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Biomedical subjects

M D Collins

Publications and source records attributed to M D Collins.

At least 235 records · Page 13Linked to original sources
PubMed1993

Development of a polymerase chain reaction test for specific identification of the urinary tract pathogen Aerococcus urinae.

A polymerase chain reaction test was developed for identification of the gram-positive urinary tract pathogen Aerococcus urinae. Oligonucleotide primers were based on highly specific sequences within the small-subunit rRNA gene. A confirmatory test based on hybridization of the amplified products to a highly specific internal probe was also developed.

Bacteriological Techniques↗
PubMed1993

Gene probes for identification of the botulinal neurotoxin gene and specific identification of neurotoxin types B, E, and F.

A polymerase chain reaction method was developed for the specific detection of the botulinum neurotoxin (BoNT) gene of Clostridium botulinum. Degenerate oligonucleotide primers, designed from the nucleotide sequence of the heavy chain of the BoNT gene, amplified a specific fragment of approximately 1.1 kb from strains of C. botulinum toxin types A, B, E, F, and G and neurotoxin-producing strains of Clostridium barati and Clostridium butyricum, but no fragment was obtained from nontoxigenic strains. The fragments amplified from several strains of C. botulinum types B, E, and F were cloned in Escherichia coli and their nucleotide sequences were determined. Sequences within this region were used to design oligonucleotide probes specific for BoNT type B (BoNT/B), BoNT/E, and BoNT/F genes. An additional probe was designed for the detection of the BoNT/F gene of C. barati, which differed in sequence from BoNT/F genes of both proteolytic and nonproteolytic strains of C. botulinum.

Amino Acid Sequence↗
PubMed1993

Development of gene probes for the specific identification of Streptococcus uberis and Streptococcus parauberis based upon large subunit rRNA gene sequences.

23S ribosomal RNa (rRNA) gene sequences of Streptococcus uberis and Strep. parauberis were determined by direct polymerase chain reaction (PCR) sequencing. Oligonucleotide probes specific for Strep. uberis and Strep. parauberis were designed from variable regions of the 23S rRNA gene sequence data. Molecular hybridizations with PCR-amplified rRNA gene targets provided a precise and reliable means of differentiating Strep. uberis and Strep. parauberis from each other and from other streptococcal species.

Bacterial Typing Techniques↗
PubMed1993

Phylogenetic analysis of some leuconostocs and related organisms as determined from large-subunit rRNA gene sequences: assessment of congruence of small- and large-subunit rRNA derived trees.

The large-subunit ribosomal RNA gene sequences of Leuconostoc carnosum, Leuc. mesenteroides, Leuc. oenos, Leuc. paramesenteroides and Lactobacillus confusus were determined by direct sequencing of enzymatically-amplified DNA. Comparative analysis of the large-subunit rDNA sequences revealed that the leuconostocs form three distinct lines of descent: Leuconostoc sensu stricto, Leuc. paramesenteroides group of organisms, and Leuc. oenos. The distance matrix tree constructed from the large-subunit sequence data was in excellent agreement with that derived from small-subunit sequences, and demonstrates the 'synchrony' of the two chronometers. The results of the present and earlier sequence analyses indicate the taxonomy of the genus Leuconostoc is in need of revision, and that the Leuc. paramesenteroides group of organisms and the species Leuc. oenos represent distinct phylogenetic units, separate from Leuconostoc sensu stricto.

Base Sequence↗
PubMed1993

Phenotypic and phylogenetic evidence for a close relationship between Lactococcus garvieae and Enterococcus seriolicida.

Cultural, biochemical and protein profiling studies were performed on L. garvieae strains isolated from diseased rainbow trout and on the fish pathogen Enterococcus seriolicida ATCC 49156. The results, confirmed by 16 rRNA sequence analyses, indicate that E. seriolicida ATCC 49156 should be reclassified in the genus Lactococcus. Contrary to previous reports, both L. garvieae and E. seriolicida were found to be beta-haemolytic.

Animals↗
PubMed1992

Studies on the ribosomal RNA operons of Listeria monocytogenes.

A 23S rRNA gene of Listeria monocytogenes was cloned into pUC19 on a 6.2-kb Pst I fragment. Hybridisation studies demonstrated the presence of the 5S and partial 16S rRNA genes within the clone. The nucleotide sequence of the region encoding the 23S rRNA was found to be highly homologous with those of other low G + C Gram-positive bacteria. The 16S-23S intergenic spacer region was amplified using PCR technology and revealed two product sizes, the larger of which contained tRNA(Ala) and tRNA(Ileu) genes. Further tRNA genes were found downstream of the 5S rRNA gene.

Base Sequence↗
PubMed1992

Sequence of the gene encoding type F neurotoxin of Clostridium botulinum.

Primers designed to conserved regions of botulinum and tetanus clostridial toxins were used to amplify DNA fragments from non-proteolytic Clostridium botulinum type F (202F) DNA using polymerase chain reaction technology. The fragments were cloned and the complete nucleotide sequence of the gene encoding type F toxin determined. Analysis of the nucleotide sequence demonstrated the presence of an open frame encoding a protein of 1274 amino acids, similar to other botulinum neurotoxins. Upstream of the toxin gene is the end of an open reading frame which encodes the C-terminus of a protein with homology to non-toxic-non-hemagglutinin component of type C progenitor toxin.

Amino Acid Sequence↗
PubMed1992

Taxonomic studies on a psychrophilic Clostridium from vacuum-packed beef: description of Clostridium estertheticum sp. nov.

Taxonomic studies were performed on an anaerobic Gram-positive, spore-forming, psychrophilic bacterium originally isolated from spoiled vacuum-packed refrigerated beef. Based on the present finding it is proposed that this unknown psychrophilic bacterium be classified as a new species of the genus Clostridium, as Clostridium estertheticum sp. nov. The type strain is NCIMB 12511.

Animals↗
PubMed1992

Evidence for a close genealogical relationship between Afipia (the causal organism of cat scratch disease), Bradyrhizobium japonicum and Blastobacter denitrificans.

The primary structures of the small subunit rRNA of Bradyrhizobium japonicum and Blastobacter denitrificans were determined by direct sequencing of enzymatically amplified DNA. Comparative sequence analysis revealed that Bradyrhizobium japonicum and Blastobacter denitrificans are members of the alpha-2 subgroup of the Proteobacteria and show a very close phylogenetic relationship with the genus Afipia.

Animals↗
PubMed1992

Comparative sequence analyses of the 16S rRNA genes of Lactobacillus minutus, Lactobacillus rimae and Streptococcus parvulus: proposal for the creation of a new genus Atopobium.

16S rRNA gene sequencing was performed on the species Lactobacillus minutus, Lactobacillus rimae and Streptococcus parvulus in order to clarify their taxonomic position. Based on comparative sequence analyses these organisms represent a hitherto unknown line of descent within the lactic acid group of bacteria for which a new genus, Atopobium gen. nov., is proposed.

Base Sequence↗
PubMed1992

Analysis of DNA encoding 23S rRNA and 16S-23S rRNA intergenic spacer regions from Plesiomonas shigelloides.

Amplification of the gene encoding 23S rRNA of Plesiomonas shigelloides by polymerase chain reaction (PCR), with primers complementary to conserved regions of 16S and the 3' end of 23S rRNA genes, resulted in a DNA fragment of approximately 3 kb. This fragment was cloned in Escherichia coli and its nucleotide sequence determined. The region encoding 23S rRNA shows high homology with the published sequences of 23S rRNA from other members of the gamma division of Proteobacteria. The sequence of the intergenic spacer region, between the 16S and 23S rRNA genes, was determined in a further two clones. In one the sequence of a single tRNA(Glu) was found which was absent from the other two. This variation in sequence suggests that the different clones may be derived from different ribosomal RNA operons.

Base Sequence↗
PubMed1992

Rapid identification of Aerococcus viridans using the polymerase chain reaction and an oligonucleotide probe.

A polymerase chain reaction/oligonucleotide probe method was developed for the specific identification of the Gram-positive bacterium Aerococcus viridans. Primers for the enzymatic amplification reaction were designed from specific sequences within the 16S rRNA. The method was also highly sensitive and 10 cfu of A. viridans could be detected in 5 h although the reliability of detection was poor in mixed cultures with Escherichia coli.

Base Sequence↗
PubMed1992

PCR cloning and nucleotide sequence determination of the 18S rRNA genes and internal transcribed spacer 1 of the protozoan parasites Cryptosporidium parvum and Cryptosporidium muris.

The genes encoding 18S rRNA and internal transcribed spacer 1 (1TS1) of Cryptosporidium parvum and Cryptosporidium muris were amplified from oocysts by PCR utilizing primers complementary to conserved regions of the 5' end of 18S and 5.8S rRNA. PCR products were cloned and the complete nucleotide sequences of two clones of each Cryptosporidium species were determined. The 18S rRNA genes of C. parvum and C. muris showed more than 99% sequence identity.

Animals↗
PubMed1992

Comparative analysis of 23S ribosomal RNA gene sequences of Bacillus anthracis and emetic Bacillus cereus determined by PCR-direct sequencing.

The primary structures of the 23S ribosomal RNA genes of Bacillus anthracis and an emetic strain of Bacillus cereus were determined by direct sequencing of enzymatically amplified chromosomal DNA. The 23S rRNA gene sequences of B. anthracis and B. cereus were found to be almost identical and showed only two differences (a single nucleotide change, and a single base insertion in B. cereus). The feasibility of using PCR-direct sequencing for the rapid sequence determination of large-subunit rRNA genes is demonstrated.

Bacillus anthracis↗
PubMed1992

Phylogenetic analysis of the genera Planococcus, Marinococcus and Sporosarcina and their relationships to members of the genus Bacillus.

A phylogenetic analysis based on 16S rRNA was performed on the genera Planococcus, Marinococcus, Sporosarcina and endospore-forming rods. In agreement with earlier 16S rRNA cataloguing data, Planococcus citreus and Sporosarcina ureae clustered with Bacillus pasteurii and other bacilli containing lysine in their cell walls. Sporosarcina halophila was shown to be genetically distinct from S. ureae and formed a loose association with the main Bacillus subtilis grouping. Marinococcus halophilus (formerly Planococcus halophilus) exhibited low levels of relatedness to all reference species examined and formed a distinct line of descent.

Bacillaceae↗
PubMed1992

Aeromonas allosaccharophila sp. nov., a new mesophilic member of the genus Aeromonas.

Phenotypic and genetic studies were performed on some atypical aeromonas strains of uncertain taxonomic position. 16S rRNA gene sequence analysis revealed that these strains represent a hitherto unknown genetic line within the genus Aeromonas, for which the name Aeromonas allosaccharophila sp. nov. is proposed. The type strain is CECT 4199.

Aeromonas↗