BEsTRF (Best Estimated T-RF) provides an environment for analyzing primers-enzymes-gene section combinations used in T-RFLP. User defined databases of DNA sequences can be explored and the resolution of user specified sets of primers and restriction endonucleases can be analyzed on either forward or reverse terminal fragments. Sequence quality, primer mismatches, insertions and delitions can be controlled and each primer-pair specific sequence collections can be exported for downstream analyses.
COBISS.SI-ID: 2450312
Mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It provides a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur totrim, screen, and align sequences, calculate distances, assign sequences to OTUs, and describe that alfa-and ß-diversity of eight marine samples previously characterized by pyrpsequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 hours using laptop computer.
COBISS.SI-ID: 2517640
Since the basic requirements for probiotic bacteria is their viability, the appropriate methods for their quantification are crucial. In this publication, the use of propidium monoazide in combination with real-time PCR using SYBR Green I chemistry was used for the first time for selective enumeration of viable Lb. acidophilus and B. animalis ssp. lactis bacteria in a lyophilised probiotic food supplement. The method which is based on the differences of bacterial cell membrane integrity was found promising for routine monitoring of quality and stability of such products.
COBISS.SI-ID: 2592625
The health concerns associated with the presence of L. monocytogenes in cheese have been demonstrated by several listeriosis outbreaks. This work demonstrates that traditional greek Graviera cheeses contaminated in retail with L. monocytogenes are at low risk regarding a potential outgrowth of the pathogen above the E.U. maximum allowable level of 100 CFU/cm2 or g, but may support its survival during storage. A cocktail of bacteriocins naturally present in cheese and consisting mainly of enterocins associated with E. faecium and plantaricin A may contribute to pathogen inhibition.
COBISS.SI-ID: 2443400
To evaluate the protective effect of C. officinalis propylene glycol extracts against oxidative DNA damage and lipid peroxidation induced by high PUFA intake in pigs. Petals extract effectively protected DNA from oxidative damage and indicated a trend towards the reduction of plasma MDA and urinary iPF2a-VI excretion. Its effect was comparable with that of vitamin E and higher of the effect of flower tops extract. Conclusion: The amount of extracts proposed for internal use by traditional medicine protects the organism against DNA damage induced by high PUFA intake.
COBISS.SI-ID: 2356616