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At least 1,027 records · Page 57Linked to original sources
PubMed1997

Enterovirus heart disease of adults: a persistent, limited organ infection in the presence of neutralizing antibodies.

Detection of enterovirus RNA in endomyocardial biopsies (EMB) by reverse transcription/polymerase chain reaction (RT-PCR) is currently the preferred diagnostic procedure in suspected enterovirus heart disease (EHD), which can present clinically as myocarditis, dilated cardiomyopathy (DCM), and arrhythmogenic right ventricular cardiomyopathy (ARVC). EMB and peripheral blood mononuclear cells (PBMC) of 44 patients with suspected EHD were examined by nested RT-PCR to investigate whether the myocardial enterovirus infection is limited to the heart or is generalized. Enterovirus RNA was detected in EMB, but not in PBMC, of 8 patients (3 of these suffered from ARVC), whereas EMB of 16 controls and PBMC of 45 controls were negative. In addition, enterovirus RNA was demonstrated in PBMC, but not in EMB, of a single patient with suspected EHD. A high sequence homology of the amplicons to coxsackievirus B3 was demonstrated in 7 patients, and to coxsackievirus B2 in two patients. In order to evaluate whether the myocardial enterovirus infection was acute or persistent, neutralization and complement fixation tests were performed for antibodies against the serotypes indicated by the nucleic acid sequences. Neutralizing antibodies were detected in the sera of all 9 patients, but complement fixing antibodies were demonstrated only in one EHD patient and in the patient positive for enterovirus RNA in PBMC. In conclusion, the molecular and serological data demonstrate that CVB3 predominates as cardiotropic enterovirus, and that the enterovirus replication is limited to the heart in EHD. Serological results support the hypothesis of myocardial enterovirus RNA persistence in spite of neutralizing antibodies.

Adult↗
PubMed1995

Cell growth inhibition by sequence-specific RNA minihelices.

RNA minihelices which reconstruct the 12 base pair acceptor-T psi C domains of transfer RNAs interact with their cognate tRNA synthetases. These substrates lack the anticodons of the genetic code and, therefore, cannot participate in steps of protein synthesis subsequent to aminoacylation. We report here that expression in Escherichia coli of either of two minihelices, each specific for a different amino acid, inhibited cell growth. Inhibition appears to be due to direct competition between the minihelix and its related tRNA for binding to their common synthetase. This competition, in turn, sharply lowers the pool of the specific charged tRNA for protein synthesis. Inhibition is relieved by single nucleotide changes which disrupt the minihelix-synthetase interaction. The results suggest that sequence-specific RNA minihelix substrates bind to cognate synthetases in vivo and can, in principle, act as cell growth regulators. Naturally occurring non-tRNA substrates for aminoacylation may serve a similar purpose.

Alanine-tRNA Ligase↗
PubMed2001

Identification of Nash1, a novel protein containing a nuclear localization signal, a sterile alpha motif, and an SH3 domain preferentially expressed in mast cells.

By using a serial analysis of gene expression (SAGE), we have identified a novel full-length cDNA that is preferentially expressed in human cord blood-derived mast cells. The predicted protein showed unique primary structure with a nuclear localization signal (NLS), a sterile alpha motif (SAM), and a Src homology 3 domain (SH3) (termed Nash1). Nash1 was mapped to human chromosome 21q11.1 and highly expressed in spleen, liver, peripheral blood, and mast cell lines. In consistent with the presence of NLS, Nash1 was localized in the nucleus. Interestingly, screening gene databases for Nash1-related sequences revealed the existence of a Nash1-related gene termed SLY that was preferentially detected in lymphoid cells. We also found at least two additional candidates for this gene family in the database. These findings suggested that Nash1 and Nash1-related proteins consisted of a novel family of signaling/adaptor proteins, and Nash1 might function as a signaling component of mast cells, possibly in the nucleus.

Adaptor Proteins, Vesicular Transport↗
PubMed1994

Conformation of the central, three-helix junction of the 5 S ribosomal RNA of Sulfolobus acidocaldarius.

The current investigation has focused on the structure of the central, three-helix junction of the 5 S ribosomal RNA from Sulfolobus acidocaldarius, a thermoacidophilic archaebacterium. The 5 S molecule from S. acidocaldarius represents a paradigm for the study of the 5 S junction (and branched RNA structures in general) due to its unusually high degree of predicted secondary structure and stability. In order to study the junction in isolation, a set of three RNA heteroduplex molecules was assembled in which pairs of helices bounding the junction were extended by 70 base-pairs per helix. Since the extended helices comprise more than 95% of the heteroduplex structure, the relative solution conformations of the heteroduplex molecules, in effect, "report" the interhelix (branch) angles bounded by the extended pairs of helices. Examination of these heteroduplex molecules, using a combination of gel electrophoresis and transient electric birefringence measurements, has revealed a tertiary structure for the central branch in which helices I and V are essentially collinear, and in which helix II is relatively free to reorient with respect to the I-V axis.

Base Sequence↗
PubMed2006

Screening and determination of gene function using randomized ribozyme and siRNA libraries.

Rapid progress in the sequencing of the genomes of model organisms, such as the mouse, rat, nematode, fly, and Arabidopsis, as well as the human genome, has provided abundant sequence information, but functions of long stretches of these genomes remain to be determined. RNA-based technologies hold promise as tools that allow us to identify the specific functions of portions of these genomes. In particular, catalytic RNAs, known also as ribozymes, can be engineered for optimization of their activities in the intracellular environment. The introduction of a library of active ribozymes into cells, with subsequent screening for phenotypic changes, can be used for the rapid identification ofa gene function. Ribozyme technology complements another RNA-based tool for the determination of gene function, which is based on libraries of small interfering RNAs (siRNAs).

Animals↗
PubMed1993

Phylogenetic relationships of Cryptococcus neoformans and some related basidiomycetous yeasts determined from partial large subunit rRNA sequences.

The genus Cryptococcus was found to be heterogeneous on the basis of partial rRNA sequences. The human-pathogenic species C. neoformans, comprising 4 serotypes and having Filobasidiella neoformans and F. bacillispora as teleomorphs, was found at a relatively large distance from Filobasidium. Serotypes B and C had identical sequences, while in A and D they were different, with D closer to B and C than to A. Filobasidiella depauperata, which lacks a yeast-like anamorph, clustered with F. neoformans. The genus Filobasidium was clearly separated from Filobasidiella and clustered with C. albidus, C. kuetzingii, C. gastricus, C. lupi, C. vishniaciae, C. bhutanensis, C. aerius, C. terreus and C. ater. The latter may represent the anamorph of Filobasidium elegans. The orange to red species of Cryptococcus, as well as C. aquaticus and C. yarrowii, were found completely unrelated with these taxa, C. macerans being affiliated to Cystofilobasidium capitatum. The genus Trichosporon was found relatively homogeneous; it includes C. humicola, C. curvatus and the filamentous species Hyalodendron lignicola. Cryptococcus flavus and C. dimennae probably belong to the Tremellales, though distances between these species are large. The positions of C. laurentii and C. luteolus remains to be determined.

Base Sequence↗
PubMed2005

Molecular identification and characterization of canine Hepatozoon species from Brazil.

Canine Hepatozoon species from Brazil was molecular identified and characterized for the first time. From 31 dogs, 7 were positive for blood smear examination and 21 positive for PCR. Partial sequences of the 18S rRNA gene from eight naturally infected dogs were analyzed. Sequences revealed that Brazilian Hepatozoon is closely related with the Japanese Hepatozoon, that has 99% nucleotide identity with Hepatozoon canis from Israel, and different from Hepatozoon americanum. These results indicate that the canine Hepatozoon species from Brazil is H. canis.

Animals↗
PubMed2000

Identification of facultatively alkaliphilic Bacillus sp. strain YN-2000 and its fatty acid composition and cell-surface aspects depending on culture pH.

Facultatively alkaliphilic Bacillus sp. strain YN-2000 was isolated from an indigo ball. Although the strain has been extensively investigated as a representative strain of alkaliphilic bacillus, its taxonomic position is not yet known. Morphological, biochemical, and physiological characteristics and chemotaxonomic properties indicated that the strain was closely related to Bacillus cohnii; this was confirmed by the high homology of the 16S rRNA sequence and the construction of a phylogenetic tree on the basis of the 16S rRNA sequence and DNA-DNA relatedness data. Strain YN-2000 contained a larger amount of unsaturated fatty acids compared with Bacillus subtilis and the obligate alkaliphile, Bacillus alcalophilus, regardless of its culture pH. When the cells were grown at pH 10, the unsaturated fatty acid content and anteiso-/iso-branched fatty acid ratio became lower than those at pH 7. This result suggests that membrane fluidity decreases when the cells are grown at pH 10 compared to those of pH 7. In the cells of strain YN-2000 grown at pH 10, the cell-surface aspect was rougher, the cell shape was longer, and the cell-surface layer was thicker compared with those of the cells grown at pH 7. The cell-surface structural change might be related to adaptation to an alkaline environment.

Alkalies↗
PubMed2005

The Amblyomma maculatum Koch, 1844 (Acari: Ixodidae: Amblyomminae) tick group: diagnostic characters, description of the larva of A. parvitarsum Neumann, 1901, 16S rDNA sequences, distribution and hosts.

A review of the largely confused Amblyomma maculatum Koch, 1844 tick group of the subgenus Anastosiella Santos Dias, 1963 (A. neumanni Ribaga, 1902, A. maculatum, A. parvitarsum Neumann, 1901, A. tigrinum Koch, 1844 and A. triste Koch, 1844) is presented together with a discussion of the diagnostic characters used for the determination of adults, nymphs and, to a lesser extent, larvae. A key for this tick group is produced, including the description of the larva of A. parvitarsum, 1901. Sequences of 16S rDNA are obtained and compared with other Amblyomma spp., including two other species currently in Anastosiella but in the ovaletick group, A. ovale Koch, 1844 and A. aureolatum (Pallas, 1772). According to the morphology and the rDNA sequences, the maculatum group is reduced to A. maculatum (Neotropical-Nearctic), A. tigrinum (Neotropical) and A. triste (Neotropical) A. neumanni and A. parvitarsum are excluded from the subgenus. The distribution is sympatric in northern South America from where A. maculatumreaches the southern Nearctic and the range of A. tigrinum extends to the southern Neotropics. These species have been found on several domestic and wild vertebrates. A. triste and A. tigrinum have been also found on man. Their role as vectors of pathogens deserves further investigation.

Americas↗
PubMed1992

Cell wall-less, free-living spirochetes in Antarctica.

The phylogeny of an Antarctic, cell wall-less, bacterial strain was determined by sequencing PCR amplified 16S rDNA, and comparison of the sequence with other bacterial 16S rRNA sequences available in databanks. Although the strain was phenotypically very similar to members of the genus Anaeroplasma, phylogenetic analyses showed it was a member of the order Spirochaetales. Until now, the order was one of the few bacterial orders in which phylogeny was reflected in a uniform morphology of its members. The viability of wall-less cells in cultures of spirochetes and spirochetal infective material warrants reinvestigation.

Antarctic Regions↗
PubMed2005

Prediction of siRNA knockdown efficiency using artificial neural network models.

Selective knockdown of gene expression by short interference RNAs (siRNAs) has allowed rapid validation of gene functions and made possible a high throughput, genome scale approach to interrogate gene function. However, randomly designed siRNAs display different knockdown efficiencies of target genes. Hence, various prediction algorithms based on siRNA functionality have recently been constructed to increase the likelihood of selecting effective siRNAs, thereby reducing the experimental cost. Toward this end, we have trained three Back-propagation and Bayesian neural network models, previously not used in this context, to predict the knockdown efficiencies of 180 experimentally verified siRNAs on their corresponding target genes. Using our input coding based primarily on RNA structure thermodynamic parameters and cross-validation method, we showed that our neural network models outperformed most other methods and are comparable to the best predicting algorithm thus far published. Furthermore, our neural network models correctly classified 74% of all siRNAs into different efficiency categories; with a correlation coefficient of 0.43 and receiver operating characteristic curve score of 0.78, thus highlighting the potential utility of this method to complement other existing siRNA classification and prediction schemes.

Algorithms↗
PubMed2005

Mutations in a conserved replication protein suppress transcriptional gene silencing in a DNA-methylation-independent manner in Arabidopsis.

Mutations in the DNA glycosylase/lyase ROS1 cause transcriptional silencing of the linked RD29A-LUC and 35S-NPTII transgenes in Arabidopsis. We report here that mutations in the Arabidopsis RPA2 locus release the silencing of 35S-NPTII but not RD29A-LUC in the ros1 mutant background. The rpa2 mutation also leads to enhanced expression of some transposons. Neither DNA methylation nor siRNAs at any of the reactivated loci are blocked by rpa2. Histone H3 methylation at lysine 4 was increased and histone H3 methylation at lysine 9 was decreased at the 35S promoter in the ros1rpa2 mutant compared to the ros1 background. RPA2 encodes a nuclear protein similar to the second subunit of the replication protein A conserved from yeast to mammals. Ectopic expression of the Arabidopsis RPA2 could complement the yeast rfa2 (rpa2) mutant. These results suggest an essential role of RPA2 in the maintenance of transcriptional gene silencing at specific loci in a DNA-methylation-independent manner. In addition, we found that rpa2 mutants are hypersensitive to the genotoxic agent methyl methanesulphonate, and the RPA2 protein interacts with ROS1 in vitro and in vivo, suggesting that RPA2 also functions together with ROS1 in DNA repair.

Amino Acid Sequence↗
PubMed2006

Data analysis of alternative splicing microarrays.

The importance of alternative splicing in drug and biomarker discovery is best understood through several example genes. For most genes, the identification, detection and particularly quantification of isoforms in different tissues and conditions remain to be carried out. As a result, the focus in drug and biomarker development is increasingly on high-throughput studies of alternative splicing. Initial strategies for the parallel analysis of alternative splicing by microarrays have been recently published. The design specificities and goals of alternative splicing microarrays, in terms of identification and quantification of multiple mRNAs from one gene, are promoting the development of novel methods of analysis.

Algorithms↗
PubMed2006

Nosema ceranae, a new microsporidian parasite in honeybees in Europe.

Twelve samples of adult honey bees from different regions of Spain from colonies with clear signs of population depletion, positive to microsporidian spores using light microscopy (1% of total positive samples analysed), were selected for molecular diagnosis. PCR specific primers for a region of the 16S rRNA gene of Microsporidia were developed and the PCR products were sequenced and compared to GenBank entries. The sequenced products of 11 out of the 12 samples were identical to the corresponding Nosema ceranae sequence. This is the first report of N. ceranae in colonies of Apis mellifera in Europe. The suggested link of the infections to clinical disease symptoms makes imperative a study of the virulence of N. ceranae in European races of honey bees.

Animals↗
PubMed2006

Early legume responses to inoculation with Rhizobium sp. NGR234.

Interactions between legumes and rhizobia are controlled by the sequential exchange of symbiotic signals. Two different techniques, 2D-PAGE electrophoresis and differential display were used to study the effects of rhizobial signals on legume development. Application of variously substituted lipo-oligo-saccharidic Nod-factors to roots of Vigna unguiculata resulted in changes in the phosphorylation patterns of microsomal proteins. Reliable amino-acid sequences were obtained for one Nod-factor enhanced protein which was highly homologous to the 57-kDa subunit from Arabidopsis thaliana vacuolar membrane H(+)-ATPase. Immuno-blotting techniques demonstrated that Nod-factors cause rapid and massive increases of this enzyme in treated roots, suggesting that H(+)-ATPases play symbiotic roles. Concomitantly, we used differential display (DD) techniques on mRNA isolated from root-hairs to analyse early root responses to NGR234. Significant matches of several DD clones to known sequences were found. Clone D2.62 was homologous to a multitude of receptor kinases including S receptor-like kinases of A. thaliana and clone D4.1 showed similarities to Lotus japonicus phosphatidylinositol transfer-like protein III and late nodulin 16. Independent confirmatory analyses of these differentially expressed clones indicated expression at very low levels.

Cell Fractionation↗
PubMed2004

A conserved non-homeodomain Hoxa9 isoform interacting with CBP is co-expressed with the 'typical' Hoxa9 protein during embryogenesis.

Various Hox genes are known to produce alternative transcripts encoding different isoforms whose physiological relevance during development is not yet understood. In this work, we analysed two different Hoxa9 mRNAs encoding a full-length protein (Hoxa9) or a protein lacking the homeodomain (Hoxa9T). First, we demonstrated that these transcripts are conserved from birds to mammals. We then showed that both transcripts are present throughout embryogenesis and that Hoxa9T transcript is particularly abundant in embryonic genital tract, kidney, forelimb and tail. We further found that both isoforms are able to interact with CBP, suggesting a competition between Hoxa9 and Hoxa9T with this protein.

Animals↗
PubMed2005

Structure, folding and mechanisms of ribozymes.

The past two years have seen exciting developments in RNA catalysis. A completely new ribozyme (possibly two) has come along and several new structures have been determined, including three different group I intron species. Although the origins of catalysis remain incompletely understood, a significant convergence of views has happened in the past year, together with the discovery of new super-fast ribozymes. There is persuasive evidence of general acid-base chemistry in nucleolytic ribozymes, whereas catalysis of peptidyl transfer in the ribosome seems to result largely from orientation and proximity effects. Lastly, important new folding-enhancing elements have been discovered.

Base Sequence↗