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At least 217 records · Page 12Linked to original sources
PubMed1976

Base sequence complexity of the stable RNA species of Drosophila melanogaster.

The base sequence complexity of Drosophila transfer RNA (tRNA), 5S RNA, and 18S + 28S ribosomal RNA was determined by analyzing the kinetics of RNA-DNA hybridization on membrane filters. We find that Drosophila tRNA is made up from about 59 basic nucleotide sequences distinguishable by hybridization, suggesting that many of the 99 tRNA species resolved by reverse phase chromatography (RPC-5) are homogenic. In contrast 5S RNA was found to contain a single family of sequences. Either 18S ribosomal RNA (rRNA) alone, or 18S + 28S rRNA together, behaved kinetically as two sequence families, and the possible basis for this unexpected result is discussed.

Animals↗
PubMed2001

[A study of methicillin -- resistant staphylococcus aureus (MRSA) in a burn unit with repetitive -- DNA -- sequence -- based PCR fingerprinting].

OBJECTIVE: To investigate the distribution and spread of MRSA in a burn ward, so as to explore the measures of the prevention, surveillance and control of hospital infection in a burn ward. METHODS: Five hundred and four specimens were isolated from the wounds and nasal vestibules of burn patients, the hands and nasal vestibules of medical staffs and lay attendants and the surfaces of various equipments. From these specimens, 58 strains of MRSA and 43 methicillin -- sensitive staphylococcus aureus (MSSA) were isolated. The genome DNA of isolated MRSA strains was analyzed by repetitive DNA -- sequence -- based PCR analysis. RESULTS: MRSA strains were isolated from the burn wounds in 22 of 41 (53.7%) patients, and 5 from the nasal vestibules. Moreover, among 19 medical staffs, MRSA strains were isolated from the hands of 9 persons, but not from the nasal vestibules. From the hands in 9 of 43 lay attendants and the nasal vestibules in 2 MRSA strains were found. Thirteen MRSA strains were isolated from 193 specimens from the surrounding items. It was indicated by repetitive DNA -- sequence -- based PCR analysis of the genome DNA of isolated MRSA strains that there existed homologous strains around the patients' wounds, in the burn wounds, on the skin of medical staffs and lay attendants and also surrounding equipments. CONCLUSION: (1) There was wide spread presence of MRSA homologous strains in the burn ward. (2) It was indicated by repetitive DNA -- sequence -- based PCR analysis of the genome DNA of isolated MRSA strains that there was cross infection among burn patients. The source of the infection of MRSA in burn ward was burn patients, and the route of the infection was hands of medical staffs and lay attendants. (3) MRSA is wide -- spread. The contamination of the hands and the environment was potential risk factor of MRSA outbreak in the burn unit.

Burn Units↗
PubMed1993

Nucleic acid sequence-based amplification (NASBA) for the identification of mycobacteria.

Nucleic acid sequence-based amplification (NASBA), an isothermal amplification technique for nucleic acids (NA), was investigated for the species-specific identification of mycobacteria. A set of primers was selected from a highly conserved region of the 16S rRNA sequence of mycobacteria sandwiching a variable sequence to perform amplification of mycobacterial RNA. Species-specific probes for the M. tuberculosis complex, M. avium-paratuberculosis, M. intracellulare and M. leprae were hybridized in-solution with the amplified nucleic acids of 10 pathogenic mycobacteria and 11 closely related bacteria, as well as with human-derived NA in an enzyme-linked gel assay (ELGA). Each probe was shown to hybridize specifically to the amplified single-stranded RNA of the corresponding species. Thirty-two clinical isolates of M. tuberculosis strains from different parts of the world were correctly identified by NASBA using the M. tuberculosis-complex-specific probe. In combination with the ELGA, NASBA could identify mycobacteria rapidly, i.e. in less than 6 h. The relative simplicity and rapidity of this technique makes it an attractive tool for species-specific identification of mycobacteria.

Base Sequence↗
PubMed2002

Identification of two new HLA-A alleles, A*2419 and A*3011, by sequence-based typing.

In this report, we describe two new HLA-A alleles, A*2419 and A* 3011, that were initially recognized by an aberrant serological pattern. Sequence-based typing revealed sequence differences with other known HLA-A alleles. Allele A*2419 showed 4 nucleotide differences with A*2404, resulting in 4 amino acid differences at codons 70, 76, 77 and 90. Compared with other A*24 alleles, A*2419 lacks the Bw4 motif, as do A*2404 and A*2428. The A*3011 allele showed 2 mismatches with A*3001, resulting in one amino acid difference at codon 80.

Alleles↗
PubMed1997

A generic sequencing based typing approach for the identification of HLA-A diversity.

Sequencing Based Typing (SBT) is a generic approach for the identification of HLA-A polymorphism. This approach includes the high resolution typing of the HLA-A broad reacting groups, HLA-A subtypes and will identify new alleles directly. The SBT approach described here uses a locus specific amplification of DNA from exon 1 to exon 5. The resulting 2,022 bp PCR product serves as a template for the subsequent sequencing reactions. Amplification is followed by direct sequencing of exons 2, 3 and 4 in both orientations with fluorescently labeled primers to define all polymorphic positions leading to a high resolution typing result. In this study the sequence of exons 2 and 3 of a panel of 49 cell lines was determined. In addition, the exon 4 region of 35 cell lines was also sequenced to evaluate the exon 4 polymorphism. The HLA-A type of most of the cells could be identified by sequencing only exons 2 and 3. However, the sequence of exon 4 was required to discriminate A*0201 from A*0209 and A*0207 from A*0215N. In this panel, an identical new "HLA-A*0103" was identified in two Caucasian samples.

Alleles↗
PubMed2005

Novel HLA-A*11 allele, A*1120, identified by sequence-based typing.

In this report, we describe the identification of a human leucocyte antigen-A*11 (HLA-A*11) nucleotide sequence variant, a new HLA-A*1120 by using sequence-based typing (SBT). The new allele was detected during routine HLA typing by high-resolution SBT. Allele A*1120 showed one nucleotide difference with A*110101 at codon 152 (GCG-->GAG) resulting in an amino acid change from alanine to glutamate. Residue 152 is located on alpha(2)-helix of HLA class I molecule and involved in peptide binding by constructing E pocket of peptide-binding groove, implying that the change of the residue 152 would affect the binding affinity of peptides to A*1120 allele.

Alleles↗
PubMed2005

Novel HLA-Cw*01 allele, Cw*010203, identified by sequence-based typing*.

In this report, we describe the identification of an human leucocyte antigen-Cw*0102 (HLA-Cw*0102) nucleotide sequence variant, a new HLA-Cw*010203, in a case - control study by using sequence-based typing. Allele HLA-Cw*010203 showed one nucleotide difference with HLA-Cw*010201 by a silent substitution at codon 130 (CTG-->CTA).

Alleles↗
PubMed2005

Novel HLA-Cw*06 allele, Cw*0612, identified by sequence-based typing.

In this report, we describe the identification of an human leucocyte antigen-Cw*06 (HLA-Cw*06) nucleotide sequence variant, a new HLA-Cw*0612. The new allele was detected during routine HLA typing by high-resolution sequence-based typing. Allele Cw*0612 showed one nucleotide difference with Cw*0602 at codon 153 (GCG-->ACG) resulting in an amino acid change from alanine to threonine.

Alleles↗
PubMed2007

dnaJ gene sequence-based assay for species identification and phylogenetic grouping in the genus Staphylococcus.

In the last few years, many attempts have been made to use conserved gene sequences for identification and for phylogenetic studies of Staphylococcus species. In an effort to identify a more reliable approach, a dnaJ gene sequence-based database was created. In this study, an approximately 883 bp portion of the dnaJ gene sequence from 45 staphylococcal type strains was compared with 16S rRNA and other conserved gene (hsp60, sodA and rpoB) sequences available in public databases. Nucleotide sequence comparisons revealed that the staphylococcal dnaJ gene showed higher discrimination (mean similarity 77.6 %) than the 16S rRNA (mean similarity 97.4 %), rpoB (mean similarity 86 %), hsp60 (mean similarity 82 %) and sodA (mean similarity 81.5 %) genes. Analysis of the dnaJ gene sequence from 20 Staphylococcus isolates representing two clinically important species showed <1 % sequence divergence. Phylogenetic data obtained from the dnaJ gene sequence were in general agreement with those of 16S rRNA gene sequence analysis and DNA-DNA reassociation studies. In conclusion, the dnaJ gene sequence-based assay is an effective alternative to currently used methods, including 16S rRNA gene sequencing, for identification and taxonomical analysis of Staphylococcus species.

Bacterial Typing Techniques↗
PubMed2004

Base-sequence-dependent sliding of proteins on DNA.

The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general validity and the implications of the results are discussed.

Base Pairing↗
PubMed2003

Determination method of sense sequence based on RT/PCR.

When novel sequences are isolated by differential display and other methods, it seems useful to determine which is a sense sequence at an early stage before further experiments. A novel sequence, named MT-001, which shows enhanced expression in the permanent ischemic rat brain, was isolated by differential display. Based on this sequence, a primer set for both direction was designed. Each primer was used to make a cDNA and PCRs performed with each cDNA and both primers. One primer used in the RT step produced a PCR product at the expected position, but another primer in the reverse direction could not. This result indicated that the primer that made the expected PCR product is antisense.

Animals↗
PubMed1978

Electron microscope study of the base sequence homology between simian virus 40 and human papovavirus BK.

The base sequence homology between the genomes of simian virus 40 (SV40) and human papovavirus BK (BKV) was studied by the heteroduplex method of Ferguson and Davis (J. Mol. Biol. 94:135-149, 1975). When mounted for microscopy in 30% formamide (Tm-35 degrees C), BKV/SV40 heteroduplexes were an average of 92% double-stranded and contained only two small nonhomologous regions that mapped near the junctions between the early and late regions of the SV40 Genome. At higher formamide concentrations, the fraction of duplex DNA in the BKV/SV40 heteroduplexes decreased, indicating significant base mismatching in the homologous regions. The strongest regions of homology were located in the late region.

BK Virus↗
PubMed1992

Mutagenic specificity in DNA base sequence by irradiation of health lamp light (UV-B) in Escherichia coli.

A shuttle vector, pZ189, carrying a bacterial suppressor tRNA marker gene, was irradiated with health lamp (HL) light containing UV-B. Plasmid mutations were scored by transforming an indicator strain of Escherichia coli carrying a suppressive blue amber mutation in the beta-galactosidase gene. Plasmid survival was also measured by transforming activity of the indicator strain. The majority of mutations induced by HL light were GC-AT transitions (69%) and the rest were transversions (31%). Some hot-spots in the mutations were observed by sequencing the suppressor gene. Mutagenic specificity in DNA base sequences induced by HL in E. coli agrees well with previous reports about 254-nm or 313-nm light effects on mammalian cells. This agreement may depend on the substitution of the inserted base instead of a G residue at the opposite site of a damaged C residue from conformational change of DNA structure in both bacterial and mammalian cells.

Animals↗
PubMed2001

LDB2000: sequence-based integrated maps of the human genome.

MOTIVATION: Integrated maps are useful for gene mapping and establishing the relationship between recombination and sequence. In this paper we describe algorithms and their implementation for constructing sequence-based integrated maps of the human chromosomes, which are presented in LDB2000, a web based resource. Gene mapping efforts are now focussing on linkage disequilibrium mapping and extension of the integrated map to represent the extent of linkage disequilibrium in different genomic regions would further increase the utility of these maps. RESULTS: Sequence-based integrated maps have been completed for chromosomes 21 and 22. These maps provide locations for genes and polymorphic markers in sequence and on genetic linkage, radiation hybrid and cytogenetic scales. Single nucleotide polymorphisms associated with genes in the maps are also included and their sequence locations indicated. Related locus information, such as aliases and expression information, can be searched on the WWW site.

Algorithms↗
PubMed2001

Detection of viable oocysts of Cryptosporidium parvum following nucleic acid sequence based amplification.

A reliable method using nucleic acid sequence based amplification (NASBA) with subsequent electrochemiluminescent detection for the specific and sensitive detection of viable oocysts of Cryptosporidium parvum in environmental samples was developed. The target molecule was a 121-nt sequence from the C. parvum heat shock protein hsp70 mRNA. Oocysts of C. parvum were isolated from environmental water via vortex flow filtration and immunomagnetic separation. A brief heat shock was applied to the oocysts and the nucleic acid purified using an optimized very simple but efficient nucleic acid extraction method. The nucleic acid was amplified in a water bath for 60-90 min with NASBA, an isothermal technique that specifically amplifies RNA molecules. Amplified RNA was hybridized with specific DNA probes and quantified with an electrochemiluminescence (ECL) detection system. We optimized the nucleic acid extraction and purification, the NASBA reaction, amplification, and detection probes. We were able to amplify and detect as few as 10 mRNA molecules. The NASBA primers as well as the ECL probes were highly specific for C. parvum in buffer and in environmental samples. Our detection limit was approximately 5 viable oocysts/sample for the assay procedure, including nucleic acid extraction, NASBA, and ECL detection. Nonviable oocysts were not detected.

Animals↗
PubMed1996

Sequence-based identification of microbial pathogens: a reconsideration of Koch's postulates.

Over 100 years ago, Robert Koch introduced his ideas about how to prove a causal relationship between a microorganism and a disease. Koch's postulates created a scientific standard for causal evidence that established the credibility of microbes as pathogens and led to the development of modern microbiology. In more recent times, Koch's postulates have evolved to accommodate a broader understanding of the host-parasite relationship as well as experimental advances. Techniques such as in situ hybridization, PCR, and representational difference analysis reveal previously uncharacterized, fastidious or uncultivated, microbial pathogens that resist the application of Koch's original postulates, but they also provide new approaches for proving disease causation. In particular, the increasing reliance on sequence-based methods for microbial identification requires a reassessment of the original postulates and the rationale that guided Koch and later revisionists. Recent investigations of Whipple's disease, human ehrlichiosis, hepatitis C, hantavirus pulmonary syndrome, and Kaposi's sarcoma illustrate some of these issues. A set of molecular guidelines for establishing disease causation with sequence-based technology is proposed, and the importance of the scientific concordance of evidence in supporting causal associations is emphasized.

Base Sequence↗