| 1. |
- Bal, Karol, et al.
(författare)
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Structure of muramic acid TMS derivative mass spectrum's base ion (m/z=185) used for quantification of bacterial peptidoglycan.
- 2002
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Ingår i: Journal of Microbiological Methods. - 1872-8359. ; 48:2-3, s. 267-270
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Tidskriftsartikel (refereegranskat)abstract
- The use of trimethylsilyl (TMS)-derivatisation for determining muramic acid in environmental and clinical samples by gas chromatography-mass spectrometry provides high detection sensitivity; however, questions have been raised as concerns the chemical structure of the entity giving the strong signal of m/z 185. In the present communication we present evidence that this entity results from the formation of a lactam structure of muramic acid upon derivatisation.
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| 2. |
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| 3. |
- Danilov, Roman, et al.
(författare)
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Comparison of usefulness of three types of artificial substrata (glass, wood and plastic) when studying settlement patterns of periphyton in lakes of different trophic status
- 2001
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Ingår i: Journal of Microbiological Methods. - 0167-7012 .- 1872-8359. ; 45:3, s. 167-170
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Tidskriftsartikel (refereegranskat)abstract
- Usefulness of three types of artificial substrata (glass, wood and plastic) was tested when studying settlement patterns of periphyton in lakes of different trophic status. Strictly eu-, meso- and oligotrophic lakes in central Sweden were chosen as objects of the study. Glass slides, glass tubes, pieces of plastic (PVC) and pieces of wood of similar dimensions were placed for 9 weeks in July-August vertically 3 cm above bottom at a total depth of ca. 30 cm. Substrata were located at well-illuminated places without any other submerged objects (like macrophytes and stones), which could potentially affect colonisation patterns by algae. Periphyton communities, which colonised both the glass tubes and the pieces of wood tested, were specific enough to enable a clear classification of the lakes studied in eu-, meso- and oligotrophic. Glass tubes turned out to be the most favourable substratum when investigating settlement patterns of periphyton in this study. Although also colonised by periphytic species, wood did not support the same diversity and abundance of species as glass did. No algae were detected on the plastics studied. The plastics were covered entirely by a slime layer of bacteria. It is discussed if the nature of plastics could have some inhibitory effects on algal growth or the slime layer itself may have prevented settlement of algal spores.
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| 4. |
- Dopson, Mark, et al.
(författare)
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First use of two-dimensional polyacrylamide gel electrophoresis to determine phylogenetic relationships.
- 2004
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Ingår i: J Microbiol Methods. - : Elsevier BV. - 0167-7012 .- 1872-8359. ; 58:3, s. 297-302
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Tidskriftsartikel (refereegranskat)abstract
- Methods for microbial classification are not always capable of distinguishing between isolates at the species level. We have previously characterised four Ferroplasma isolates that were >98.9% similar at the 16S rDNA level, the isolates showed marked phenotypic differences, and one isolate was borderline on the 70% species boundary from DNA-DNA similarity data. In this study we have used statistical comparisons of two-dimensional polyacylamide gel electrophoresis gels for classification of closely related isolates. From the protein profile similarities an un-rooted tree was constructed that was congruent with a tree derived from DNA-DNA similarities.
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| 5. |
- Kisand, Veljo, et al.
(författare)
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Limited resolution of 16S rDNA DGGE caused by melting properties and closely related DNA sequences
- 2003
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Ingår i: Journal of Microbiological Methods. - 0167-7012 .- 1872-8359. ; 54:2, s. 183-191
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Tidskriftsartikel (refereegranskat)abstract
- The phylogenetic affiliation of 91 operational taxonomic units, randomly sampled from three aquatic microcosm experiments, was investigated by two PCR based and one culture dependent method. The occurrence of multiple melting domains and poor coupling between Tin and DGGE retardation was demonstrated to cause poor resolution at the species level in PCR-DGGE analysis of microbial communities. We also showed that the problem of multiple melting domains was particularly prone for brackish water bacterioplankton in the Flavobacterium genus, providing characteristic band morphology for this genus. Banding patterns from DGGE analysis may therefore be misinterpreted in terms of the species richness in natural bacterial communities, when using commonly applied universal primers. (C) 2003 Elsevier Science B.V. All rights reserved.
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| 6. |
- Szponar, Bogumila, et al.
(författare)
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Limitations in the use of 3-hydroxy fatty acid analysis to determine endotoxin in mammalian samples
- 2002
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Ingår i: Journal of Microbiological Methods. - 1872-8359 .- 0167-7012. ; 50:3, s. 283-289
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Tidskriftsartikel (refereegranskat)abstract
- 3-Hydroxy fatty acids (3-OH FAs) of 10-18-carbon chain lengths are constituents of the lipopolysaccharide of Gram-negative bacteria. These acids are used as chemical markers for determining endotoxin in environmental samples. The present communication addresses the question whether this type of analysis also would be applicable to mammalian samples. Low levels (6.1 +/- 1.6-94.0 +/- 23.2 pmol/ml) of the studied 3-OH FAs were detected in blood from both conventional and germ-fine rats. The levels were considerably higher (0.0-1.06 +/- 0.17 nmol/mg) in livers. The amounts of the 3-OH FAs did not differ between the two groups of rats. All analyses were made by gas chromatography-tandem mass spectrometry (GC-MSMS) for unequivocal identification. The results illustrate a limitation in using 3-OH FA analysis to determine endotoxin in mammalian samples since these acids may represent not only endotoxin but also products from mammalian mitochondrial fatty acid beta-oxidation. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 7. |
- Tavares, F, et al.
(författare)
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A simple, rapid and non-destructive procedure to extract cell wall-associated proteins from Frankia
- 2000
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Ingår i: Journal of Microbiological Methods. - 0167-7012 .- 1872-8359. ; 39:2, s. 171-178
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Tidskriftsartikel (refereegranskat)abstract
- A simple cell fractionation procedure was developed to extract cell wall-associated proteins from the nitrogen-fixing actinomycete Frankia. The method was based on washing Frankia mycelia in 62.5 mM Tris-HCl (pH 6.8) buffer supplemented with 0.1% Triton X-100 as solubilizing agent. Cell wall-associated proteins were efficiently extracted in less than 10 min, recovering approximately 94.5+/-7.44 pg protein per extraction procedure from exponentially growing cells, corresponding to 50 ml of culture. The amount of cell lysis occurring during the cell wall extraction was estimated to be 1.50+/-0.51%. Three peptidoglycan hydrolases with apparent molecular masses of 4.7, 12.1, and 17.8 kDa were detected by zymography in the cell wall-associated protein fraction. On the contrary, no cell wall lytic enzyme was detected in the cytoplasmic protein fraction. These results indicate that the present method enables a specific extraction of cell wall-associated proteins. Moreover, fluorescein isothiocyanate (FITC) labelling of the cell surface proteins showed an efficient removal of cell wall-associated proteins. Growth of the treated Frankia cells (i.e. cells from which the cell wall-associated proteins were removed) in semi-solid media suggested that these cells were still viable. This technique is of importance for functionality studies of cell wall-associated proteins, particularly for bacteria where traditional cell fractionation methods are difficult to be applied. (C) 2000 Elsevier Science B.V. All rights reserved.
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| 8. |
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| 9. |
- Wang, Mei, et al.
(författare)
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T-RFLP combined with principal component analysis and 16S rRNA gene sequencing: an effective strategy for comparison of fecal microbiota in infants of different ages
- 2004
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Ingår i: Journal of Microbiological Methods. - : Elsevier BV. - 1872-8359 .- 0167-7012. ; 59:1, s. 53-69
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Tidskriftsartikel (refereegranskat)abstract
- The fecal microbiota of two healthy Swedish infants was monitored over time by terminal restriction fragment length polymorphism (T-RFLP) analysis of amplified 16S rRNA genes. Principal component analysis (PCA) of the T-RFLP profiles revealed that the fecal flora in both infants was quite stable during breast-feeding and a major change occurred after weaning. The two infants had different sets of microbiota at all sampling time points. 16S rDNA clone libraries were constructed and the predominant terminal restriction fragments (T-RFs) were identified by comparing T-RFLP patterns in the fecal community with that of corresponding 16S rDNA clones. Sequence analysis indicated that the infants were initially colonized mostly by members of Enterobacteriaceae, Veillonella, Enterococcus, Streptococcus, Staphylococcus and Bacteroides. The members of Enterobacteriaceae and Bacteroides were predominant during breast-feeding in both infants. However, Enterobacteriaceae decreased while members of clostridia increased after weaning. T-RFLP in combination with PCA and 16S rRNA gene sequencing was shown to be an effective strategy for comparing fecal microbiota in infants and pointing out the major changes. (C) 2004 Elsevier B.V. All rights reserved.
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