Random amplified polymorphic DNA and restriction enzyme analysis of PCR amplified rDNA in taxonomy: two identification techniques for food‐borne yeasts

Baleiras-Couto, Margarida; Vogels, Jack; Hofstra, H.; Veld, J.H.J. Huis in‘t; Vossen, J.M.B.M. van der

doi:10.1111/j.1365-2672.1995.tb03173.x

Cited by 60 publications

(23 citation statements)

References 32 publications

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“…Furthermore, using these three primers in combination con®rms the relatedness ®ndings, because the oligonucleotides randomly target regions of the genome and the use of multiple primers leads to diversi®cation of the zones ampli®ed. Moreover, RAPD tells us about the phylogenetic links between strains (Baleiras Couto et al 1995). The strains of the species G. fragrans and G. capitatum show only 20% homology with the strains of G. candidum.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity among Geotrichum candidum strains from various substrates studied using RAM and RAPD-PCR

et al. 2002

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Aims: Assessment of genetic diversity within the species Geotrichum candidum and development of tools to trace the strains that play an important role in the agro food industry. Methods and Results: RAM‐PCR and RAPD‐PCR techniques were assessed for their ability to discriminate 57 strains of various morphotypes, substrates and geographical origin. The techniques were complementary and, when combined, allowed us to discriminate isolates. Moreover, we established a link between a taxon and its occupation of an ecological niche, which should not be confused with the substrate of isolation. Conclusions: We observed a high degree of diversity, which could be linked to the variety of the ecological niches chosen and to the high degree of morphological polymorphism encountered within the species. Significance and Impact of the Study: Used in combination, RAM‐PCR and RAPD‐PCR permit traceability and monitoring systems for G. candidum strains during food processing.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity among Geotrichum candidum strains from various substrates studied using RAM and RAPD-PCR

et al. 2002

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“…The complete NTS region was amplified with the primers NTS F and nts R (Gibco Brl). The sequence of the primers were: 5¢-TGA ACG CCT CTA AGY CAG AAT C for NTS F and 5¢-TTA TAC TTA GAC ATG CAT GGC for NTS R. Final concentrations in the PCR mixture were described by Baleiras Couto et al 1995. The PCR program utilized was as follows: 5 min at 94°C, followed by 30 cycles of 30 s at 94°C, 1 min at 57°C and 3 min at 72°C; then the mixture was heated at 72°C for 2 min and subsequently cooled at 4°C.…”

Section: Amplification and Restriction Analysis Of Nts Regionmentioning

confidence: 99%

“…Over the last decade molecular techniques for the identification and typing of micro-organisms have been widely studied. Thus, the applicability of molecular techniques, such as the RAPD method (Baleiras Couto et al 1994) and restriction enzyme analysis of PCR-amplified small subunits (Baleiras Couto et al 1995) have been demonstrated as a tool for taxonomic purposes providing information on the species level.…”

Section: Introductionmentioning

confidence: 99%

Typing of Saccharomyces cerevisiae and Kloeckera apiculata strains from Aglianico wine

Caruso

Capece

Salzano

et al. 2002

Lett Appl Microbiol

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Aims: Kloeckera apiculata and Saccharomyces cerevisiae yeast species are dominant, respectively, at the early and at the following stages of wine fermentation. In the present study, PCR fingerprinting and NTS region amplification and restriction were applied as techniques for monitoring yeast population performing Aglianico of Vulture grape must fermentation. Methods and Results: Thirty S. cerevisiae and 30 K. apiculata strains were typed by PCR fingerprinting with (GAC)5 and (GTG)5 primers and by complete NTS region amplification followed by restriction with HaeIII and MspI enzymes. S. cerevisiae strains generated two patterns with (GAC)5 primer, while (GTG)5 primer yielded a higher genetic polymorphism. Conversely, in K. apiculata Aglianico wine strains (GAC)5 and (GTG)5 primers generated the same profile for all strains. Restriction analysis of the amplified NTS region gave the same profile for all strains within the same species, except for one strain of S. cerevisiae. Conclusions: The PCR fingerprinting technique was useful in discriminating at strain level S. cerevisiae, particularly with the primer (GTG)5. RFLP patterns generated from the NTS region of the two species can be more easily compared than the patterns resulting from PCR fingerprinting, thus RFLP is more suitable for the rapid monitoring of the species involved in different stages of fermentation. Significance and Impact of the Study: The molecular techniques used allow discrimination of S. cerevisiae at strain level and monitoring of the ratio of S. cerevisiae/K. apiculata during the fermentation process. Thus, their application can assure technological adjustments in a suitable time.

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“…Some of the first applications of PCA and cluster analysis to the study of DNA and RNA fragments of several biological systems in the field of microbiology were done by Couto et al (1995), Johansson et al (1995) and Boon et al (2002). The study by Boon et al (2002) reported the diversity of bacterial groups of activated sludge samples that received waste water from four different types of industry by PCR-DGGE.…”

Section: Microbiologymentioning

confidence: 99%

Multivariate Statistical Tools for the Evaluation of Proteomic 2D-maps:Recent Achievements and Applications

Marengo¹,

Robotti²,

Bobba

2007

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Two dimensional polyacrylamide gel electrophoresis (2D-PAGE) maps represent an unavoidable tool in many fields connected with proteome research, such as development of new diagnostic assays or new drugs. Unfortunately the information contained in the maps is often so complex that its recognition and extraction usually requires complex statistical treatments. Statistics accompanies many phases of 2D-PAGE maps management -from the spot revelation to maps matching, as well as the extraction and rationalisation of useful information. This review describes and reports the most recent achievements in the field of statistical tools applied to proteome research by two-dimensional gel electrophoresis (2D-GE). The first section is devoted to briefly describe the theoretical aspects of the multivariate methods mostly adopted in this field such as Principal Component Analysis, Cluster Analysis, Classification methods, Artificial Neural Networks. The most recent applications are then described explaining the analysis of spot volume datasets from standard differential analysis as well as the direct analysis of 2D maps images. Applications are also reported about the use of multivariate tools in the analysis of DNA and RNA profiles.

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Random amplified polymorphic DNA and restriction enzyme analysis of PCR amplified rDNA in taxonomy: two identification techniques for food‐borne yeasts

Cited by 60 publications

References 32 publications

Genetic diversity among Geotrichum candidum strains from various substrates studied using RAM and RAPD-PCR

Genetic diversity among Geotrichum candidum strains from various substrates studied using RAM and RAPD-PCR

Typing of Saccharomyces cerevisiae and Kloeckera apiculata strains from Aglianico wine

Multivariate Statistical Tools for the Evaluation of Proteomic 2D-maps:Recent Achievements and Applications

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