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At least 379 records · Page 21Linked to original sources
PubMed1993

The phylogenetic position of the Aspidobothrea within the parasitic flatworms inferred from ribosomal RNA sequence data.

Sequence data from parts of the small subunit ribosomal RNA gene (18s rRNA) from an aspidobothrean and two digeneans have been added to a published data set which includes sequences from a number of parasitic and non-parasitic flatworms. Parsimony and distance matrix analyses of the data were carried out. Tests for particular clades were done using bootstrap resampling methods, and tests of particular topologies done using 4- and 5-taxon tests. The aspidobothrean Lobatostoma manteri emerges from near the base of the Neodermata, but whether as a sister group to the rest of the Neodermata or as a sister to the Digenea alone cannot be determined from the number of nucleotide sites available. Gyrocotyle is included with the cestodes in a very strongly supported clade in all analyses. There is evidence that the Monogenea is a paraphyletic group, although more data are needed to confirm this possibility.

Animals↗
PubMed1994

Phylogeny of dermatophytes and dimorphic fungi based on large subunit ribosomal RNA sequence comparisons.

The phylogeny of dermatophytes and dimorphic fungi was considered using the large-subunit of ribosomal RNA (25S rRNA). Aligned sequences of 595 nucleotides covering the two most divergent domains D1 and D2, permitted a comparison of phylogenetic relationships at different levels. The dimorphic species (Onygenaceae) were significantly separated from dermatophytes (Arthrodermataceae) and from a third group including geophilic or very weakly pathogenic species (Onygenaceae and Gymnoascaceae). On a species level, the varietal status of Histoplasma duboisii and Histoplasma farciminosum, as close relations of Histoplasma capsulatum, was confirmed. The dimorphic fungus Emmonsia parva, in spite of a completely different parasitic form (adiaspores instead of yeast-like cells), clustered with Blastomyces dermatitidis which has a perfect form resembling that of H. capsulatum. From our data, teleomorphs of E. parva, Paracoccidioides brasiliensis and H. farciminosum, three dimorphic fungi known only under their anamorphic states, should belong to the family of Onygenaceae and the genus Ajellomyces. Among Arthrodermataceae, and family containing the most keratinophilic species, it was not possible to establish a clear hierarchy of species. Only Ctenomyces serratus, the species adapted to degrade keratin of feathers, Trichophyton ajelloi and Trichophyton terrestre were significantly separated. The speciation of true dermatophytes resulted most likely from a very recent evolution by adaptation to parasitism. Among species used as outgroups, the two emerging pathogens Pseudallescheria boydii (Scedosporium apiospermum) and Scedosporium prolificans (Scedosporium inflatum) were shown to be closely related to each other.

Arthrodermataceae↗
PubMed1994

Phylogenetic relationships among Vairimorpha and Nosema species (Microspora) based on ribosomal RNA sequence data.

A portion (approximately 350 nucleotides) of the large subunit ribosomal RNA (rRNA) 5' to the 580 region (Escherichia coli numbering) was sequenced using the reverse transcriptase dideoxy method and compared for several species of Nosema and Vairimorpha. Comparison among Nosema species suggests that this genus is composed of several unrelated groups. The group which includes the type species, Nosema bombycis, consists of closely related species found primarily in Lepidoptera. Other Nosema species sequenced (Nosema kingi, Nosema algerae, and Nosema locustae) do not appear to be closely related to each other or to the lepidopteran Nosema group. Comparison among the Vairimorpha species indicates that two distinct but very closely related groups exist. The Lymantria group consists of species isolated from the gypsy moth, Lymantria dispar, while the Vairimorpha necatrix group consists of species isolated from other Lepidoptera. Intergeneric comparison of the sequence data suggests that the lepidopteran Nosema species are closely related to the Vairimorpha species.

Animals↗
PubMed1985

Self-catalyzed cyclization of the intervening sequence RNA of Tetrahymena: inhibition by intercalating dyes.

The intervening sequence (IVS) excised from the pre-rRNA of Tetrahymena undergoes a self-catalyzed cleavage-ligation reaction to form a covalently closed circular RNA. This cyclization reaction is kinetically inhibited by ethidium bromide (50% inhibition at 22 +/- 14 microM, greater than 99% inhibition at 53 +/- 16 microM for a 20 minute reaction). The dye does not alter the sites of the cyclization reaction, but it does increase the relative amount of reaction at a minor site 19 nucleotides from the 5' end of the IVS. The reversibility of the inhibition and the relative inhibitory strength of acridine orange, ethidium and proflavine suggest that inhibition is due to intercalation of the dye in functionally important secondary or tertiary structures of the IVS. The concentration of dye required to inhibit cyclization is much higher than expected from the known binding constants of such dyes to tRNA. At high Mg2+ to Na+ ratios, conditions which should stabilize RNA structure, a subpopulation of the IVS RNA molecules is resistant to ethidium inhibition, even at 200 microM ethidium. These data are interpreted as reflecting two conformational isomers of the IVS that differ in their reactivity and in their sensitivity to dye binding.

Acridine Orange↗
PubMed1988

Total chemical synthesis of a 77-nucleotide-long RNA sequence having methionine-acceptance activity.

Chemical synthesis is described of a 77-nucleotide-long RNA molecule that has the sequence of an Escherichia coli Ado-47-containing tRNA(fMet) species in which the modified nucleosides have been substituted by their unmodified parent nucleosides. The sequence was assembled on a solid-phase, controlled-pore glass support in a stepwise manner with an automated DNA synthesizer. The ribonucleotide building blocks used were fully protected 5'-monomethoxytrityl-2'-silyl-3'-N,N-diisopropylaminophosphoram idites. p-Nitro-phenylethyl groups were used to protect the O6 of guanine residues. The fully deprotected tRNA analogue was characterized by polyacrylamide gel electrophoresis (sizing), terminal nucleotide analysis, sequencing, and total enzyme degradation, all of which indicated that the sequence was correct and contained only 3-5 linkages. The 77-mer was then assayed for amino acid acceptor activity by using E. coli methionyl-tRNA synthetase. The results indicated that the synthetic product, lacking modified bases, is a substrate for the enzyme and has an amino acid acceptance 11% of that of the major native species, tRNA(fMet) containing 7-methylguanosine at position 47.

Base Sequence↗
PubMed2000

Comparison of human immunodeficiency virus type 1 RNA sequence heterogeneity in cerebrospinal fluid and plasma.

The source of human immunodeficiency virus type 1 (HIV-1) RNA in cerebrospinal fluid (CSF) during HIV-1 infection is uncertain. The sequence heterogeneity of HIV-1 RNA in simultaneous CSF and plasma samples was characterized for five patients at the baseline and during the first week of antiretroviral therapy by two commercial genotyping methodologies. In individual subjects, the sequences in CSF samples differed significantly from those in plasma. In contrast, the viral sequences in CSF at the baseline did not differ from the sequences in CSF during treatment. Similarly, viral sequences in plasma did not vary over this interval. This study provides evidence that HIV-1 RNA in CSF and plasma arise from distinct compartments.

Anti-HIV Agents↗
PubMed2001

RNA sequences involved in transcriptional termination of respiratory syncytial virus.

RNA signals at the ends of the genes of respiratory syncytial (RS) virus direct polyadenylation and termination of viral transcription. These gene ends contain two conserved regions, a pentanucleotide and a tract of uridylate (U) residues, separated by an A/U-rich central region that is less well conserved. The U tract is thought to be the template for polyadenylation of viral mRNAs by reiterative transcription. The cis-acting requirements for termination were investigated by mutagenesis of the matrix (M) gene end (3'-UCAAUUAUUUUUU-5') in a dicistronic RNA replicon. Termination efficiencies were quantitated by intracellular metabolic labeling of monocistronic mRNAs and the dicistronic readthrough RNAs that result when termination fails to occur. All three regions of the gene end were necessary for termination. Mutation of each of the first 8 nucleotides of the M gene end to all other nucleotides showed that nucleotides 2 to 6 were important for termination and intolerant of change, whereas nucleotides 1 and 7 were tolerant of change. At position 8, A or U allowed termination, but G or C did not. Both the length and the position of the U tract were important for termination. U residues at positions 9 to 12 were necessary, while additional U residues at position 8, and especially position 13, enhanced termination efficiency. Altering the length of the central region abolished termination, suggesting that the position of the U tract with respect to the 3'-UCAAU-5' sequence was critical. The termination efficiencies of each of the 10 genes of RS virus are different. Since transcription is obligatorily sequential and termination of each gene is required for transcription of the next gene downstream, these differences may contribute to gene regulation. In agreement with our data, the naturally occurring gene ends of RS virus that terminate inefficiently have short U tracts or other sequence features that correlated with decreased termination when similar mutations were analyzed in RNA replicons.

RNA, Viral↗
PubMed1989

Increased viral pathogenicity after insertion of a 28S ribosomal RNA sequence into the haemagglutinin gene of an influenza virus.

The haemagglutinin glycoprotein HA of influenza viruses is responsible for the attachment of the virus to neuraminic acid-containing receptors at the cell surface and subsequent penetration by triggering fusion of the viral envelope with cellular membranes. To express full activity of the newly synthesized precursor, HA has to be modified by post-translational proteolytic cleavage into the polypeptides HA1 and HA2 by cellular enzymes. If proteases suitable for cleavage are not present in the host cell, the resulting virus particles are non-infectious. During adaptation of the apathogenic influenza virus A/turkey/Oregon/71 to chicken embryo cells, which are not permissive for HA cleavage, we obtained an infectious virus variant with increased pathogenicity. Sequence analysis revealed that during adaptation 54 nucleotides were inserted into the HA gene; their sequence corresponds to a region of the 28S ribosomal RNA. This insertion is probably responsible for increased cleavability of HA, as well as for infectivity and pathogenicity of the adapted virus.

Base Sequence↗
PubMed1977

The distribution of poly(A)+ and poly(A)- protamine messenger RNA sequences in the developing trout testis.

Protamine messenger RNA was isolated in a very pure form from trout testes and used as a template for the synthesis of labeled complementary DNA (cDNA) of high specifiv activity. The cDNA was found to be a full-length transcript of protamine messenger RNA and was used as a probe for hybridization reactions with RNA preparations isolated from three subcellular compartments of differentiating trout testis cells. The RNA populations from the nuclei, polysomes, and postribosomal supernatant of these cells were fractionated into poly(A)-containing [poly(A)+] and poly(A)-free [poly(A)-] RNA to determine the distribution of these two forms of protamine mRNA in these cell compartments. At the early protamine stage of testis development, polysomal and postribosomal supernatant fractions contain almost equal quantities of poly(A)+ protamine mRNA, but poly(A)- protamine mRNA was found almost entirely in the polysomes.

Animals↗
PubMed1998

Dissecting RNA recombination in vitro: role of RNA sequences and the viral replicase.

Molecular mechanisms of RNA recombination were studied in turnip crinkle carmovirus (TCV), which has a uniquely high recombination frequency and non-random crossover site distribution among the recombining TCV-associated satellite RNAs. To test the previously proposed replicase-driven template-switching mechanism for recombination, a partially purified TCV replicase preparation (RdRp) was programed with RNAs resembling the putative in vivo recombination intermediates. Analysis of the in vitro RdRp products revealed efficient generation of 3'-terminal extension products. Initiation of 3'-terminal extension occurred at or close to the base of a hairpin that was a recombination hotspot in vivo. Efficient generation of the 3'-terminal extension products depended on two factors: (i) a hairpin structure in the acceptor RNA region and (ii) a short base-paired region formed between the acceptor RNA and the nascent RNA synthesized from the donor RNA template. The hairpin structure bound to the RdRp, and thus is probably involved in its recruitment. The probable role of the base-paired region is to hold the 3' terminus near the RdRp bound to the hairpin structure to facilitate 3'-terminal extension. These regions were also required for in vivo RNA recombination between TCV-associated sat-RNA C and sat-RNA D, giving crucial and direct support for a replicase-driven template-switching mechanism of RNA recombination.

Binding Sites↗
PubMed1983

A new approach to the classification of human leukaemias: measurement of the relative abundance of a specific RNA sequence by means of molecular hybridisation.

A recombinant plasmid library representing polyadenylated RNAs in the leucocytes of a Ph1-positive chronic granulocytic leukaemia (CGL) has been constructed. One recombinant (designated pCG14) isolated from this library contains a DNA sequence complementary to a small polyadenylated RNA that is abundant in RNA from CGL leucocytes. The relative concentrations of pCG14 RNA in the RNAs from a variety of normal and leukaemic leucocytes and human haemopoietic cell lines have been measured with a molecular hybridisation assay. This has shown that pCG14 RNA is 10 to 50 times more abundant in RNA from CGL leucocytes than in the RNAs from these other cells. The data indicate that the occurrence of pCG14 RNA in high abundance is sufficiently characteristic of a CGL leucocyte population to distinguish it from other populations of leucocytes. They suggest that the measurement of the concentrations of specific RNA species in leucocyte RNA by means of molecular hybridisation with cloned complementary DNAs may provide additional markers for the objective classification of human leukaemias which could be particularly useful since the method exploits a criterion different from any currently in use.

Autoradiography↗
PubMed1996

Invariant U2 RNA sequences bordering the branchpoint recognition region are essential for interaction with yeast SF3a and SF3b subunits.

U2 small nuclear RNA (snRNA) contains a sequence (GUAGUA) that pairs with the intron branchpoint during splicing. This sequence is contained within a longer invariant sequence of unknown secondary structure and function that extends between U2 and I and stem IIa. A part of this region has been proposed to pair with U6 in a structure called helix III. We made mutations to test the function of these nucleotides in yeast U2 snRNA. Most single base changes cause no obvious growth defects; however, several single and double mutations are lethal or conditional lethal and cause a block before the first step of splicing. We used U6 compensatory mutations to assess the contribution of helix III and found that if it forms, helix III is dispensable for splicing in Saccharomyces cerevisiae. On the other hand, mutations in known protein components of the splicing apparatus suppress or enhance the phenotypes of mutations within the invariant sequence that connect the branchpoint recognition sequence to stem IIa. Lethal mutations in the region are suppressed by Cus1-54p, a mutant yeast splicing factor homologous to a mammalian SF3b subunit. Synthetic lethal interactions show that this region collaborates with the DEAD-box protein Prp5p and the yeast SF3a subunits Prp9p, Prp11p, and Prp21p. Together, the data show that the highly conserved RNA element downstream of the branchpoint recognition sequence of U2 snRNA in yeast cells functions primarily with the proteins that make up SF3 rather than with U6 snRNA.

Base Sequence↗
PubMed2002

Description of Enteromyxum scophthalmi gen. nov., sp. nov. (Myxozoa), an intestinal parasite of turbot (Scophthalmus maximus L.) using morphological and ribosomal RNA sequence data.

A new Myxozoa species causing enteritis and death in cultured turbot, Scophthalmus maximus, is described at light and electron microscope levels. In addition, small subunit ribosomal RNA gene sequences (SSU rDNA) from the new species and from similar myxozoans were obtained and used for phylogenetic inference, as complementary criteria to resolve its taxonomic classification. The new parasite is closely related to Myxidium leei, another enteric histozoic species from marine fish. However, the ascription of M. leei to the genus Myxidium was based on weak morphological evidence and is not supported by our rDNA data analysis. A close relationship with Zschokkella, the other morphologically related myxozoan genus is also not supported. The combined morphological and molecular study results in the establishment of the new genus Enteromyxum to accommodate the new species E. scophthalmi, and the former M. leei, which is transferred to the new genus as Enteromyxum leei (Diamant, Lom & Dyková 1994) n. comb. This genus of marine, histozoic and enteric myxozoans includes significant parasite species for marine finfish culture.

Animals↗
PubMed1989

Partial RNA sequencing of eight supposed derivatives of type 3 poliovirus/USA/Saukett/50 reveals remarkable differences between three apparent substrains.

Eight supposed derivatives of type 3 poliovirus/USA/Saukett/50 could be divided in three subgroups differing from each other as much as from the independent P3/Sabin strain as judged by partial genomic sequences covering about 25% of the portion of RNA coding for the structural proteins. This suggests that strains designated as Saukett in different laboratories are derived from three separate but related American isolates of type 3 poliovirus. Deduced amino acid sequence of the "Saukett" strains revealed amino acid substitutions at all known major antigenic sites compared with P3/Sabin or P3/Finland/23127/84 strain, but also between individual Saukett strains. These substitutions may be responsible for the known antigenic differences between the studied strains.

Amino Acid Sequence↗
PubMed1993

RNA sequence of astrovirus: distinctive genomic organization and a putative retrovirus-like ribosomal frameshifting signal that directs the viral replicase synthesis.

The genomic RNA of human astrovirus was sequenced and found to contain 6797 nt organized into three open reading frames (1a, 1b, and 2). A potential ribosomal frameshift site identified in the overlap region of open reading frames 1a and 1b consists of a "shifty" heptanucleotide and an RNA stem-loop structure that closely resemble those at the gag-pro junction of some retroviruses. This translation frame-shift may result in the suppression of in-frame amber termination at the end of open reading frame 1a and the synthesis of a nonstructural, fusion polyprotein that contains the putative protease and RNA-dependent RNA polymerase. Comparative sequence analysis indicated that the protease and polymerase of astrovirus are only distantly related to the respective enzymes of other positive-strand RNA viruses. The astrovirus polyprotein lacks the RNA helicase domain typical of other positive-strand RNA viruses of similar genome size. The genomic organization and expression strategy of astrovirus, with the protease and the polymerase brought together by predicted frameshift, most closely resembled those of plant leuteoviruses. Specific features of the sequence and genomic organization support the classification of astroviruses as an additional family of positive-strand RNA viruses, designated Astroviridae.

Base Sequence↗
PubMed1994

Ribosomal RNA sequence phylogeny is not congruent with ascospore morphology among species in Ceratocystis sensu stricto.

The genus Ceratocystis sensu stricto includes important fungal pathogens of woody and herbaceous plants. This genus is distinguished from species in Ceratocystis sensu lato by the presence of Chalara anamorphs. Ascospore shape has been used extensively in delineating Ceratocystis taxa, which show a large variety of ascospore shapes. Sequence analysis of one region of he 18S ribosomal RNA subunit and two regions of the 28S ribosomal RNA subunit showed that there was a majority of multiple substitutions at nucleotide sites and that there was a low transition/transversion ratio, T = 0.72. Both of these results suggest that these are well established, old species. Ascospore morphology, for the most part, was not congruent with the molecular phylogeny, and the use of morphological characters may be misleading in the taxonomy of these species.

Ascomycota↗
PubMed1998

Brazilian isolates of Trypanosoma cruzi from humans and triatomines classified into two lineages using mini-exon and ribosomal RNA sequences.

Traditional molecular and biochemical methods, such as schizodeme analysis, karyotyping, DNA fingerprinting, and enzyme electrophoretic profiles, have shown a large variability among Trypanosoma cruzi isolates. In contrast to those results, polymerase chain reaction (PCR) amplification of sequences from the 24S alpha ribosomal RNA gene and from the mini-exon gene nontranscribed spacer indicated a dimorphism among T. cruzi isolates, which enabled the definition of two major parasite lineages. In the present study, 86 T. cruzi field stocks (68 isolated from humans with defined presentations of Chagas' disease and 18 from triatomines) derived from four Brazilian geographic areas were typed by the PCR assay based on the DNA sequences of the mini-exon and 24S alpha rRNA genes. These stocks were ordered into the two major T. cruzi lineages. Lineage 1 was associated mainly with human isolates and lineage 2 with the sylvatic cycle of the parasite.

Animals↗
PubMed1985

RNA sequence and transcriptional properties of the 3' end of the Newcastle disease virus genome.

The 3' end of the genomic RNA of Newcastle disease virus (NDV) has been sequenced and the leader RNA defined. Using hybridization to a 3'-end-labeled genome, leader RNA species from in vitro transcription reactions and from infected cell extracts were found to be 47 and 53 nucleotides long. In addition, the start site of the 3'-proximal mRNA was determined by sequence analysis of in vitro [beta-82P]GTP-labeled transcription products. The genomic sequence extending beyond the leader region demonstrated an open reading frame for at least 42 amino acids and probably represents the amino terminus of the nucleocapsid protein (NP). The terminal 8 nucleotides of the NDV genome were identical to those of measles virus and Sendai virus while the sequence of the distal half of the leader region was more similar to that of vesicular stomatitis virus. These data argue for strong evolutionary relatedness between the paramyxovirus and rhabdovirus groups.

Animals↗