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Other Sequences (other + sequence)
Selected AbstractsActivity and sequence characterization of two cysteine proteases in the digestive tract of the reduviid bug Triatoma infestansINSECT MOLECULAR BIOLOGY, Issue 6 2004A. H. Kollien Abstract Cathepsin B- and cathepsin L-like activities were identified in gut extracts of the blood-sucking bug Triatoma infestans using specific substrates and inhibitors. Activities decreased during the first 2 days after feeding but increased to a maximum value at 5 and 10 days post feeding. The deduced 332 and 328 amino acid sequences showed high levels of identity (50,60%) to other insect cathepsin B- and L-like proteases, respectively. The three amino acid residues of the catalytic domain, CHN, and the GCNGG motif were conserved in both cathepsins, but the occluding loop, characterizing B-like cathepsins, was present only in one. ERFNIN and GNFD motifs occurred in the other sequence, defining it as cathepsin L-like. The cathepsin B-like gene was expressed at low, constitutive levels in unfed and fed T. infestans. [source] HCV RNA-dependent RNA polymerase replicates in vitro the 3, terminal region of the minus-strand viral RNA more efficiently than the 3, terminal region of the plus RNAFEBS JOURNAL, Issue 22 2001Sandrine Reigadas The NS5B protein, or RNA-dependent RNA polymerase of the hepatitis virus type C, catalyzes the replication of the viral genomic RNA. Little is known about the recognition domains of the viral genome by the NS5B. To better understand the initiation of RNA synthesis on HCV genomic RNA, we used in vitro transcribed RNAs as templates for in vitro RNA synthesis catalyzed by the HCV NS5B. These RNA templates contained different regions of the 3, end of either the plus or the minus RNA strands. Large differences were obtained depending on the template. A few products shorter than the template were synthesized by using the 3, UTR of the (+) strand RNA. In contrast the 341 nucleotides at the 3, end of the HCV minus-strand RNA were efficiently copied by the purified HCV NS5B in vitro. At least three elements were found to be involved in the high efficiency of the RNA synthesis directed by the HCV NS5B with templates derived from the 3, end of the minus-strand RNA: (a) the presence of a C residue as the 3, terminal nucleotide; (b) one or two G residues at positions +2 and +3; (c) other sequences and/or structures inside the following 42-nucleotide stretch. These results indicate that the 3, end of the minus-strand RNA of HCV possesses some sequences and structure elements well recognized by the purified NS5B. [source] Comparison of ferucarbotran-enhanced fluid-attenuated inversion-recovery echo-planar, T2-weighted turbo spin-echo, T2*-weighted gradient-echo, and diffusion-weighted echo-planar imaging for detection of malignant liver lesionsJOURNAL OF MAGNETIC RESONANCE IMAGING, Issue 3 2010Yoshihiko Fukukura MD Abstract Purpose: To compare the diagnostic accuracy of superparamagnetic iron oxide (SPIO)-enhanced fluid-attenuated inversion-recovery echo-planar imaging (FLAIR EPI) for malignant liver tumors with that of T2-weighted turbo spin-echo (TSE), T2*-weighted gradient-echo (GRE), and diffusion-weighted echo-planar imaging (DW EPI). Materials and Methods: SPIO-enhanced magnetic resonance imaging (MRI) that included FLAIR EPI, T2-weighted TSE, T2*-weighted GRE, and DW EPI sequences was performed using a 3 T system in 54 consecutive patients who underwent surgical exploration with intraoperative ultrasonography. A total of 88 malignant liver tumors were evaluated. Images were reviewed independently by two blinded observers who used a 5-point confidence scale to identify lesions. Results were correlated with results of histopathologic findings and surgical exploration with intraoperative ultrasonography. The accuracy of each MRI sequence was measured with jackknife alternative free-response receiver operating characteristic analysis. The sensitivity of each observer with each MRI sequence was compared with McNemar's test. Results: Accuracy values were significantly higher with FLAIR EPI sequence (0.93) than with T2*-weighted GRE (0.80) or DW EPI sequences (0.80) (P < 0.05). Sensitivity was significantly higher with the FLAIR EPI sequence than with any of the other sequences. Conclusion: SPIO-enhanced FLAIR EPI sequence was more accurate in the diagnosis of malignant liver tumors than T2*-weighted GRE and DW EPI sequences. SPIO-enhanced FLAIR EPI sequence is helpful for the detection of malignant liver tumors. J. Magn. Reson. Imaging 2010;31:607,616. ©2010 Wiley-Liss, Inc. [source] Multiple spin-echo spectroscopic imaging for rapid quantitative assessment of N-acetylaspartate and lactate in acute strokeMAGNETIC RESONANCE IN MEDICINE, Issue 2 2004Astrid Stengel Abstract Monitoring the signal levels of lactate (Lac) and N-acetylaspartate (NAA) by chemical shift imaging can provide additional knowledge about tissue damage in acute stroke. Despite the need for this metabolic information, spectroscopic imaging (SI) has not been used routinely for acute stroke patients, mainly due to the long acquisition time required. The presented data demonstrate that the application of a fast multiple spin-echo (MSE) SI sequence can reduce the measurement time to 6 min (four spin echoes per echo train, 32 × 32 matrix). Quantification of Lac and NAA in terms of absolute concentrations (i.e., mmol/l) can be achieved by means of the phantom replacement approach, with correction terms for the longitudinal and transversal relaxation adapted to the multiple spin-echo sequence. In this pilot study of 10 stroke patients (symptom onset < 24 hr), metabolite concentrations obtained from MSE-SI add important information regarding tissue viability that is not provided by other sequences (e.g., diffusion-weighted imaging (DWI) and perfusion-weighted imaging (PWI)). Metabolic changes extended beyond the borders of the apparent diffusion coefficient (ADC) lesion in nine of the 10 patients, showing a rise in Lac concentrations up to 18 mmol/l, while NAA levels sometimes dropped below the detection level. Considerable differences among the patients in terms of the Lac concentrations and the size of the SI-ADC mismatch were observed. Magn Reson Med 52:228,238, 2004. © 2004 Wiley-Liss, Inc. [source] First-generation SNP/InDel markers tagging loci for pathogen resistance in the potato genomePLANT BIOTECHNOLOGY JOURNAL, Issue 6 2003Andreas M. Rickert Summary A panel of 17 tetraploid and 11 diploid potato genotypes was screened by comparative sequence analysis of polymerase chain reaction (PCR) products for single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), in regions of the potato genome where genes for qualitative and/or quantitative resistance to different pathogens have been localized. Most SNP and InDel markers were derived from bacterial artificial chromosome (BAC) insertions that contain sequences similar to the family of plant genes for pathogen resistance having nucleotide-binding-site and leucine-rich-repeat domains (NBS-LRR-type genes). Forty-four such NBS-LRR-type genes containing BAC-insertions were mapped to 14 loci, which tag most known resistance quantitative trait loci (QTL) in potato. Resistance QTL not linked to known resistance-gene-like (RGL) sequences were tagged with other markers. In total, 78 genomic DNA fragments with an overall length of 31 kb were comparatively sequenced in the panel of 28 genotypes. 1498 SNPs and 127 InDels were identified, which corresponded, on average, to one SNP every 21 base pairs and one InDel every 243 base pairs. The nucleotide diversity of the tetraploid genotypes (, = 0.72 × 10,3) was lower when compared with diploid genotypes (, = 2.31 × 10,3). RGL sequences showed higher nucleotide diversity when compared with other sequences, suggesting evolution by divergent selection. Information on sequences, sequence similarities, SNPs and InDels is provided in a database that can be queried via the Internet. [source] Serological and molecular detection of Tomato chlorosis virus and Tomato infectious chlorosis virus in tomatoPLANT PATHOLOGY, Issue 2 2009M. Jacquemond Tomato chlorosis virus (ToCV) and Tomato infectious chlorosis virus (TICV) are two criniviruses inducing similar yellowing symptoms in tomato. An approximately 4 kb central region of the genomic RNA2 of French ToCV and TICV isolates was sequenced. TICV, for which no other sequences were available, appeared as a distant species in the genus, being close only to LIYV (Lettuce infectious yellows virus) for some, but not all, proteins. ToCV has more than 98% nucleotide identity with isolates from the US and Spain, and sequencing the CP gene of several isolates collected in different regions in southern France during 2 years suggested a unique origin. Polyclonal antisera were produced using capsid proteins of both viruses expressed in Escherichia coli. DAS-ELISA assays were developed for routine diagnosis and conditions for preparing samples for an optimized detection were determined. No cross-reactions were observed. However, some false-negative results, corresponding to samples giving ELISA readings close to the detection limit were regularly detected, particularly for ToCV (approximately 5% of the samples). A triplex RT-PCR assay was thus developed, which allowed detection of both viruses in a one-step protocol. An internal PCR control was included, which in addition showed that it could be used as a control for the entire RT-PCR procedure. Finally, combining DAS-ELISA in a first round, and triplex RT-PCR for doubtful samples, appeared the best way to achieve a reliable diagnosis of these viruses. [source] Ribosomal DNA pseudogenes are widespread in the eucalypt group (Myrtaceae): implications for phylogenetic analysisCLADISTICS, Issue 2 2008Michael J. Bayly Pseudogenes from the 18S,5.8S,26S cistron of nuclear ribosomal DNA are reported in the eucalypt group (Myrtaceae), which includes seven genera. Putative pseudogenes are identified by a range of sequence comparisons including: the number of CpG and CpNpG methylation sites, GC content, estimated secondary structure stability of internal transcribed spacer transcripts, the presence of conserved motifs, patterns of sequence relationships and inferred substitution patterns. These comparisons indicate that pseudogenes are widespread, being evident in Eucalyptus (subgenera Eucalyptus and Eudesmia), Corymbia (extracodical sections Rufaria, Ochraria and Blakearia), Angophora, Stockwellia quadrifida and Arillastrum gummiferum. At least six sequences used in previous phylogenetic studies are identified as pseudogenes, and a further 10 pseudogenes are newly sequenced here. Gene trees place pseudogenes in a number of distinct lineages: pseudogenes from Eucalyptus group with other Eucalyptus sequences, those from Corymbia and Angophora group with other Corymbia/Angophora sequences, that from Stockwellia groups with other sequences from the Eucalyptopsis group, and that from Arillastrum is placed as sister to the other included sequence of Arillastrum. Some pseudogenes in Eucalyptus, Corymbia and Angophora represent "deep" ribosomal DNA paralogues that pre-date species differentiation in these groups, and a recombination analysis shows no evidence of recombination between putative pseudogenes and their functional counterparts. The presence of divergent paralogues presents both challenges and opportunities for the reconstruction of eucalypt phylogenies using ribosomal DNA sequences. Phylogenetic data sets should include only orthologous sequences, but different paralogues potentially provide additional, independent, character sets for phylogenetic analyses. © The Willi Hennig Society 2007. [source] | |||||||||||||