Analysis of nucleic acid profiles

Towner, K. J.

doi:10.1007/978-94-011-1506-3_2

Cited by 7 publications

(5 citation statements)

References 160 publications

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“…It should be noted that most published data reporting plasmid size have been obtained from fragment size standards and interpreted by semilogarithmic interpolation. Considerable size errors can be generated, complicating comparisons of DNA fragments reported from different laboratories (Towmer and Cockayne 1993). Thus, in this study, we used the migration distance or R F value of each band to show the plasmid profile.…”

Section: Resultsmentioning

confidence: 99%

Analysis of Salmonella enteritidis strains isolated from food-poisoning cases in Taiwan by pulsed field gel electrophoresis, plasmid profile and phage typing

Tsen¹,

Lin²

2001

J Appl Microbiol

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Aims: To establish the molecular typing data for Salmonella enteritidis due to its increasing role in Salmonella infections in Taiwan. Methods and Results: Sixty-three Salm. enteritidis strains isolated from related and unrelated patients suffering from food-borne poisoning during 1991±97 were collected and subjected to pulsed ®eld gel electrophoresis (PFGE), plasmid analysis and phage typing. For PFGE, XbaI, SpeI and NotI restriction enzymes were used for chromosomal DNA digestion. The results showed that, for these 63 Salmonella strains, 10 PFGE pattern combinations were found. Of these, pattern X3 S3 N3 was the major subtype, since 46 strains isolated from different locations at different times during 1991±97 showed this PFGE pattern. Plasmid analysis showed only three plasmid pro®les and phage typing showed that most of the Salmonella strains were of the phage type PT4. Conclusions: Most of the Salm. enteritidis strains circulating in Taiwan are of very similar genetic types or are highly related and that strains of PFGE pattern X3 S3 N3 are the prevalent and recirculating strains of Salm. enteritidis which caused food-poisoning cases in Taiwan in 1991±97. Signi®cance and Impact of the Study: This study provides information that in Salmonella infection, certain subtypes of Salm. enteritidis should be scrutinized.

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Section: Resultsmentioning

confidence: 99%

Analysis of Salmonella enteritidis strains isolated from food-poisoning cases in Taiwan by pulsed field gel electrophoresis, plasmid profile and phage typing

Tsen¹,

Lin²

2001

J Appl Microbiol

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“…Afterward, numerous rapid mini-prep methods for isolation of plasmid DNA on a small scale have been developed that can be applied to large numbers of bacterial isolates for typing purposes and epidemiological studies (Towner and Cockayne, 1993). The best yields are obtained with smaller plasmids, partly because of their large copy numbers and because they are less prone to physical damage during the isolation process; but, also plasmids > 100 kb in size can be visualized if appropriate care in handling is taken (Towner and Cockayne, 1993). By using the Maxi Prep., commercial ready kits (Qiagen), sharp and clear patterns were obtained, but in more than 2 h using large volumes of cultivated bacteria (500 ml) which recompensed plasmid yield loses and high costs as well (Figure 4).…”

Section: Resultsmentioning

confidence: 99%

“…Once plasmid DNA has been precipitated, it should be visualized before analysis. This step is normally achieved by electrophoresis through an agarose gel (Towner and Cockayne, 1993) such as horizontal slab agarose gel with a concentration of 0.7% in 1 x Tris acetate EDTA (TAE) buffer.…”

Section: Agarose Gel Electrophoresis Of Plasmid Dnamentioning

confidence: 99%

Rapid mini-prep isolation of high quality small and large plasmids from phytopathogenic Gram negative bacteria

Abdullah¹,

Khalid²,

Sobhy³

et al. 2013

Afr. J. Microbiol. Res.

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A simple and cheap method of plasmid DNA preparation from phytopathogenic Gram-negative bacteria (Xanthomonad, Erwinia stewartii) is presented here. In this method, in place of the high-priced chemicals and commercial kits, available and cheap chemicals were used for rapid isolation of small and large plasmids from different Gram negative bacteria. The time also was reduced by using this method giving a high quality plasmid production as demonstrated on the agarose gel, which make this method be used on a preparative scale to isolate sufficient quantities of plasmid DNA required for restriction analysis, cloning, or transformation experiments. A down scaled-protocol is also very useful for rapidly screening the wild plasmids in a large numbers of bacterial isolates in the experiments where hundreds of colonies should be screened for their plasmid contents such as in studying plasmid curing; antibiotic and heavy metal resistant bacteria or; xenobiotic compound degrading bacteria.

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“…According to Towner and Cockayne (1993), the molecular approach is a common way to find a new genus/species. The 16S rRNA gene sequencing is particularly useful as the 16S rRNA gene is present in all bacteria and is a universal target for bacterial identification that is highly accurate, reliable and reproducible (Kolbert and Persing, 1999;Drancourt et al, 2004).…”

Section: Discussionmentioning

confidence: 99%

Isolation and characterization of a biodegrading 3-chloropropionic acid Burkholderia cepacia WH1 isolated from abandoned agricultural land

Muslem

Huyop

Zakaria

et al. 2015

Asia-Pacific Journal of Molecular Biology and Biotechnology

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The widespread use of herbicides that may contain the recalcitrant halogenated compound 3-chloropropionic acid poses significant environmental hazards and may prove detrimental to human kind. Therefore, it is important that an environmentally friendly bio-based method to detoxify such substance is developed. Consequently, the research detailed here investigated the isolation and identification of a bacterial strain that could degrade 3-chloropropionic acid (3CP) as its sole carbon source. A dehalogenase producing bacteria capable of utilizing 3CP was successfully isolated from abandoned agricultural land and designated strain WH1. Analysis of 16s rRNA as well as biochemical and morphological tests found that the strain WH1 showed a 96% sequence identity with and characteristics similar to that of Burkholderia cepacia. Analysis of phylogeny and BIOLOG confirmed that the strain WH1 was indeed B. cepacia. The bacteria grew well at 37°C in media containing 10 mM 3CP but exhibited a rather slow doubling time of 43.62 h, with an optimum chloride ion release of 0.194 µmol Cl − /mL. Most importantly, analysis by high perfomance chromatography revealed that the B. cepacia isolate effectively degraded ~100% of available 10 mM 3CP. This is the first report detailing a B. cepacia strain able to competently utilize 3CP as its sole carbon source.

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Analysis of nucleic acid profiles

Cited by 7 publications

References 160 publications

Analysis of Salmonella enteritidis strains isolated from food-poisoning cases in Taiwan by pulsed field gel electrophoresis, plasmid profile and phage typing

Analysis of Salmonella enteritidis strains isolated from food-poisoning cases in Taiwan by pulsed field gel electrophoresis, plasmid profile and phage typing

Rapid mini-prep isolation of high quality small and large plasmids from phytopathogenic Gram negative bacteria

Isolation and characterization of a biodegrading 3-chloropropionic acid Burkholderia cepacia WH1 isolated from abandoned agricultural land

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