136,171 research outputs found
FUNCTIONAL ANALYSIS OF 5'-FLANKING REGION OF CYTOCHROME P450 GENES THROUGH MOLECULAR CLONING AND TRANSFECTION IN VITRO AND IN VIVO
No full textCytochrome P450 (CYP) enzymes are an important class of heme-containing proteins that catalyze oxidation reactions leading toward the removal of a wide variety of endogenous and exogenous substrates including prescription drugs. The activities of CYP enzymes are regulated primarily at the transcription level involving the regulatory sequences at the 5'-flanking region of the CYP genes. The objective of this dissertation study was to characterize the function of the 5'-flanking sequences of selected CYP genes primarily responsible for drug metabolism. Various sequences from the 5'-flanking regions of different CYP genes (CYP1A2, CYP2C9, CYP2C18, CYP2D6, CYP2E1, and CYP3A4) were cloned in expression vectors and tested for their activity in driving reporter gene expression in mouse livers and in transfected HepG2, 293, and BL-6 cells under optimized conditions. It was demonstrated that among the tested 5'-flanking regions of CYP genes, the CYP2D6 promoter showed the highest activity both in vivo and in vitro. The activities of various 5'-flanking regions of CYP genes in sustaining transgene expression were then tested in mouse liver and compared to those of other promoter sequences. As a result, the CYP2D6 promoter showed the highest activity and its activity was comparable to that of many established promoters. The mechanism underlying CYP promoter activities in vivo and in vitro were then studied using the CYP2C9 promoter as a model. Activities of various 5'-flanking sequences of CYP2C9 were evaluated by using deletion mutations of plasmid constructs in combination with transfection in mouse livers and in HepG2 cells. Finally, the role of PXR and CAR nuclear receptors in regulating CYP2C9 activation was investigated. The results show that both CAR and PXR are essential for CYP2C9 activation and that the regulatory elements reside in the proximal 1-2 kb region upstream of the CYP2C9 gene
Characterizing flanking transmission paths in the NRC-IRC flanking facility
No full textThis paper is the third of a series of papers that provide an overview of work conducted by NRC in the past years on flanking transmission. In the previous papers the measurement system and the new NRC-IRC Flanking Facility are described1,2. The ISO 10848 method for measuring flanking paths is time-consuming and not feasible for a facility of this complexity. This paper describes the methodology used in the Flanking Facility to systematically measure airborne sound transmission through the individual flanking paths for the 6 junctions of the specimen.Ce document est le troisi\ue8me d?une s\ue9rie qui fournit une vue d?ensemble des travaux dirig\ue9s par le CNRC au cours des derni\ue8res ann\ue9es portant sur la transmission indirecte des sons. Dans les travaux ant\ue9rieurs, on d\ue9crivait le syst\ue8me de mesure ainsi que la nouvelle installation d?essai de transmission indirecte de l?IRC-CNRC. La m\ue9thode ISO 10848 de mesure des voies de transmission indirecte demande beaucoup de temps et se r\ue9v\ue8le non praticable pour une installation d?une telle complexit\ue9. On d\ue9crit dans ce document la m\ue9thodologie employ\ue9e dans l?installation d?essai de transmission indirecte, dans le but de mesurer syst\ue9matiquent la transmission des bruits a\ue9riens par les voies indirectes individuelles pour les 6 jonctions du sp\ue9cimen.Peer reviewed: YesNRC publication: Ye
Clade D microsatellite flanking region sequences
No full textExample flanking sequences of loci 88 and 93 (sensu Wham et al. 2011) for Symbiodinium trenchii, S. boreum, and S. eurythalpos
The diploid origins of allopolyploid rose species studied using single nucleotide polymorphism haplotypes flanking a microsatellite repeat
No full textThe taxonomy of the genus Rosa is complex, not least because of hybridisations between species. We aimed to develop a method to connect the diploid Rosa taxa to the allopolyploid taxa to which they contributed, based on the sharing of haplotypes. For this we used an SNPSTR marker, which combines a short tandem repeat (STR; microsatellite) marker with single nucleotide polymorphisms (SNPs) in the flanking sequences. In total, 53 different sequences (haplotypes) were obtained for the SNPSTR marker, Rc06, from 20 diploid and 35 polyploid accessions from various species of Rosa. Most accessions of the diploid species had only one allele, while accessions of the polyploid species each contained two-to-five different alleles. Twelve SNPs were detected in the flanking sequences, which alone formed a total of 18 different haplotypes. A maximum likelihood dendrogram revealed five groups of haplotypes. Diploid species in the same Section of the genus Rosa contained SNP haplotypes from only one haplotype group. In contrast, polyploid species contained haplotypes from different haplotype groups. Identical SNP haplotypes were shared between polyploid species and diploid species from more than one Section of the genus Rosa. There were three different polymorphic repeat regions in the STR region. The STR repeat contained eight additional SNPs, but these contributed little to the resolution of the haplotype groups. Our results support hypotheses on diploid Rosa species that contributed to polyploid taxa. Finding different sets of haplotypes in different groups of species within the Sections Synstylae and Pimpinellifoliae supports the hypothesis that these may be paraphyletic
MeSH term explosion and author rank improve expert recommendations
No full textInformation overload is an often-cited phenomenon that reduces the productivity, efficiency and efficacy of scientists. One challenge for scientists is to find appropriate collaborators in their research. The literature describes various solutions to the problem of expertise location, but most current approaches do not appear to be very suitable for expert recommendations in biomedical research. In this study, we present the development and initial evaluation of a vector space model-based algorithm to calculate researcher similarity using four inputs: 1) MeSH terms of publications; 2) MeSH terms and author rank; 3) exploded MeSH terms; and 4) exploded MeSH terms and author rank. We developed and evaluated the algorithm using a data set of 17,525 authors and their 22,542 papers. On average, our algorithms correctly predicted 2.5 of the top 5/10 coauthors of individual scientists. Exploded MeSH and author rank outperformed all other algorithms in accuracy, followed closely by MeSH and author rank. Our results show that the accuracy of MeSH term-based matching can be enhanced with other metadata such as author rank
Dealing With Flanking Transmission in Wood Framed
No full textthis document is published in / Une version de ce document se trouve dans: Canadian Acoustics, v. 31, no. 3, Sept. 2003, pp. 52-53 http://irc.nrc-cnrc.gc.ca/ircpubs DEALING WITH FLANKING TRANSMISSION IN WOOD FRAMED CONSTRUCTION J. D. Quirt, T. R. T. Nightingale, and R. E. Halliwell, National Research Council Canada, Institute for Research in Construction Ottawa, Ontario K1A 0R6, Canada 1
D-seq identifies dihydrouridine sites in mRNAs.
No full text(A) Plots of cDNA end positions in ALD6 and SEC63 mRNAs. D peaks are highlighted. Scale in RPM and bp. (B) Distribution of D sites among mRNA features, and background distribution of features for all sites interrogated for D. (C) SDS-PAGE gels showing Top7 protein produced from U and D containing mRNAs with 4 different test codons. Denaturing glyoxal agarose gel showing mRNA integrity. All 4 test constructs showed no significant difference in protein produced per mRNA +/‒ D. Schematic of U/D mRNAs with U/D positions highlighted in red. (D) Plots of cDNA end positions for intronic D in RPL30 mRNA. D peak is highlighted. Scale in RPM and bp. (E) DUS KO strain has increased ratio of RPL30 intron mapping reads to exon mapping reads (p t test). Model of regulation of RPL30 pre-mRNA splicing by RPL30 protein. (F) mRNA sequences flanking Ds have higher DMS reactivity indicating greater flexibility. Plot of median DMS-induced mutation rate in 25 nt window flanking D site. Red trace is median DMS reactivity surrounding D positions. Black dots are median DMS reactivity for randomly selected set of background positions. Blue is p-value for difference in DMS reactivity for sequences flanking D or background sites. (G) D has multiple impacts on RNA structure. D both promotes loop formation and antagonizes duplex formation. The data underlying this figure can be found in S3 Table. D-seq, dihydrouridine sequencing; DMS, dimethyl sulfate; DUS, dihydrouridine synthase.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Flanking Residues Are Central to DO11.10 T Cell Hybridoma Stimulation by Ovalbumin 323–339
No full textBenjamin M. Roy is with UT Austin and University of Minnesota; Dmitriy V. Zhukov is with UT Austin; Jennifer A. Maynard is with UT Austin.T cell activation requires formation of a tri-molecular interaction between a major histocompatibility complex (MHC), peptide, and T cell receptor. In a common model system, the ovalbumin epitope 323–339 binds the murine class II MHC, I-Ad, in at least three distinct registers. The DO11.10 T cell recognizes the least stable of these, as determined by peptide-MHC dissociation rates. Using exogenous peptides and peptide insertions into a carrier protein in combination with IL-2 secretion assays, we show that the alternate registers do not competitively inhibit display of the active register four. In contrast, this weakly binding register is stabilized by the presence of N-terminal flanking residues active in MHC binding. The DO11.10 hybridoma is sensitive to the presence of specific wild-type residues extending to at least the P-3 peptide position. Transfer of the P-4 to P-2 flanking residues to a hen egg lysozyme epitope also presented by I-Ad increases the activity of that epitope substantially. These results illustrate the inherent complexity in delineating the interaction of multiple registers based on traditional thermodynamic measurements and demonstrate the potential of flanking residue modification for increasing the activity of weakly bound epitopes. The latter technique represents an alternative to substitution of anchor residues within a weakly bound register, which we show can significantly decrease the activity of the epitope to a responding T cell.Funding for this project was provided by the Packard Foundation, NSF DBI-0964137 and NIH 1R01GM095638 to JAM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Chemical Engineerin
Features of the TE and flanking sequences.
No full textGC content in the TE (A) and 1kb flanking sequence (B). Proportion of sites methylatable in the CG context in the TE (C) and 1kb flanking sequence (D), methylatable in the CHG context in the TE (E) and 1kb flanking sequence (F), proportion of sites methylatable in the CHH context in the TE (G) and 1kb flanking sequence (H). Proportion of sites containing a TG or CA dinucleotide in the TE (I) and 1kb flanking sequence (J). Proportion of sites in MNase hypersensitive regions in root in TE (K) and 1kb flank (L), and shoot in TE (M) and 1kb flank (N). Proportion of segregating sites in the TE (O) and 1kb flank (P). (TIF)</p
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