of a resonator design to compensate for the thermal lensing effects.

  18. Characterizing exploration behavior in spatial neglect: omissions and repetitive search.

    PubMed

    Olk, Bettina; Harvey, Monika

    2006-11-01

    In search tasks, patients with spatial neglect typically fail to respond to stimuli on the contralesional side. Such behavior has been associated with hyperattention to the ipsilesional side and a deficit in disengaging from attended stimuli. The present study investigated whether such explanations can also account for a further kind of behavior frequently shown by neglect patients: repetitive returns to previously indicated stimuli, particularly on the ipsilesional side. A group of neglect patients was tested along with a group of healthy participants and a patient control group without neglect. Participants performed an exploration task in which they searched for targets defined by their shape or for all stimuli either with the aid of vision or blindfolded. The results showed differential effects of reducing the salience of visual stimuli by blindfolding. For a subgroup of patients, detection rate improved, while for others the percentage of omissions increased. However, contrary to the control groups, blindfolding had no effect on repetitive search in the neglect group, inconsistent with hyperattention, a disengage or impaired working memory deficits. The rate of repetitive returns to previously indicated locations did not seem to be associated with the percentage of omitted stimuli, suggesting that repetitive returns may be best explained by a disruption of systematic search and lack of volitional control in spatial neglect. The results further underline the importance of considering repetitive search behavior in addition to omissions in standard neglect assessments. PMID:16979143

  19. Quantifying Repetitive Speech in Autism Spectrum Disorders and Language Impairment

    PubMed Central

    van Santen, Jan P. H.; Sproat, Richard W.; Hill, Alison Presmanes

    2013-01-01

    We report on an automatic technique for quantifying two types of repetitive speech: repetitions of what the child says him/herself (self-repeats) and of what is uttered by an interlocutor (echolalia). We apply this technique to a sample of 111 children between the ages of four and eight: 42 typically developing children (TD), 19 children with specific language impairment (SLI), 25 children with autism spectrum disorders (ASD) plus language impairment (ALI), and 25 children with ASD with normal, non-impaired language (ALN). The results indicate robust differences in echolalia between the TD and ASD groups as a whole (ALN + ALI), and between TD and ALN children. There were no significant differences between ALI and SLI children for echolalia or self-repetitions. The results confirm previous findings that children with ASD repeat the language of others more than other populations of children. On the other hand, self-repetition does not appear to be significantly more frequent in ASD, nor does it matter whether the child’s echolalia occurred within one (immediate) or two turns (near-immediate) of the adult’s original utterance. Furthermore, non-significant differences between ALN and SLI, between TD and SLI, and between ALI and TD are suggestive that echolalia may not be specific to ALN or to ASD in general. One important innovation of this work is an objective fully automatic technique for assessing the amount of repetition in a transcript of a child’s utterances. PMID:23661504

  20. Verbal repetition in primary progressive aphasia and Alzheimer's disease.

    PubMed

    Leyton, Cristian E; Savage, Sharon; Irish, Muireann; Schubert, Samantha; Piguet, Olivier; Ballard, Kirrie J; Hodges, John R

    2014-01-01

    We aimed to explore the nature of verbal repetition deficits and infer the cognitive systems involved in primary progressive aphasia (PPA) and Alzheimer's disease (AD). A total of 63 patients (13 semantic variant (sv-PPA), 17 nonfluent/agrammatic variant (nfv-PPA), 10 logopenic variant (lv-PPA), 23 AD) and 13 matched healthy controls completed a battery of tests that included naming, word comprehension, digit span, repetition of multisyllabic single words, monosyllabic word span presented under similar and dissimilar phonological conditions, and sentence repetition. All patient groups displayed some level of impairment, however, specific patterns emerged in each variant. Participants with sv-PPA were the least impaired, showing marginal difficulties exclusively for sentence repetition, whereas those with lv-PPA had the worst overall performance. Cases with nfv-PPA showed compromised repetition of multisyllabic and phonologically similar words. The deficit in cases with AD was confined to span tasks. These distinctive patterns of language impairments can assist in the differential diagnosis of PPA variants and point toward the vulnerability of specific cognitive systems in each syndrome. PMID:24662100

  1. Physical chromosome mapping of repetitive DNA sequences in Nile tilapia Oreochromis niloticus: evidences for a differential distribution of repetitive elements in the sex chromosomes.

    PubMed

    Ferreira, Irani A; Martins, Cesar

    2008-06-01

    Repetitive DNAs have been extensively applied as physical chromosome markers on comparative studies, identification of chromosome rearrangements and sex chromosomes, chromosome evolution analysis, and applied genetics. Here we report the characterization of repetitive DNA sequences from the Nile tilapia (Oreochromis niloticus) genome by construction and screening of plasmid library enriched with repetitive DNAs, analysis of a BAC-based physical map, and hybridization to chromosomes. The physical mapping of BACs enriched with repetitive sequences and C(o)t-1 DNA (DNA enriched for highly and moderately repetitive DNA sequences) to chromosomes using FISH showed a predominant distribution of repetitive elements in the centromeric and telomeric regions and along the entire length of the largest chromosome pair (X and Y sex chromosomes) of the species. The distribution of repetitive DNAs differed significantly between the p arm of X and Y chromosomes. These findings suggest that repetitive DNAs have had an important role in the differentiation of sex chromosomes. PMID:17395473

  2. Scale resolving simulations of the water flow through a rod bundle with split-type spacer grid

    NASA Astrophysics Data System (ADS)

    Matyushenko, A. A.; Garbaruk, A. V.

    2014-12-01

    Unsteady isothermal turbulent flow in periodic sub-channel of 5×5 rod bundle with split-type spacer grid is investigated using modern Scale Resolving Simulation methods: Wall Modelling Large Eddy Simulation (WMLES) and Scale Adapting Simulation (SAS). Solutions obtained with both methods show complicated swirling flow dissipating over the distance from spacer grid and are in a good agreement with the experimental data except an area in close vicinity of the vanes.

  3. Modifying exchange-spring behavior of CoPt/NiFe bilayer by inserting a Pt or Ru spacer

    SciTech Connect

    Hsu, Jen-Hwa Tsai, C. L.; Lee, C.-M.; Saravanan, P.

    2015-05-07

    We herein explore the possibility of obtaining tunable tilted magnetic anisotropy in ordered-CoPt (5 nm)/NiFe(t{sub NiFe}) bilayers through modifying their exchange spring behavior by inserting Pt and Ru-spacers. The tuning process of tilt angle magnetization of NiFe-layer was systematically investigated by varying the Pt or Ru thickness (t{sub Pt} or t{sub Ru}) from 0 to 8 nm at different thicknesses of NiFe (t{sub NiFe} = 1.5, 4.0, and 6.0 nm). Polar magneto-optic Kerr effect (p-MOKE) studies reveal that the bilayers grown in absence of spacers exhibit almost a rectangular hysteresis loop. With the insertion of Pt-spacer, the loop becomes more and more tilted as t{sub Pt} increases; whereas, in the case of Ru-spacer, the nature of the loops is not simply changing in one direction. The estimated SQR{sub ⊥} (= θ{sub r}/θ{sub s}) values from the p-MOKE loops are found to monotonically decrease with increasing t{sub Pt} when t{sub Pt} ≦ 4 nm. In contrast, in the case of Ru-spacer, an oscillatory behavior for the SQR{sub ⊥} values is apparent when t{sub Ru} ≦ 4 nm. As a result, an oscillatory tilted angle of NiFe spin configuration was obtained in the case of Ru-spacer; while a decoupling effect was prominent for the Pt-spacer. The results of present study reveal that the insertion of Pt and Ru-spacers as an appropriate means for realizing tunable tilted magnetic anisotropy in the CoPt/NiFe exchange springs.

  4. Repetition blindness for faces reflects identity coding but not emotion coding.

    PubMed

    Buttle, Heather

    2010-02-01

    Repetition blindness for visually presented stimuli occurs when only one of two similar items is available to a viewer's conscious awareness. The objective of this experiment was to investigate repetition blindness for faces and to observe whether encoding of similar emotions displayed on different individuals' faces produced repetition blindness. A further aim was to assess whether such an effect could be modulated by attentional task demands (sex judgment or expression judgment). Faces were presented so that four within-participant conditions could be compared: Complete repetition, same emotion/different Identity repetition, same identity/different Emotion repetition, and No repetition trials. The data revealed repetition blindness for Complete and same identity/different Emotion repetitions, but not for same emotion/different Identity repetitions. The lack of an "emotion blindness" effect supports previous reports that emotional expressions do not necessarily lead to automatic attentional biases. PMID:20391889

  5. A Rationale for Going Back to the Future: Use of Disposable Spacers for Pressurised Metered Dose Inhalers

    PubMed Central

    Sanders, Mark; Bruin, Ronald

    2015-01-01

    The introduction of pressurised metered dose inhalers (MDIs) in the mid-1950s completely transformed respiratory treatment. Despite decades of availability and healthcare support and development of teaching aids and devices to promote better use, poor pMDI user technique remains a persistent issue. The main pMDI user aid is the spacer/valved holding chamber (VHC) device. Spacer/chamber features (size, shape, configuration, construction material, and hygiene considerations) can vie with clinical effectiveness (to deliver the same dose as a correctly used pMDI), user convenience, cost, and accessibility. Unsurprisingly, improvised, low-cost alternatives (plastic drink bottles, paper cups, and paper towel rolls) have been pressed into seemingly effective service. A UK law change permitting schools to hold emergency inhalers and spacers has prompted a development project to design a low-cost, user-friendly, disposable, and recyclable spacer. This paper spacer requires neither preuse priming nor washing, and has demonstrated reproducible lung delivery of salbutamol sulphate pMDI, comparable to an industry-standard VHC, an alternative paperboard VHC, and pMDI alone. This new device appears to perform better than these other VHC devices at the low flow rates thought achievable by paediatric patients. The data suggest that this disposable spacer may have a place in the single-use emergency setting. PMID:26491563

  6. The estimation of size and position of contaminating particle adhering to the insulating spacer surface in gas-insulated systems

    NASA Astrophysics Data System (ADS)

    Khan, Yasin; Nur Budiman, Firmansiah; Béroual, Abderrahmane; Hussain Malik, Nazar; Al-Arainy, Abdulrehman Ali

    2013-05-01

    The presence of metallic particles has been recognized as a dangerous threat in gas-insulated substation (GIS). Such particles are initially free and move toward higher electric field regions such as triple junction i.e., spacer-electrode-gas interface. However, once these particles reach the spacer surface, they adhere to the spacer easily due to electrostatic image forces. From insulation point of view, the triple junction is the weakest point in GIS. The presence of such metallic particles on the spacer surface deteriorates the insulation strength. Thus, in order to improve the reliability of GIS, it is important to identify the size and the position of the particle adhering to the insulating spacer surface. One of the most promising methods to carry out such identification is by recognizing the partial discharges (PDs) provoked by such particles. This paper is aimed to discuss the particle size and position estimation by using the PD patterns and statistical analysis. The PD patterns were acquired using IEC 60270 method. Measurements were made to determine various PD signals caused by particle of different sizes at different locations on the spacer surface. The acquired PD patterns were characterized by a number of statistical parameters. The results show that the implemented technique could be used to distinguish between various particle sizes and positions at different SF6 pressures with a fairly high accuracy.

  7. A Rationale for Going Back to the Future: Use of Disposable Spacers for Pressurised Metered Dose Inhalers.

    PubMed

    Sanders, Mark; Bruin, Ronald

    2015-01-01

    The introduction of pressurised metered dose inhalers (MDIs) in the mid-1950s completely transformed respiratory treatment. Despite decades of availability and healthcare support and development of teaching aids and devices to promote better use, poor pMDI user technique remains a persistent issue. The main pMDI user aid is the spacer/valved holding chamber (VHC) device. Spacer/chamber features (size, shape, configuration, construction material, and hygiene considerations) can vie with clinical effectiveness (to deliver the same dose as a correctly used pMDI), user convenience, cost, and accessibility. Unsurprisingly, improvised, low-cost alternatives (plastic drink bottles, paper cups, and paper towel rolls) have been pressed into seemingly effective service. A UK law change permitting schools to hold emergency inhalers and spacers has prompted a development project to design a low-cost, user-friendly, disposable, and recyclable spacer. This paper spacer requires neither preuse priming nor washing, and has demonstrated reproducible lung delivery of salbutamol sulphate pMDI, comparable to an industry-standard VHC, an alternative paperboard VHC, and pMDI alone. This new device appears to perform better than these other VHC devices at the low flow rates thought achievable by paediatric patients. The data suggest that this disposable spacer may have a place in the single-use emergency setting. PMID:26491563

  8. The non-signaling extracellular spacer domain of chimeric antigen receptors is decisive for in vivo antitumor activity

    PubMed Central

    Hudecek, Michael; Sommermeyer, Daniel; Kosasih, Paula L.; Silva-Benedict, Anne; Liu, Lingfeng; Rader, Christoph; Jensen, Michael C.; Riddell, Stanley R.

    2015-01-01

    The use of synthetic chimeric antigen receptors (CAR) to redirect T cells to recognize tumor provides a powerful new approach to cancer immunotherapy; however the attributes of CARs that ensure optimal in vivo tumor recognition remain to be defined. Here, we analyze the influence of length and composition of IgG-derived extracellular spacer domains on the function of CARs. Our studies demonstrate that CD19-CARs with a long spacer from IgG4 hinge-CH2-CH3 are functional in vitro but lack antitumor activity in vivo due to interaction between the Fc domain within the spacer and the Fc receptor-bearing myeloid cells, leading to activation-induced T-cell death. We demonstrate that in vivo persistence and antitumor effects of CAR-T-cells with a long spacer can be restored by modifying distinct regions in the CH2 domain that are essential for Fc receptor binding. Our studies demonstrate that modifications that abrogate binding to Fc receptors are crucial for CARs in which a long spacer is obligatory for tumor recognition as shown here for a ROR1-specific CAR. These results demonstrate that the length and composition of the extracellular spacer domain that lacks intrinsic signaling function can be decisive in the design of CARs for optimal in vivo activity. PMID:25212991

  9. Immobilization of pectinase on silica-based supports: Impacts of particle size and spacer arm on the activity.

    PubMed

    Alagöz, Dilek; Tükel, S Seyhan; Yildirim, Deniz

    2016-06-01

    The pectinase was separately immobilized onto Florisil and nano silica supports through both glutaraldehyde and 3-glyoxypropyltrietoxysilane spacer arms. The effects of spacer arm, particle size of support and ionic liquids on the activities of pectinase preparations were investigated. The immobilization of pectinase onto Florisil and nano silica through 3-glyoxypropyltrietoxysilane spacer arm completely led to inactivation of enzyme; however, 10 and 75% pectinase activity were retained when it was immobilized through glutaraldehyde spacer arm onto Florisil and nano silica, respectively. The pectinase immobilized onto nano silica through glutaraldehyde spacer arm showed 6.3-fold higher catalytic efficiency than that of the pectinase immobilized onto Florisil through same spacer arm. A 2.3-fold increase in thermal stability of pectinase was provided upon immobilization onto nano silica at 35°C. The effects of IL/buffer mixture and volume ratio of IL/buffer mixture on the catalytic activities of free and immobilized pectinase preparations were also tested. All the pectinase preparations showed highest activity in 10% (v/v) 1-butyl-3-methylimidazolium hexafluorophosphate containing medium and their activities significantly affected from the concentration of 1-butyl-3-methylimidazolium hexafluorophosphate. PMID:26964525

  10. Multiple cellular mechanisms prevent chromosomal rearrangements involving repetitive DNA

    PubMed Central

    George, Carolyn M.; Alani, Eric

    2012-01-01

    Repetitive DNA is present in the eukaryotic genome in the form of segmental duplications, tandem and interspersed repeats, and satellites. Repetitive sequences can be beneficial by serving specific cellular functions (e.g. centromeric and telomeric DNA) and by providing a rapid means for adaptive evolution. However, such elements are also substrates for deleterious chromosomal rearrangements that affect fitness and promote human disease. Recent studies analyzing the role of nuclear organization in DNA repair and factors that suppress non-allelic homologous recombination have provided insights into how genome stability is maintained in eukaryotes. In this review we outline the types of repetitive sequences seen in eukaryotic genomes and how recombination mechanisms are regulated at the DNA sequence, cell organization, chromatin structure, and cell cycle control levels to prevent chromosomal rearrangements involving these sequences. PMID:22494239

  11. Association between repetitive work and occupational cold exposure.

    PubMed

    Buzanello, Márcia Rosângela; Moro, Antônio Renato Pereira

    2012-01-01

    Occupational cold exposure is an important risk factor that increases stress at work and can induce many health effects like diseases and symptoms related to cold, including work-related musculoskeletal disorders. The methodological procedures were performed to measure these environmental variables as recommended by the ISO 7726/85. For the analysis of repetitiveness was used the OCRA checklist and evaluation of musculoskeletal morbidity conducted by the Nordic Musculoskeletal Questionnaire. So the objective of this study was to investigate the correlation between cold environmental variables and prevalence of musculoskeletal morbidity in the repetitive work. Was found association between work in cutting and boning sector (occupational cold and repetitive work) and the presence of musculoskeletal morbidity, with a significance of 99%. PMID:22317689

  12. [Repetitive facilitative exercise: recent evidence and development for combination therapy].

    PubMed

    Shimodozono, Megumi

    2013-01-01

    Repetitive facilitative exercise (RFE), a combination of high-dose (high frequency) of repetitions and neurofacilitation, is a recently developed approach to the rehabilitation of stroke-related limb impairment. We conducted a randomized controlled evaluation of RFE compared with a duration-matched conventional rehabilitation program in the treatment of subacute stroke-related upper extremity impairment (Shimodozono et al. 2013). RFE demonstrated both statistically and clinically significant benefits over conventional rehabilitation both on the Action Research Arm Test, which is designed to measure dexterity and function, and on the Fugl-Meyer Arm scores, which was chosen as measure of motor control. In the case-series study, the beneficial effect of RFE is also reported in the treatment of chronic phase of stroke. More research is needed, but RFE could conceivably be integrated with other approaches such as vibration, neuromuscular electrical stimulation, repetitive transcranial magnetic stimulation, botulinum toxin, and robotics to achieve further improvement in its capabilities. PMID:24291952

  13. Patterns of tandem repetition in plant whole genome assemblies.

    PubMed

    Navajas-Pérez, Rafael; Paterson, Andrew H

    2009-06-01

    Tandem repeats often confound large genome assemblies. A survey of tandemly arrayed repetitive sequences was carried out in whole genome sequences of the green alga Chlamydomonas reinhardtii, the moss Physcomitrella patens, the monocots rice and sorghum, and the dicots Arabidopsis thaliana, poplar, grapevine, and papaya, in order to test how these assemblies deal with this fraction of DNA. Our results suggest that plant genome assemblies preferentially include tandem repeats composed of shorter monomeric units (especially dinucleotide and 9-30-bp repeats), while higher repetitive units pose more difficulties to assemble. Nevertheless, notwithstanding that currently available sequencing technologies struggle with higher arrays of repeated DNA, major well-known repetitive elements including centromeric and telomeric repeats as well as high copy-number genes, were found to be reasonably well represented. A database including all tandem repeat sequences characterized here was created to benefit future comparative genomic analyses. PMID:19242726

  14. Repetition-based credibility enhancement of unfamiliar faces.

    PubMed

    Brown, Alan S; Brown, Lori A; Zoccoli, Sandy L

    2002-01-01

    This experiment demonstrated that rating the credibility of nonfamous faces results in a significant increase in rated credibility on a subsequent encounter relative to new nonfamous faces. The degree of credibility enhancement is comparable for both honesty and sincerity ratings and at both short (2-day) and long (14-day) interrating intervals. Furthermore, credibility enhancement was independent of recognition; ratings were significantly higher for repeated faces, regardless of whether they were remembered. Although female faces were rated more credible than male faces, there was no gender difference in the degree of credibility enhancement with repetition. Conditional analyses revealed that actual, rather than perceived, repetition formed the basis of credibility enhancement. Future research should compare repetition effects on both credibility and affect as well as the durability of such effects over time. PMID:12041008

  15. Salamander Hox clusters contain repetitive DNA and expanded non-coding regions: a typical Hox structure for non-mammalian tetrapod vertebrates?

    PubMed Central

    2013-01-01

    Hox genes encode transcription factors that regulate embryonic and post-embryonic developmental processes. The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding and non-coding sequences. The potential for evolutionary changes in Hox cluster structure is thought to be low among vertebrates; however, recent studies of a few non-mammalian taxa suggest greater variation than originally thought. Using next generation sequencing of large genomic fragments (>100 kb) from the red spotted newt (Notophthalamus viridescens), we found that the arrangement of Hox cluster genes was conserved relative to orthologous regions from other vertebrates, but the length of introns and intergenic regions varied. In particular, the distance between hoxd13 and hoxd11 is longer in newt than orthologous regions from vertebrate species with expanded Hox clusters and is predicted to exceed the length of the entire HoxD clusters (hoxd13–hoxd4) of humans, mice, and frogs. Many repetitive DNA sequences were identified for newt Hox clusters, including an enrichment of DNA transposon-like sequences relative to non-coding genomic fragments. Our results suggest that Hox cluster expansion and transposon accumulation are common features of non-mammalian tetrapod vertebrates. PMID:23561734

  16. Oral Language Skills Moderate Nonword Repetition Skills in Children with Dyslexia: A Meta-Analysis of the Role of Nonword Repetition Skills in Dyslexia

    ERIC Educational Resources Information Center

    Melby-Lervag, Monica; Lervag, Arne

    2012-01-01

    We present a meta-analysis reviewing studies that have focused on the relationship between dyslexia and nonword repetition. The results show that children with dyslexia have poorer nonword repetition skills when compared to both chronological-age and reading-level controls. However, the severity of the nonword repetition problem varies…

  17. High-repetition-rate short-pulse gas discharge.

    PubMed

    Tulip, J; Seguin, H; Mace, P N

    1979-09-01

    A high-average-power short-pulse gas discharge is described. This consists of a volume-preionized transverse discharge of the type used in gas lasers driven by a Blumlein energy storage circuit. The Blumlein circuit is fabricated from coaxial cable, is pulse-charged from a high-repetition-rate Marx-bank generator, and is switched by a high-repetition-rate segmented rail gap. The operation of this discharge under conditions typical of rare-gas halide lasers is described. A maximum of 900 pps was obtained, giving a power flow into the discharge of 30 kW. PMID:18699678

  18. Short-cavity high-repetition-rate CO2 laser

    NASA Astrophysics Data System (ADS)

    Klopper, Wouter; Bagrova, Kalina; du Pisanie, Johan; Ronander, Einar; Meyer, Jan A.; von Bergmann, Hubertus M.

    1994-09-01

    We report on the construction and optimization of a TEA CO2 laser with a discharge volume of 15 cm3 and cavity length of 20 cm. Such a short cavity facilitates single longitudinal mode operation. A roots blower is employed to achieve the necessary gas flow rate for high-repetition-frequency operation in a compact design. Output has been obtained at 1 kHz and a stable discharge to a repetition rate of 2 kHz has been demonstrated. The laser is part of a program aimed at the development of an efficient laser system for molecular laser isotope separation. Additional applications in materials processing are envisioned.

  19. Prediction of Muscle Performance During Dynamic Repetitive Exercise

    NASA Technical Reports Server (NTRS)

    Byerly, D. L.; Byerly, K. A.; Sognier, M. A.; Squires, W. G.

    2002-01-01

    A method for predicting human muscle performance was developed. Eight test subjects performed a repetitive dynamic exercise to failure using a Lordex spinal machine. Electromyography (EMG) data was collected from the erector spinae. Evaluation of the EMG data using a 5th order Autoregressive (AR) model and statistical regression analysis revealed that an AR parameter, the mean average magnitude of AR poles, can predict performance to failure as early as the second repetition of the exercise. Potential applications to the space program include evaluating on-orbit countermeasure effectiveness, maximizing post-flight recovery, and future real-time monitoring capability during Extravehicular Activity.

  20. Interaction of repetitively pulsed high energy laser radiation with matter

    NASA Astrophysics Data System (ADS)

    Hugenschmidt, M.

    1986-05-01

    Laser target interaction processes and methods of improving the overall energy balance are discussed. This can be achieved with high repetition rate pulsed lasers even for initially highly reflecting materials, such as metals. Experiments were performed using a pulsed CO2 laser at mean powers up to 2 KW and repetition rates up to 100 Hz. The rates of temperature rise of aluminum for example are increased by more than a factor of 3 as compared to cw-radiation of comparable power density. Similar improvements are found for the overall absorptivities, that are increased by more than an order of magnitude.