Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.1.30.2 (endonuclease)
18,621 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Pseudomonas pseudomallei isolates from 62 human, 17 animal, 3 soil and 3 water samples were examined by genomic DNA digestion with PstI. Five major (RE I, II, III, IV, V) reproducible restriction patterns were observed, with most (56/62) of the human isolates displaying RE I (30/62), II (5/62), III (15/62), IV (4/62), V (2/62), and the animal (16/17), soil (2/3), water (3/3) isolates showing predominantly RE II profiles. Six human and one soil isolates showed patterns different from those of RE I to V. Restriction endonuclease analysis may be applied in epidemiological studies of melioidosis.
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PMID:Comparison of Pseudomonas pseudomallei from humans, animals, soil and water by restriction endonuclease analysis. 757 Jan 38

The spread in Europe of a single multiresistant strain of Pseudomonas aeruginosa serotype O12 has been suggested. This bacterium was responsible for a nosocomial outbreak in our hospital in 1988-1989. Three different epidemiological methods were used to analyze 30 strains isolated during five consecutive years. Protein profile analysis and chromosomal DNA fingerprinting with four different enzymes revealed closely related patterns. rRNA gene restriction fragment length analysis performed with a digoxigenin-labelled probe showed identical hybridization patterns with four to six bands according to the endonuclease used. Combination of the three typing methods showed genotypic homogeneity of these Pseudomonas aeruginosa O12 strains, despite a relative increase in their antibiotic resistance.
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PMID:Genotypic homogeneity of nosocomial Pseudomonas aeruginosa O12 strains demonstrated by analysis of protein profiles, DNA fingerprints and rRNA gene restriction patterns. 768 79

A rapid direct-extraction method was used to obtain DNA from environmental soil samples. Heat, enzymes, and guanidine isothiocyanate were utilized to lyse cells. The DNA was purified by agarose gel electrophoresis, amplified with 16S rRNA-based primers by use of the polymerase chain reaction, and then digested with the restriction endonuclease PalI. The extraction method was used to obtain DNA from a variety of plants, bacteria, and fungi including Gossypium hirsucum (cotton), Pseudomonas, Bacillus, Streptomyces, and Colletotrichum. Up to 100 micrograms DNA/g (wet weight) of soil and 400 micrograms DNA/g of plant material were recovered. Restriction endonuclease analysis patterns of amplified rDNA from pure microbial cultures and plant species contained three to five different DNA fragments. Amplified rDNA of mixed population DNA extracts from soil samples, digested with the restriction endonuclease PalI, contained 12-20 DNA fragments, appearing as sample "fingerprints." Results from eight environmental soil samples that were analyzed suggest that the amplified rDNA fingerprints can be used to help characterize the genetic and biological diversity of the microbial populations in these samples.
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PMID:An effective method to extract DNA from environmental samples for polymerase chain reaction amplification and DNA fingerprint analysis. 776 20

The intra-species differentiation of Pseudomonas aeruginosa was analysed by comparing the polymorphism of esterases by conventional polyacrylamide-agarose gel electrophoresis, the physicochemical properties of the variants of the major esterase P3 and the restriction fragment length polymorphism of ribosomal RNA gene regions (ribotyping) to O-serotyping for several panels of strains selected from among a series of 257 clinical isolates and two references strains, (ATCC nos. 10145 and 27853). The electrophoretic variation of four main kinds of esterase (P1-P4) and 11 additional esterases distinguished by their spectra of hydrolytic activity with synthetic substrates and by their sensitivity to di-isopropylfluorophosphate, allowed the discrimination of 67 zymotypes. Thirty-two esterase P3 variants were characterized by their pI, electrophoretic mobilities and titration curve analyses. They were distributed into two groups which, by these molecular criteria, seem to be distantly related. Combination of the patterns resulting from HindIII, EcoRI and BclI restriction endonuclease digestions allowed the discrimination of 33 ribotypes among 134 strains. The strains exhibiting esterase P3 variants of group 2 presented a distinct ribotype and belonged to serotype (O)12. They could constitute a distinct group within the species. For the majority of the strains, the absence of correlation between zymotype, ribotype and serotype argues for a high level of heterogeneity within P. aeruginosa and indicates that the parallel use of the first two methods represent a potential tool for epidemiological study.
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PMID:Genetic heterogeneity of Pseudomonas aeruginosa clinical isolates revealed by esterase electrophoretic polymorphism and restriction fragment length polymorphism of the ribosomal RNA gene region. 790 49

A sample of 30 fluorescent pseudomonads isolated from the phyllosphere of sugar beet throughout a single growing season and shown to be closely related on the basis of fatty acid methyl ester (FAME) analysis was subjected to detailed phenotypic and genotypic characterization. Phenotypic traits were assessed on the basis of biochemical properties, assimilation of sole carbon sources, FAME analysis, organic pyrolysate content (MS-pyrolysis), and total cellular protein profiles. With the exception of total cellular protein profiles, numerical analysis of the data revealed two main clusters, each of which was divided into several subclusters. Numerical analysis of total cellular protein data failed to differentiate isolates into two main clusters, but nevertheless grouped isolates into six subclusters. On the basis of biochemical and carbon source assimilation profiles, 19 isolates were identified as Pseudomonas fluorescens biovar V, eight isolates as P. fluorescens biovar III and three isolates as P. syringae pathovar syringae. In general, all methods of phenotypic analysis grouped isolates according to time of sampling and leaf type. Genome analysis was undertaken by pulsed-field gel electrophoresis (PFGE) of PacI, SpeI, SwaI and XbaI macrorestriction fragments and revealed the presence of eight distinct genomic (clonal) groups. These groups correlated closely with the clusters generated by numerical analysis of phenotypic data, but there was no correlation between macrorestriction fragment profile and isolate identification; in fact the variation in macrorestriction fragment patterns within P. fluorescens biovars was as great as the variation detected between biovars, and between P. fluorescens and P. syringae. Statistical evaluation of macrorestriction fragment patterns revealed two examples of recent strain divergence: one was due to the presence of a 400 kbp plasmid within one isolate of a collection of nine otherwise genomically identical isolates, and the other was observed between two phenotypically similar isolates sampled 220 d apart. Genetic variation was expressed in terms of nucleotide diversity (pi) and pairwise comparisons yielded values ranging from 0.0029 to 0.1517. The mean intrapopulation genetic variation was high (0.0993), but limited genetic variation was detected among isolates sampled on each occasion. Taken together this suggests a population comprised of a variety of apparently distantly related clones (genomic groups), each adapted to local conditions. Genome sizes were estimated from the sum of SpeI restriction fragments and ranged from 4.2 to 5.5 Mbp. Examination of the distribution of XbaI, SpeI, SwaI and PacI restriction endonuclease sites showed that the distribution of SpeI sites differed significantly from the expected (random) distribution.
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PMID:Phenotypic and genotypic diversity of fluorescent pseudomonads isolated from field-grown sugar beet. 795 85

PCR was used to detect Pseudomonas aeruginosa from water samples by amplifying a 396-bp region of the exotoxin A (ETA) structural gene sequence. The identify of the amplified 396-bp fragment was confirmed by digesting it with PvuI restriction endonuclease, which produced the predicted 246- and 150-bp fragments. Specific primers amplified ETA-positive P. aeruginosa DNA, whereas other species of Pseudomonas and GC-rich bacteria did not yield any 396-bp fragment. The specificity and sensitivity of the assay were 100 and 96%, respectively, which confirms the assay's reliability for diagnostic and epidemiological studies. The assay can detect as few as 5 to 10 cells in a 10-ml water sample or 0.1 pg of P. aeruginosa DNA per reaction mixture (5 microliters) by ethidium bromide staining of an agarose gel. Ten-times-lower concentrations were detected by hybridization with a digoxigenin-labeled oligonucleotide probe internal to the PCR product. With this PCR method, ETA-positive P. aeruginosa was detected in animal cage water samples at a level of 40 cells per ml. This method is rapid and less cumbersome than other diagnostic methods for the identification of P. aeruginosa strains. The method described can be used to detect a low level of P. aeruginosa from environmental and clinical samples without the use of selective media or additional biochemical tests.
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PMID:Detection of Pseudomonas aeruginosa from clinical and environmental samples by amplification of the exotoxin A gene using PCR. 798 47

A self-transmissible 2,4-dichlorophenoxyacetic acid (2,4-D)-degradative plasmid, pKA2, has been identified in a new 2,4-D-degrading strain, Alcaligenes paradoxus 2811P, isolated from agricultural soil. pKA2 occurred as a 42.9-kb plasmid in strain 2811P. A derivative strain, 2811C, was isolated from a stock culture in which the entire pKA2 plasmid was apparently integrated into the host chromosome without loss of the 2,4-D+ phenotype. This interpretation is based on the disappearance of a free plasmid DNA band, a shift in the tfdA-hybridizing band to the chromosome, loss of transmissibility of the 2,4-D+ trait, and appropriate shifts in Southern hybridization bands of plasmid DNA compared with whole-cell DNA. The integrated plasmid of strain 2811C was excised either precisely or imprecisely after continued transfer on 2,4-D-containing medium. This suggests that a chromosome-free plasmid cycle may occur to optimize fitness under conditions of specific resource fluctuation. Another new 2,4-D-degrading strain, Pseudomonas pickettii 712, which was isolated from the same field plot but at a different time, was found to carry a plasmid that is nearly identical to pKA2. The plasmid of this strain, pKA4, is 40.9 kb long and has features in common with pKA2, such as high self-transmissibility, hybridization only to the tfdA gene among the 2,4-D-metabolic genes of 2,4-D-degradative plasmid pJP4, and similar restriction endonuclease-generated fragments. Furthermore, the genetic homology between the two plasmids was high since all fragments of pKA2 hybridized to pKA4. These results suggest that these two plasmids are closely related and thus their occurrence in two genera in nature is the result of natural horizontal gene transfer.
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PMID:Integration and excision of a 2,4-dichlorophenoxyacetic acid-degradative plasmid in Alcaligenes paradoxus and evidence of its natural intergeneric transfer. 807 Dec 3

The prevalence of possible cross-transmission of selected bacteria (Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae, Pseudomonas aeruginosa, Staphylococcus aureus, and enterococci) among infected patients was evaluated in five intensive care units (ICUs) over 6 months. A total of 284 isolates from clinical specimens were typed by plasmid profile analysis (E. coli, K. pneumoniae, and E. cloacae), restriction endonuclease analysis of plasmid DNA (S. aureus), and/or pulse-field gel electrophoresis of chromosomal DNA (P. aeruginosa, enterococci, S. aureus, and other bacteria without plasmid DNA). By typing criteria, only 13% of the 177 isolates obtained after > 2 days in an ICU were classified as possibly cross-transmitted. Many patients whose cultures yielded bacteria of an identical type may have been the sources rather than the recipients of these organisms. Episodes of possible cross-transmission were scattered among all ICUs, usually affected only two patients, and were associated with most bacterial species. These data suggest that endemic bacterial cross-transmission in ICUs is relatively infrequent and that cross-transmitted bacteria are not common causes of endemic ICU-related nosocomial infections.
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PMID:Assessment of bacterial cross-transmission as a cause of infections in patients in intensive care units. 808 55

The genotypic diversity of 40 presumably epidemiologically unrelated strains of Pseudomonas aeruginosa belonging to nine different O-serotypes was analysed according to ribosomal DNA fingerprints. Ribotyping was performed with a digoxigenin-labelled DNA probe and four restriction endonucleases. Characteristic banding patterns of three to 12 bands were obtained with the different endonucleases. Among the 40 strains, eight, nine, 10 and 29 different ribotypes were differentiated with EcoRI, the combination EcoRI+HindIII, BamHI and PvuII, respectively. Poor correlations were noted between the results of serotyping and those of ribotyping. With the latter method, indices of discrimination were calculated for each enzyme from the data of the 40 unrelated strains: the values ranged from 0.678 for EcoRI to 0.979 for PvuII. Epidemiologically related samples were also tested; this enabled assessment of whether the method was able to cluster strains from a common origin with each of the enzymes tested. Ribotyping with PvuII endonuclease is proposed for screening large numbers of P. aeruginosa strains in epidemiological studies. Additional enzymes could be used to further increase the discrimination between isolates found to be indistinguishable with PvuII enzyme.
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PMID:Differentiation of Pseudomonas aeruginosa strains by ribotyping: high discriminatory power by using a single restriction endonuclease. 815 79

A novel transposon (Tn) mutagenesis system for Gram- non-enteric bacteria was developed which allowed rapid and one-step cloning of the mutated region in Escherichia coli. The Tn constructed was Tn1722-299Km, a Tn1722 derivative containing a KmR gene and the entire sequence of an E. coli-specific plasmid, pACYC184. The hybrid plasmid consisting of Tn1722-299Km and the transfer genes of plasmid R388 was conjugally transferred from E. coli to Pseudomonas putida or P. aeruginosa, and selection of the transconjugants expressing the Tn-specified resistance genes led to isolation of insertion mutants of the recipient strain. The presence of the pACYC184 replicon in the Tn greatly facilitated rapid and easy cloning of the mutated region in E. coli through (i) mini-scale preparation of the genomic DNA from the Tn-inserted mutant, (ii) digestion of the DNA with an appropriate restriction endonuclease, (iii) self-ligation, and (iv) transformation of E. coli to recover the plasmid carrying the Tn-specified resistance marker. This procedure was successfully adapted to clone the Tn-inserted trpBA region of P. putida. Such a cloned region was further employed to isolate the wild-type allele of the trpBA region without construction of a genomic library.
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PMID:A mutagenesis system utilizing a Tn1722 derivative containing an Escherichia coli-specific vector plasmid: application to Pseudomonas species. 829 12


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