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Journal ArticleDOI

Molecular phylogenetic analysis of Vibrio cholerae O1 El Tor strains isolated before, during and after the O139 outbreak based on the intergenomic heterogeneity of the 16S-23S rRNA intergenic spacer regions

01 Dec 2005-Journal of Biosciences (Springer India)-Vol. 30, Iss: 5, pp 619-625

TL;DR: Phylogenetic analysis conducted with all three ISR classes showed that the pre-O 139 serogroup and post-O139 serogroups O1 El Tor strains arose out of two independent clones, which was congruent with the observation made by earlier workers suggesting that analyses of ISR-C andISR-h, instead of all fiveISR classes, could be successfully used to study phylogeny in this organism.

AbstractWe have cloned, sequenced and analysed all the five classes of the intergenic (16S-23S rRNA) spacer region (ISR) associated with the eightrrn operons (rrna-rrnh) ofVibrio cholerae serogroup O1 El Tor strains isolated before, during and after the O139 outbreak. ISR classes ‘a’ and ‘g’ were found to be invariant, ISR-B (ISRb and ISRe) exhibited very little variation, whereas ISR-C (ISRc, ISRd, and ISRf) and ISRh showed the maximum variation. Phylogenetic analysis conducted with all three ISR classes (ISR-B, ISR-C and ISRh) showed that the pre-O139 serogroup and post-O139 serogroup O1 El Tor strains arose out of two independent clones, which was congruent with the observation made by earlier workers suggesting that analyses of ISR-C and ISR-h, instead of all five ISR classes, could be successfully used to study phylogeny in this organism.

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Journal ArticleDOI
TL;DR: This review examines the current application of molecular techniques for the characterization of microbial communities in contaminated soil and water and methods that directly link microbial phylogeny to its ecological function at contaminated sites as well as high throughput methods for complex microbial community studies.
Abstract: Traditionally, the identification and characterization of microbial communities in contaminated soil and water has previously been limited to those microorganisms that are culturable. The application of molecular techniques to study microbial populations at contaminated sites without the need for culturing has led to the discovery of unique and previously unrecognized microorganisms as well as complex microbial diversity in contaminated soil and water which shows an exciting opportunity for bioremediation strategies. Nucleic acid extraction from contaminated sites and their subsequent amplification by polymerase chain reaction (PCR) has proved extremely useful in assessing the changes in microbial community structure by several microbial community profiling techniques. This review examines the current application of molecular techniques for the characterization of microbial communities in contaminated soil and water. Techniques that identify and quantify microbial population and catabolic genes involved in biodegradation are examined. In addition, methods that directly link microbial phylogeny to its ecological function at contaminated sites as well as high throughput methods for complex microbial community studies are discussed.

188 citations


Cites background from "Molecular phylogenetic analysis of ..."

  • ..., 2003), Vibrio (Chun et al., 2002; Ghatak et al., 2005) and other medically important microorganisms....

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Journal ArticleDOI
Abstract: Traditional methods of typing Vibrio cholerae define virulent strains according to their recognition by sera directed against the known epidemic serogroups O1 and O139, overlooking potentially virulent non-O1/non-O139 strains. Here, we have undertaken the characterization of eight clinical isolates of non-O1/non-O139 V. cholerae, collected during cholera outbreaks in Brazil. Seven of these were typed as O26 and one, 17155, was defined as non-typable. A PCR-based approach has previously detected in these strains several virulence genes derived from the CTXvarphi prophage and generally associated with pathogenic strains. Here, the presence of the O1-specific wbeN gene was investigated through PCR and found to be restricted to strain 17155, as well as one of the O26 strains, 4756, although neither strain was recognized by O1-specific antisera. The same two isolates were the only strains able to express the cholera toxin in culture, assayed by western blotting. They also possessed four repeats of the heptanucleotide TTTTGAT upstream of the ctxAB genes encoding the cholera toxin. The remaining strains possessed only two intact repeats, whereas pathogenic O1 possessed four to six repeats. To define their evolutionary relationships, selected 16S-23S intergenic rRNA spacer regions were sequenced from the various strains and the resulting sequences used to build phylogenetic trees. Strains 4756 and 17155 always clustered with control O1 strains, whereas the remaining O26 strains clustered separately. These results confirm that, despite their serological phenotype, these two strains are genotypically related to O1 strains and potentially able to produce epidemic cholera.

15 citations


DOI
23 Jan 2014
TL;DR: The potential for the use of molecular methods in toxicological risk assessment and in developing bioremediation strategies is expanding rapidly as new methodologies become available.
Abstract: Over the past 40 years, research on the microbial degradation of polycyclic aromatic hydrocarbons (PAHs) has resulted in the isolation of numerous genera of bacteria, fungi and algae capable of degrading PAHs. With the development of biology, molecular techniques such as PCR, fingerprinting technique (mainly DGGE/TGGE), ARDRA, TRFLP, FISH, RISA and gene reporter technique have been intensively applied to gain further insight into the mechanism of PAHs degradation. Further recent developments in moleclar microbial ecology like genotypic profiling, ultrafast genome pyrosequencing, metagenomics, metatranscriptomics, metaproteomics and metabolomics along with bioinformatics tools offer new tools that facilitates molecular analyses of microbial populations at contaminated and bioremediated sites. Information provided by such analyses aids in the evaluation of the effectiveness of bioremediation and the formulation of strategies that might accelerate bioremediation. The potential for the use of molecular methods in toxicological risk assessment and in developing bioremediation strategies is expanding rapidly as new methodologies become available. In this paper we present an overview of some molecular methods we feel have the most potential for use in assessment and monitoring in the field.

11 citations


Additional excerpts

  • ...RISA has been used to distinguish between different strains and closely related species of Staphylococcus [73,74], Bacillus [75,76], Vibrio [77,78], and other medically important microorganisms....

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Journal ArticleDOI
TL;DR: The application of molecular microbiology techniques Studying microbial populations in polluted sites without the need for culturing has led to the discovery of novel and unrecog nized populations.
Abstract: Molecular microbiology techniques have revolutionized microbial ecology by paving the way for rapid, high -throughput methods for culture -independent assessment and exploitation of microbial communities present in complex ecosystems like crude oil/hydrocarbon polluted soil. The soil microbial community is relatively diversewith a high level of prokaryotic diversity. This soil species pool represents a gold mine for genes involved in the biodegradation of different classes of pollutants. Currently, less than 1% of this diversity is culturable by traditional cultivation techniques. The application of molecular microbiology techniquesinstudyingmicrobial populations in polluted sites without the need for culturing has led to the discovery of novel and unrecog nized

10 citations


Additional excerpts

  • ...RISA has been used to distinguish between different strains and closely related species of Staphylococcus [118,119], Bacillus [120,121], Vibrio [122,123], and other medically important microorganisms....

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References
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Book
15 Jan 2001
Abstract: Molecular Cloning has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential. Molecular Cloning, Fourth Edition, by the celebrated founding author Joe Sambrook and new co-author, the distinguished HHMI investigator Michael Green, preserves the highly praised detail and clarity of previous editions and includes specific chapters and protocols commissioned for the book from expert practitioners at Yale, U Mass, Rockefeller University, Texas Tech, Cold Spring Harbor Laboratory, Washington University, and other leading institutions. The theoretical and historical underpinnings of techniques are prominent features of the presentation throughout, information that does much to help trouble-shoot experimental problems. For the fourth edition of this classic work, the content has been entirely recast to include nucleic-acid based methods selected as the most widely used and valuable in molecular and cellular biology laboratories. Core chapters from the third edition have been revised to feature current strategies and approaches to the preparation and cloning of nucleic acids, gene transfer, and expression analysis. They are augmented by 12 new chapters which show how DNA, RNA, and proteins should be prepared, evaluated, and manipulated, and how data generation and analysis can be handled. The new content includes methods for studying interactions between cellular components, such as microarrays, next-generation sequencing technologies, RNA interference, and epigenetic analysis using DNA methylation techniques and chromatin immunoprecipitation. To make sense of the wealth of data produced by these techniques, a bioinformatics chapter describes the use of analytical tools for comparing sequences of genes and proteins and identifying common expression patterns among sets of genes. Building on thirty years of trust, reliability, and authority, the fourth edition of Mol

215,117 citations


Journal ArticleDOI
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Abstract: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straight-forward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.

81,150 citations


"Molecular phylogenetic analysis of ..." refers methods in this paper

  • ...Various ISRs so identified were then subjected to automated DNA sequencing followed by Blast analysis (Altschul et al 1990)....

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Journal ArticleDOI
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.

61,038 citations


"Molecular phylogenetic analysis of ..." refers methods in this paper

  • ...3.2 Sequence analysis of the ISRs Nucleotide sequences for a particular ISR for all strains studied were aligned using Clustal W (Thompson et al 1994)....

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  • ...Nucleotide sequences for a particular ISR for all strains studied were aligned using Clustal W ( Thompson et al 1994 )....

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  • ...Nucleotide sequences for a particular ISR were aligned using Clustal W ( Thompson et al 1994 )....

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  • ...2.5 Phylogenetic analysis Nucleotide sequences for a particular ISR were aligned using Clustal W (Thompson et al 1994)....

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Journal ArticleDOI
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

54,096 citations


"Molecular phylogenetic analysis of ..." refers background or methods in this paper

  • ...The methods used were neighbour-joining (NJ) (Saitou and Nei 1987), and maximum parsimony (MP)....

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  • ...For the NJ (Saitou and Nei 1987) and MP analysis the tDNA regions were also included as they were found to be homologous among the strains for all three ISRs tested....

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  • ...The methods used were neighbour-joining (NJ) ( Saitou and Nei 1987 ), and maximum parsimony (MP)....

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  • ...For the NJ ( Saitou and Nei 1987 ) and MP analysis the tDNA regions were also included as they were found to be homologous among the strains for all three ISRs tested....

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Journal Article

16,846 citations