Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Direct RNA sequencing”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources
PubMed1993

Targeting RNA for degradation with a (2'-5')oligoadenylate-antisense chimera.

Antisense oligonucleotides hold considerable promise both as research tools for inhibiting gene expression and as agents for the treatment of a myriad of human diseases. However, targeted destruction of RNA has been difficult to achieve in a versatile, efficient, and reliable manner. We have developed an effective strategy for cleaving unique RNA sequences with 2-5A-dependent RNase, an endoribonuclease that mediates inhibitory effects of interferon on virus infection and is activated by 5'-phosphorylated 2'-5'-linked oligoadenylates known as 2-5A [pn5' A2'(p5' A2')mp5'A], resulting in the cleavage of single-stranded RNA predominantly after UpUp and UpAp sequences. To direct 2-5A-dependent RNase to cleave unique RNA sequences, p5' A2' p5' A2'p5'A was covalently linked to an antisense oligonucleotide to yield a chimeric molecule (2-5A:AS). The antisense oligonucleotide component of 2-5A:AS bound a specific RNA sequence while the accompanying 2-5A component activated 2-5A-dependent RNase, thereby causing the cleavage of the RNA in the targeted sequence. This strategy was demonstrated by inducing specific cleavage within a modified human immunodeficiency virus type 1 vif mRNA in a cell-free system from human lymphoblastoid cells. Because 2-5A-dependent RNase is present in most mammalian cells, the control of gene expression based on this technology--including therapies for cancer, viral infections, and certain genetic diseases--can be envisioned.

Adenine Nucleotides↗
PubMed1998

Three novel integrin beta3 subunit missense mutations (H280P, C560F, and G579S) in thrombasthenia, including one (H280P) prevalent in Japanese patients.

We analyzed three unrelated Japanese patients with type II Glanzmann thrombasthenia (GT) for associated mutations. Polymerase chain reaction and subsequent direct sequencing of platelet RNA and genomic DNA revealed three single nucleotide substitutions of the integrin beta3 subunit gene (His (CAT)-280 to Pro (CCT), Cys (TGT)-560 to Phe (TTT), and Gly(GGC)-579 to Ser(AGC)). Interestingly, the three unrelated patients all had the H280P mutation; one was homozygous and the other two heterozygous for this mutation. Ectopic expression of wild type and mutant complexes in Chinese hamster ovary cells revealed decreased surface expression of the mutated alphaIIbbeta3 complexes, thus demonstrating that these mutations may result in the mild GT phenotypes. The identification of three unrelated patients having the same mutation (H280P) suggests that this mutation might be prevalent in the Japanese thrombasthenic population.

Aged↗
PubMed1992

A redefinition of the Asp-Asp domain of reverse transcriptases.

The rules defining the Asp-Asp domain of RNA-dependent polymerases deduced by Argos (1988) were tested in a set of 53 putative reverse transcriptases (RTs) sequences. Since it was found that some of these rules are not followed by RTs coded by bacteria, group II introns, and non-LTR retrotransposons, we present here a more strict definition of the Asp-Asp domain.

Amino Acid Sequence↗
PubMed1995

Preparation of cDNA-silica using reverse transcriptase and its DNA sequence determination.

A new method for producing macroporous silica (suitable for high-performance liquid chromatography) with covalently attached DNA is presented. The method uses (dT)18-silica as a primer, annealed to a poly(A)-RNA template, which is then transcribed using reverse transcriptase. The RNA template is eluted and single-stranded cDNA-silica is recovered. The cDNA-silica can be sequenced using the dideoxy method. These methods provide a facile method for producing cDNA-silica of demonstrable authenticity and provide a unique approach to DNA and RNA sequencing.

Base Sequence↗
PubMed1990

Type I (R1) and type II (R2) ribosomal DNA insertions of Drosophila melanogaster are retrotransposable elements closely related to those of Bombyx mori.

Approximately 50% of the ribosomal DNA (rDNA) units of Drosophila melanogaster are inactivated by two different 28 S RNA ribosomal gene insertions (type I and type II). We present here the nucleotide sequence of complete type I and type II elements. Conceptual translation of these sequences revealed open reading frames (ORFs) encoding amino acid residues conserved in all retrotransposable elements. Full-length type I elements are 5.35 x 10(3) base-pairs in length and contain two overlapping ORFs. The smaller ORF (471 amino acid residues) has similarity to gag genes, while the larger ORF (1021 residues) has similarity to pol genes. Full-length type II elements are 3.6 x 10(3) base-pairs and contain one large ORF (1056 residues) that appears to represent a gag-pol fusion. Type I and type II elements are similar in structure, in the proteins they encode, and in insertion specificity to the R1Bm and R2Bm retrotransposable elements of Bombyx mori. We suggest that the D. melanogaster elements be called R1Dm and R2Dm, to reflect their structure as retrotransposons. Comparison of the R1 and R2 elements from these two widely different species revealed regions of the ORF that are likely to play an important role in the propagation of the elements. Four distinct regions of sequence conservation separated by regions of little or no sequence similarity were detected for both the R1 and R2 elements: (1) cysteine motifs of the gag gene, with three such motifs for R1 and one motif for R2; (2) a reverse transcriptase domain; (3) an integrase domain located carboxyl terminal to the reverse transcriptase region; and (4) a small region amino terminal to the reverse transcriptase domain, whose function is not known. The level of identity of the amino acid residues for these segments is 28 to 34% between the R1 elements, and 34 to 39% for the R2 elements. Finally, it may be predicted that the mechanism of unequal crossover might eventually eliminate R1 and R2 from the rDNA locus. The long history of selection at the protein level exhibited by these elements indicates that it is their active transposition that maintains them in the locus. The high level of sequence homogeneity between copies of each element within the same species is consistent with the high turnover rate expected to result from these processes.

Amino Acid Sequence↗
PubMed1989

Nucleotide sequence of the avian influenza A/Mallard/NY/6750/78 virus polymerase genes.

The avian influenza A/Mallard/NY/6750/78 virus is currently being evaluated as a donor of attenuating genes in the construction of live avian-human influenza A reassortant virus vaccines for use in humans. We determined the nucleotide sequences of the three polymerase gene segments of this virus. This completes the nucleotide sequence of the six transferrable genes of the avian donor virus. Comparison of the nucleotide and deduced amino acid sequences of the non-glycoprotein genes of the avian A/Mallard/78 virus with representative avian and human influenza A viruses suggests that the PB1 gene of H2N2 subtype human influenza A viruses may have been derived from a non-human, possibly avian influenza A virus by genetic reassortment. In addition, several regions of conserved amino acids with potential functional significance were identified in the deduced amino acid sequences of the polymerase proteins.

Amino Acid Sequence↗
PubMedDate not supplied

Molecular cloning of two west African HIV2 isolates that replicate well in macrophages.

HIV2 strains were isolated from a Gambian with neuro-AIDS (HIV2D194) and from an asymptomatic Ghanian (HIV2D205). Like HIV1 biological subtype c, both isolates grew slowly and induced few or no syncytia, but eventually produced high levels of particle-associated reverse transcriptase (RT) in cultures of fresh peripheral blood lymphocytes. Each produced even higher levels of RT in fresh human macrophages, especially HIV2D194, where maximal RT values of 1,800,000 cpm/ml supernatant of approximately 30,000 cells were measured. The viruses were molecularly cloned after a single passage in culture. Restriction site analysis showed heterogeneity within each isolate. Nucleotide sequence analysis of HIV2D194 revealed that, genetically, it is a member of the prototypic HIV2 family, displaying 12% divergence vs. HIV2ROD and HIV2NIHZ. In contrast, HIV2D205 is the most highly divergent HIV2 strain yet described: it is equidistant in relation between the known HIV2 strains and the SIVMAC isolates (23-24% nucleotide sequence divergence).

Africa, Western↗
PubMed2005

Nucleotide sequence of the matrix protein gene of avian paramyxovirus, serotype 3b: evidence on another member of the suggested new genus of the subfamily Paramyxovirinae.

The complete nucleotide sequence of the gene encoding the matrix protein (M) of the avian paramyxovirus, serotype 3b (APMV-3b), has been determined by means of the direct sequencing of viral RNA using reverse transcriptase reaction. The adjacent portions of the neighboring phosphoprotein (P) and fusion (F) protein genes were also sequenced that permitted to determine the consensus sequence of the viral genome, the poly(A) tract, downstream and upstream non-coding portions of the P and F genes, respectively, as well as the corresponding intergenic regions. The gene is 1478 nucleotides long with a protein-coding sequence of 1194 nucleotides. The deduced protein consists of 398 amino acids with a calculated MW 44,465. According to the multalignment and phylogenetic analyses, the APMV-3b M protein has shown the closest relatedness towards Newcastle disease virus (NDV) which has recently been suggested to be excluded from the Rubulavirus genus and assigned (together with APMV-6) to a new Avulavirus genus within the subfamily Paramyxovirinae of the Paramyxoviridae family. On the basis of the M protein genetic multalignment, phylogenetic relationships, bipartite nuclear localization signal identification in combination with the cysteine residues distribution, and by the degree of intrageneric heterogeneity, the APMV-3b is proposed to be another member (together with NDV and APMV-6) of the new genus.

Amino Acid Sequence↗
PubMed2000

Prevalence of diabetes mellitus in patients with end-stage liver cirrhosis due to hepatitis C, alcohol, or cholestatic disease.

BACKGROUND/AIMS: The aims were to study: 1) the prevalence of diabetes mellitus in patients with end-stage liver cirrhosis due to hepatitis C, alcohol, or cholestatic liver disease, 2) viral and host immunogenetic factors that may predispose to diabetes, and 3) liver transplantation outcome in patients with or without diabetes. METHODS: Fasting blood glucose values of patients who underwent liver transplantation because of hepatitis C-related cirrhosis (73 patients) were compared with those of patients with cirrhosis due to cholestatic (78 patients) or alcoholic liver disease (53 patients) and to a general population. Data on diabetes prevalence in a population without liver cirrhosis was based on the prevalence of diabetes in Olmsted County, Minnesota, residents. HLA was determined using serologic assays. Hepatitis C virus genotypes were determined with polymerase chain reaction amplification and direct sequencing. Hepatitis G RNA was detected with polymerase chain reaction. Liver transplantation outcome in patients with or without diabetes was determined with rejection, retransplantation, or death at 1 year after transplantation as end points. RESULTS: Of 64 patients with hepatitis C alone, 16 (25%) had diabetes before transplantation compared with 1 of 78 (1.3%) with cholestatic liver disease (p= 0.0001) and 10 of 53 (19%) with alcoholic liver disease (p=0.36). Nine patients had hepatitis C plus cholestatic liver disease; one of these (11%) had diabetes. The prevalence of diabetes in patients with cholestatic liver cirrhosis was not different from that of the general population. The frequency of hepatitis G virus coinfection, HLA-DR3, or HLA-DR4 in hepatitis C and diabetes was not different from that of hepatitis C alone. The distribution of hepatitis C virus genotype was similar in those with and those without diabetes. Diabetes was not associated with increased risk of rejection, retransplantation, or death at 1 year after transplantation, and had no impact on overall survival after transplantation. CONCLUSIONS: 1) The risk of diabetes is not increased in patients with liver cirrhosis due to cholestatic liver disease but is in patients with liver cirrhosis due to hepatitis C or alcoholic liver disease; 2) cofactors (age, sex, body mass index, hepatitis G virus coinfection, hepatitis C virus genotype, or HLA-DR3/DR4) did not explain the increased risk of diabetes in patients with hepatitis C; 3) diabetes before liver transplantation did not change the outcome at 1 year after transplantation or survival.

Adult↗
PubMed2002

Accurate translocation of mRNA by the ribosome requires a peptidyl group or its analog on the tRNA moving into the 30S P site.

The ribosome must accurately translocate mRNA to maintain the reading frame. Here, we monitor the position of mRNA within the ribosome before and after EF-G-catalyzed translocation near the initiation site. When a deacylated tRNA that is translocated to the 30S P site recognizes other nearby codons, movement of tRNA and mRNA often becomes uncoupled. Instead of moving in the 5' direction by 3 nucleotides, the mRNA slips backward, repositioning the tRNA on an out-of-frame codon more optimally spaced from the Shine-Dalgarno sequence. In contrast, when peptidyl-tRNA or its analog (N-acetyl-aminoacyl-tRNA) is translocated in the same context, translocation of mRNA is highly accurate. If aminoacyl-tRNA is translocated, an intermediate level of translocational accuracy is observed. Thus, translocational accuracy depends on the acylation state of the tRNA entering the 30S P site.

Bacteriophage T7↗
PubMed1993

Active site labeling of HIV-1 reverse transcriptase.

The human immunodeficiency virus-1 reverse transcriptase (HIV-1 RT) heterodimer (M(r) = 66,000 and M(r) = 51,000) has been photoaffinity labeled using 4-thiodeoxyuridine triphosphate (S4-dUTP) as a probe. A nascent polymerization complex was assembled from a single-stranded DNA template, a 12-mer DNA primer, and the necessary dNTPs (one of which was alpha-32P-labeled) to extend the primer to produce the n-1 product. The photoaffinity probe was then uniquely added at the 3'-terminal position of the extended primer bound at the catalytic site and photolyzed. The larger subunit (p66) was exclusively derivatized. The unique radioactive peptide resulting from proteolysis was isolated and identified by amino acid sequencing.

Acquired Immunodeficiency Syndrome↗
PubMed1998

Novel point mutations in the alphaIIb subunit (Phe289-->Ser, Glu324-->Lys and Gln747-->Pro) causing thrombasthenic phenotypes in four Japanese patients.

We analysed the molecular basis of Glanzmann thrombasthenia (GT) in four Japanese patients with type I or type II disease. Polymerase chain reaction (PCR) and subsequent direct sequencing of platelet RNA and genomic DNA revealed three single nucleotide substitutions of the alphaIIb gene, which were confirmed by allele-specific PCR or restriction analysis. One patient with type I GT had a T to C base substitution in exon 11 resulting in a Phe (TTT)-289 to Ser (TCT) mutation (F289S) of the subunit. Another type I patient had a G to A base substitution in exon 12 resulting in a Glu (GAA)-324 to Lys (AAA) mutation (E324K). Interestingly, two unrelated patients with type II GT shared an A to C base substitution in exon 2 3, a region previously not associated with GT, resulting in a Gln (CAA)-747 to Pro (CCA) mutation (Q747P). To analyse the effects of these mutations on alphaII(b)beta3 surface expression, the wild-type alphaIIb cDNA or mutant alphaIIb cDNAs were transfected into Chinese hamster ovary (CHO) cells together with a wild-type beta3 cDNA. Flow cytometric analysis using an anti-alphaII(b)beta3 complex antibody revealed that 50.6% of CHO cells with wild-type alphaII(b)beta3 expressed complexes, whereas only 1 6%, 7.7% and 31.3% of cells, with IIb(F289S)beta3, alphaIIb(E324K)beta3 and alphaIIb(Q747P)beta3 expressed complexes, respectively. Our data indicate that these three novel point mutations in the alphaIIb subunit may hamper surface expression of the alphaII(b)beta3 complex, thus resulting in the quantitative GT phenotypes of platelets from these patients.

Adult↗
PubMed1995

The formation of the 2',5'-phosphodiester linkage in the cDNA priming reaction by bacterial reverse transcriptase in a cell-free system.

Bacterial reverse transcriptase (RT) is responsible for synthesis of multicopy single-stranded DNA (msDNA) consisting of single-stranded DNA linked to an internal guanosine residue of RNA by an unusual 2',5'-phosphodiester linkage. Here we purified a bacterial RT to homogeneity from Escherichia coli harboring the RT gene from retron-Ec73. The purified RT-Ec73 was able to synthesize msDNA in a cell-free system using an RNA template produced in vitro by T7 RNA polymerase. The in vitro synthesized msDNA was released from the template RNA only when treated with yeast debranching enzyme DBR1, a specific nuclease for a 2',5'-phosphodiester linkage. The position of the branching G residue in the template RNA and the DNA sequence of the cell-free product were identical to those of msDNA-Ec73 synthesized in vivo. These results clearly demonstrate that the formation of the 2',5'-phosphodiester linkage in msDNA synthesis is carried out by RT itself.

Base Sequence↗
PubMed2000

Evolution of hepatitis B virus polymerase gene sequence during famciclovir therapy for chronic hepatitis B.

Prolonged administration of nucleoside analogues for chronic hepatitis B may result in the emergence of hepatitis B viral polymerase mutants. To gain insight into the mechanism involved in the virus's resistance to famciclovir, the amino acid sequences of the terminal protein and reverse-transcriptase (RT) domains of the viral polymerase were determined during therapy among 28 patients. The antiviral response was independent of viral genotypes, and nonresponse to famciclovir was associated with a complex variability of the RT domain. No mutation in the YMDD motif was observed, whereas an L528M mutation was clearly selected by famciclovir treatment in 2 patients, as well as 14 novel mutations in 7 patients. Clone sequence analysis of the RT domains of patients undergoing retreatment with famciclovir and/or lamivudine showed the selection of a preexisting drug-resistant mutant in one case and indicated that sequential antiviral therapy may allow the rapid selection of resistant strains.

2-Aminopurine↗
PubMed1999

Influenza B virus encephalitis.

Acute encephalitis and postinfectious encephalopathy have been reported infrequently in association with influenza A and B virus infections. We report herein a case of a 6-year-old girl with acute influenza B virus encephalitis resulting in neurological sequelae. The diagnosis was made by isolation of influenza B virus from the nasopharynx, seroconversion to influenza B, and reverse transcription polymerase chain reaction (RT-PCR) identification of the virus from the patient's cerebrospinal fluid. Direct sequencing of viral RNA from the patient's nasopharynx and cerebrospinal fluid revealed identical nucleotide sequences in the HA1 region of the hemagglutinin gene. This is the first report of influenza B virus encephalitis diagnosed by use of RT-PCR and illustrates the need for increased awareness of influenza virus as a cause of acute encephalitis. PCR may be a useful tool for diagnosing future cases.

Cerebrospinal Fluid↗
PubMed2006

Resistance mutational analysis of HIV type 1 subtype C among rural South African drug-naive patients prior to large-scale availability of antiretrovirals.

Baseline HIV-1 resistance data are important for resistance monitoring purposes especially in regions initiating large-scale antiretroviral treatment programs. We examined 40 protease and 35 reverse transcriptase amino acid sequences of HIV-1 subtype C from drug inexperienced patients from rural settings in South Africa for resistance mutations. Samples were collected between 2001 and 2004 prior to the availability of antiretrovirals through public health institutions. Ninety-five percent of patients had no major mutations in the protease gene, although substitutions M46L (2.5%) and G73S (2.5%), which according to the Stanford Genotypic Resistance Interpretation Algorithm are considered major mutations, were detected. In addition, a high prevalence of minor mutations was observed in the protease, with at least three minor resistance-associated mutations in 37% of the isolates. An isoleucine insertion at codon 37 was detected in one sequence. Most of the RT sequences were wild-type, although V118I (8.5%) and Y318F (5.7%) associated with resistance to lamivudine and nevirapine, respectively, were observed. Our data suggest that major resistance mutations among the drug-inexperienced population in South Africa may be rare, and routine resistance testing before the initiation of therapy in this initial stage of the treatment program may not be necessary.

Amino Acid Sequence↗