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Selected AbstractsNew computational algorithm for the prediction of protein folding typesINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 1 2001Nikola, tambuk Abstract We present a new computational algorithm for the prediction of a secondary protein structure. The method enables the evaluation of ,- and ,-protein folding types from the nucleotide sequences. The procedure is based on the reflected Gray code algorithm of nucleotide,amino acid relationships, and represents the extension of Swanson's procedure in Ref. 4. It is shown that six-digit binary notation of each codon enables the prediction of ,- and ,-protein folds by means of the error-correcting linear block triple-check code. We tested the validity of the method on the test set of 140 proteins (70 ,- and 70 ,-folds). The test set consisted of standard ,- and ,-protein classes from Jpred and SCOP databases, with nucleotide sequence available in the GenBank database. 100% accurate classification of ,- and ,-protein folds, based on 39 dipeptide addresses derived by the error-correcting coding procedure was obtained by means of the logistic regression analysis (p<0.00000001). Classification tree and machine learning sequential minimal optimization (SMO) classifier confirmed the results by means 97.1% and 90% accurate classification, respectively. Protein fold prediction quality tested by means of leave-one-out cross-validation was a satisfactory 82.1% for the logistic regression and 81.4% for the SMO classifier. The presented procedure of computational analysis can be helpful in detecting the type of protein folding from the newly sequenced exon regions. The method enables quick, simple, and accurate prediction of ,- and ,-protein folds from the nucleotide sequence on a personal computer. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 84: 13,22, 2001 [source] Phylogenetic relatedness and plant invader success across two spatial scalesDIVERSITY AND DISTRIBUTIONS, Issue 3 2009Marc W. Cadotte ABSTRACT Aim, Successful invaders often possess similar ecological traits that contribute to success in new regions, and thus under niche conservatism, invader success should be phylogenetically clustered. We asked if the degree to which non-native plant species are phylogenetically related is a predictor of invasion success at two spatial scales. Location, Australia , the whole continent and Royal National Park (south-eastern Australia). Methods, We used non-native plant species occupancy in Royal National Park, as well as estimated continental occupancy of these species from herbarium records. We then estimated phylogenetic relationships using molecular data from three gene sequences available on GenBank (matK, rbcL and ITS1). We tested for phylogenetic signals in occupancy using Blomberg's K. Results, Whereas most non-native plants were relatively scarce, there was a strong phylogenetic signal for continental occupancy, driven by the clustering of successful species in Asteraceae, Caryophyllaceae, Poaceae and Solanaceae. However, we failed to detect a phylogenetic signal at the park scale. Main Conclusions, Our results reveal that at a large spatial scale, invader success is phylogenetically clustered where ecological traits promoting success appear to be shared among close relatives, indicating that phylogenetic relationships can be useful predictors of invasion success at large spatial scales. At a smaller, landscape scale, there was no evidence of phylogenetic clustering of invasion success, and thus, relatedness plays a much reduced role in determining the relative success of invaders. [source] Application of nr-DNA ITS sequence for identification of Fusarium culmorum isolates,EPPO BULLETIN, Issue 3-4 2000P. K. Mishra Variation within the internal transcribed spacers (ITS1 and ITS2) and 5.8S ribosomal DNA region of 60 Fusarium culmorum isolates (section Discolor), representing different hosts and diverse geographical origins was examined by polymerase chain reaction (PCR), coupled with sequencing. Phylogenetic relationships of these F. culmorum isolates were estimated in relation to Fusarium spp. from this and other sections of the form-genus, using sequences available from Genbank. The amplified ITS region was approximately 570 bp long in 56 isolates and approximately 585 bp in four other isolates. The inferred phylogeny distinguished clearly four isolates supplied as F. culmorum. These isolates differed in both morphology and sequence from the remaining F. culmorum material. Sequence analysis revealed that the remaining 56 isolates were divided into three ITS types, within which the divergence was extremely low. ITS sequence comparison among the Fusarium isolates showed two major clades, one comprising sections Discolor, Sporotrichiella and Gibbosum and the other comprising Elegans, Liseola, Martiella and Roseum. These results demonstrate the use of the ITS region to resolve the identification and taxonomic problems of Fusarium spp. especially at sectional level but demonstrate the need to develop some other molecular markers for identification at the level of species or race. [source] The two N-glycans present on bovine Pofut1 are differently involved in its solubility and activityFEBS JOURNAL, Issue 5 2007Céline Loriol O-Fucosylation is a post-translational glycosylation in which an O -fucose is covalently attached to the hydroxyl group of a specific serine or threonine residue. This modification occurs within the consensus sequence C2X4,5(S/T)C3 present on epidermal growth factor-like repeats of several proteins, including the Notch receptors and their ligands. The enzyme responsible for the addition of O -fucose to epidermal growth factor-like repeats is protein O -fucosyltransferase 1. Protein O -fucosyltransferase 1-mediated O -fucosylation is essential in Notch signaling, folding and targeting to the cell surface. Here, we studied the expression pattern of protein O -fucosyltransferase 1 in cattle and showed that the active enzyme is present in all tissues examined from embryo and adult as a glycoprotein with two N-glycans. By comparing protein O -fucosyltransferase 1 sequences available in databases, we observed that mammalian protein O -fucosyltransferase 1 enzymes possess two putative N-glycosylation sites, and that only the first is conserved among bilaterians. To gain more insight regarding the significance of N-glycans on protein O -fucosyltransferase 1, we substituted, by site-directed mutagenesis, bovine protein O -fucosyltransferase 1 N65, N163 or both, with L or Q. We demonstrated that the loss of N-glycan on N163 caused a slight decrease in protein O -fucosyltransferase 1 activity. In contrast, glycosylation of N65 was crucial for protein O -fucosyltransferase 1 functionality. Loss of glycosylation at N65 resulted in aggregation of protein O -fucosyltransferase 1, suggesting that N-glycosylation at this site is essential for proper folding of the enzyme. [source] Identification of microsatellite DNA markers for population structure analysis in Indian major carp, Cirrhinus mrigala (Hamilton-Buchanan, 1882)JOURNAL OF APPLIED ICHTHYOLOGY, Issue 2 2004K. K. Lal Summary Forty-four primer sequences available for four cyprinid fishes were tested to amplify microsatellite loci in Indian major carp, Cirrhinus mrigala. A total of 12 loci were successfully amplified with clear scorable patterns and five thereof were polymorphic. Suitability of the identified polymorphic loci in population structure analysis of C. mrigala was assessed. Genetic variation was examined in 76 specimens collected from five different rivers. The mean observed heterozygosity ranged from 0.247 to 0.333. Significant heterogeneity in allele frequencies was detected, indicating that the samples analysed did not belong to homogenous populations. The identified microsatellite markers are promising for the analysis of intraspecific divergence in C. mrigala across its distribution range. [source] ANALYSIS OF EXPRESSED SEQUENCE TAGS (ESTS) FROM THE POLAR DIATOM FRAGILARIOPSIS CYLINDRUS,JOURNAL OF PHYCOLOGY, Issue 1 2006Thomas Mock Analysis of expressed sequence tags (ESTs) was performed to gain insights into cold adaptation in the polar diatom Fragilariopsis cylindrus Grunow. The EST library was generated from RNA isolated 5 days after F. cylindrus cells were shifted from approximately +5° C to ,1.8°C. A total of 1376 ESTs were sequenced from a non-normalized cDNA library and assembled into 996 tentative unique sequences. About 27% of the ESTs displayed similarity (tBLASTX, e -value of ,10,4) to predicted proteins in the centric diatom Thalassiosira pseudonana Hasle & Heindal. Eleven additional algae and plant data bases were used for annotation of sequences not covered by Thalassiosira sequences (7%). Most of the ESTs were similar to genes encoding proteins responsible for translation, ribosomal structure, and biogenesis (3%), followed by genes encoding proteins for amino acid transport and metabolism and post-translational modifications. Interestingly, 66% of all the EST sequences from F. cylindrus displayed no similarity (e -value ,10,4) to sequences from the 12 non-redundant databases. Even 6 of the 10 strong to moderately expressed sequences in this EST library could not be identified. Adaptation of F. cylindrus to freezing temperatures of seawater may require a complex protein metabolism and possibly also genes, which were highly expressed but still unknown. However, it could also mean that due to low temperatures, there might have been a stronger pressure to adapt amino acid sequences, making it more difficult to identify these unknown sequences and/or that there are still few protist sequences available for comparison. [source] The Presence of Phytoplasma in Black Currant Infected with the Blackcurrant Reversion DiseaseJOURNAL OF PHYTOPATHOLOGY, Issue 11-12 2004Abstract A plant of black currant cv. Karl,tejnský dlouhohrozen showing symptoms of the severe Russian (R) form of the blackcurrant reversion disease (BCRD) was shown to contain phytoplasma bodies measuring 530,750 nm. Phytoplasma infection was confirmed by polymerase chain reaction (PCR) with the universal primer pair R16F1/R16R0, followed by PCR with the primer pair fU5/rU3. A comparison of the sequence of an amplification product of approximately 880 bp with sequences available in the GenBank confirmed the classification of the phytoplasma in the 16SrI (Aster yellows group). This is the first evidence of the natural occurrence of phytoplasma infection in black currant. Blackcurrant reversion virus (BRV), the cause of BCRD, was confirmed in the plant by RT-PCR. A 481 nt cDNA fragment of BRV was sequenced and compared with sequences in GenBank. Rhabdovirus-like particles were also observed in the plant by electron microscopy. [source] Hemagglutinating activity and corresponding putative sequence identity from Curcuma aromatica rhizomeJOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE, Issue 6 2008Ponpimol Tiptara Abstract BACKGROUND:Curcuma aromatica is a medicinal plant belonging to the Zingiberaceae family with an incomplete genome sequence. It has been reported that extract from the rhizome of this plant contains haemagglutinating activity. In this study the profile of fractions containing hemagglutinating activity is described. RESULTS: Following extraction with saline buffer, the protein solution was fractionated by ammonium sulfate precipitation. Ion-exchange chromatography was completed on fast-flow SP-Sepharose, as well as gel filtration chromatography on Superdex 75. The active fractions were then separated by one-dimensional sodium dodecyl sulfate,polyacrylamide gel electrophoresis and labeled proteins were digested with trypsin. The digest bands were analyzed by reversed-phase liquid chromatography,tandem mass spectrometry. Inferred peptide sequences were used in Mascot searching and mass spectrometry-driven BLAST (MS-BLAST) homology searches allowed the recognition of related proteins in other species of Viridiplantae. Six putative proteins from nine bands showed similarity with lectin sequences. CONCLUSION: This study reports the identification of six lectins from the Curcuma aromatica rhizome achieved by mass spectrometry using MS-BLAST algorithms to search for homology between de novo determined peptide sequences and protein sequences available in sequence databases. Copyright © 2008 Society of Chemical Industry [source] Isolation of microsatellite loci in artichoke (Cynara cardunculus L. var. scolymus)MOLECULAR ECOLOGY RESOURCES, Issue 1 2003A. Acquadro Abstract We report the development of nine microsatellite markers in globe artichoke (Cynara cardunculus L. var. scolymus). Four markers were obtained from sequences available in GenBank and five were isolated using a biotin/streptavidin capture technique for (CA)n and (CT)n motifs directly from artichoke genomic DNA. Polymorphism was explored in 15 artichoke accessions that represent the genetic variation within cultivated varietal types. Inter-specific amplification was tested using cultivated cardoon (C. cardunculus L. var. altilis DC.) and wild cardoon (C. cardunculus L. var. sylvestris Lam.). Primers and conditions for polymerase chain reaction (PCR) amplification of detected loci are described. [source] Characterization of microsatellite loci in the diploid legume Medicago truncatula (barrel medic)MOLECULAR ECOLOGY RESOURCES, Issue 1-2 2001E. Baquerizo-Audiot Abstract We report the development of nine microsatellite markers in the diploid legume Medicago truncatula. Five markers were obtained from microsatellite-enriched genome libraries and four from sequences available in GenBank. Polymorphism was explored with plants from a natural population and cross-amplification was tested in other Medicago and three other legume genera. [source] On the unreliability of published DNA sequencesNEW PHYTOLOGIST, Issue 1 2003Paul D. Bridge Summary ,,Here, the reliability of published fungal nucleic acid sequences is tested by the critical re-evaluation of 206 named sequences obtained from public-access databases. ,,Sequences from the ribosomal RNA (rRNA) gene cluster were examined as these are commonly used to establish fungal phylogeny and evolution, and are also increasingly employed in the identification of fungi from nonculture based studies. ,,Fifty-one rRNA internal transcribed spacer (ITS) sequences were obtained for species of Amanita, 55 ITS sequences were obtained for species of Phoma and 100 rRNA small subunit sequences were obtained from representative genera of the order Helotiales. In each case, the fungal group was selected partly on the basis of sequences deposited by three or more laboratories in order to avoid sample bias. The results suggest that up to 20% of the sequences available for each group may be unreliable, and this proportion is supported by additional informal observations. [source] Determination of self-incompatible genotypes in sweet cherry (Prunus avium L.) accessions and cultivars of the German Fruit Gene Bank and from private collectionsPLANT BREEDING, Issue 5 2007M. Schuster Abstract Sweet cherries are self-incompatible because of a gametophytic self-incompatibility system. S alleles in the style and pollen determine the crossing relationships. Knowledge of the S allele constitution of cultivars is very important for cherry growers and breeders, and recently, molecular methods have been developed to distinguish the S alleles in sweet cherries. The S allele genotypes of 149 sweet cherry cultivars and clones, including 126 not previously genotyped, were determined by using PCR analysis. Thirteen different S alleles in 40 combinations were distinguished and nine new incompatibility groups were documented. Two new S alleles were identified in five local sweet cherry processing cultivars from southwestern Germany using the second intron primers. The sequence of these alleles was determined and compared to all known sequences available in the NCBI database. The sequences obtained showed high similarities to the alleles S19 and S22, previously described only in wild cherries, Prunus avium L. [source] | |||||||||||||