A high-throughput, medium-discrimination method for preliminary typing and selecting non-identical isolates of lactic acid bacteria in cheeses was developed. RAMP, a PCR with one microsatellite-targeted and one random primer, was used for preliminary typing of 1119 isolates of lactic acid bacteria from Slovak Bryndza cheese. A total of 59 genotypes were identified based on RAMP profiles consisting of 12-23 DNA fragments of 150-3000 bp. For example, 18, 17, 13 and 7 different RAMP-types were identified in Lactobacillus brevis, L. plantarum, L. paracasei and L. fermentum, respectively. The method facilitated well reproducible, medium-discrimination typing of Lactobacillus spp. and Pediococcus spp. at a subspecies level and proved to be suitable for preliminary typing of lactic acid bacteria isolated from cheese.
- MeSH
- Acidosis, Lactic metabolism MeSH
- DNA, Bacterial genetics MeSH
- DNA Fingerprinting methods MeSH
- DNA Primers genetics MeSH
- Genotype MeSH
- Lactobacillaceae genetics isolation & purification classification MeSH
- Microsatellite Repeats MeSH
- Cheese microbiology MeSH
- Random Amplified Polymorphic DNA Technique methods MeSH
The population structure of the fungal pathogen Pyrenophora teres, collected mainly from different regions of the Czech and Slovak Republics, was examined using a microsatellite analyses (SSR). Among 305 P. teres f. teres (PTT) and 82 P. teres f. maculata (PTM) isolates that were collected, the overall gene diversity was similar (ĥ = 0.12 and ĥ = 0.13, respectively). A high level of genetic differentiation (FST = 0.46; P < 0.001) indicated the existence of population structure. Nine clusters that were found using a Bayesian approach represent the genetic structure of the studied P. teres populations. Two clusters consisted of PTM populations; PTT populations formed another seven clusters. An exact test of population differentiation confirmed the results that were generated by Structure. There was no difference between naturally infected populations over time, and genetic distance did not correlate with geographical distance. The facts that all individuals had unique multilocus genotypes and that the hypothesis of random mating could not be rejected in several populations or subpopulations serve as evidence that a mixed mating system plays a role in the P. teres life cycle. Despite the fact that the genetic differentiation value between PTT and PTM (FST = 0.30; P < 0.001) is lower than it is between the populations within each form (FST = 0.40 (PTT); FST = 0.35 (PTM); P < 0.001) and that individuals with mixed PTT and PTM genomes were found, the two forms of P. teres form genetically separate populations. Therefore, it can be assumed that these populations have most likely undergone speciation.
- MeSH
- Ascomycota classification genetics isolation & purification MeSH
- Phylogeny MeSH
- Genetic Variation * MeSH
- Genotype MeSH
- Microsatellite Repeats * MeSH
- Molecular Typing MeSH
- Mycological Typing Techniques MeSH
- Cluster Analysis MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czech Republic MeSH
- Slovakia MeSH
Ramularia collo-cygni (Rcc) is a major pathogen of barley that causes economically serious yield losses. Disease epidemics during the growing season are mainly propagated by asexual air-borne spores of Rcc, but it is thought that Rcc undergoes sexual reproduction during its life cycle and may also disperse by means of sexual ascospores. To obtain population genetic information from which to infer the extent of sexual reproduction and local genotype dispersal in Rcc, and by implication the pathogen's ability to adapt to fungicides and resistant cultivars, we developed ten polymorphic microsatellite markers, for which primers are presented. We used these markers to analyse the population genetic structure of this cereal pathogen in two geographically distant populations from the Czech Republic (n=30) and the United Kingdom (n=60) that had been sampled in a spatially explicit manner. Genetic diversity at the microsatellite loci was substantial, Ht=0.392 and Ht=0.411 in the Czech and UK populations respectively, and the populations were moderately differentiated at these loci (Θ=0.111, P<0.01). In both populations the multilocus genotypic diversity was very high (one clonal pair per population, resulting in >96% unique genotypes in each of the populations) and there was a lack of linkage disequilibrium among loci, strongly suggesting that sexual reproduction is an important component of the life cycle of Rcc. In an analysis of spatial genetic structure, kinship coefficients in all distance classes were very low (-0.0533 to 0.0142 in the Czech and -0.0268 to 0.0042 in the Scottish population) and non-significant (P>0.05) indicating lack of subpopulation structuring at the field scale and implying extensive dissemination of spores. These results suggest that Rcc possesses a high evolutionary potential for developing resistance to fungicides and overcoming host resistance genes, and argue for the development of an integrated disease management system that does not rely solely on fungicide applications.
- MeSH
- Ascomycota classification genetics isolation & purification MeSH
- DNA Primers genetics MeSH
- Genetic Variation * MeSH
- Genotype MeSH
- Hordeum microbiology MeSH
- Microsatellite Repeats * MeSH
- Molecular Typing methods MeSH
- Mycological Typing Techniques methods MeSH
- Plant Diseases microbiology MeSH
- Genetics, Population MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Czech Republic MeSH
- United Kingdom MeSH
The detection of microsatellite instability (MSI) is a standard part of mutational analysis in hereditary nonpolyposis colorectal cancers (HNPCC). A characteristic phenotypic feature of MSI indicates loss of mismatch repair (MMR) in tumour cells. We studied MSI in 205 tumours from 152 patients with HNPCC. Of these, 37 patients fulfilled the Amsterdam criteria, 72 patients were familial and 43 were sporadic cases. We used the method of fragmentation analysis (ABI Prism 310 Genetic Analyzer) with fluorescent labelled primers; three mononucleotide (BAT-RII, BAT-25, BAT-26) and five dinucleotide (D2S123, D3S1029, D5S346, D17S250, D18S58) repeat loci were analysed. We detected 75 tumours with a high degree of MSI (MSI-H), 12 tumours with a low degree of MSI (MSI-L) and 118 tumours with stable microsatellites (MSS). We found a loss of heterozygozity (LOH) in 44 MSS tumours. In 30 patients with MSI-H tumours mutation in one of mismatch repair genes was detected.
- MeSH
- Colorectal Neoplasms, Hereditary Nonpolyposis diagnosis genetics MeSH
- DNA Primers analysis genetics MeSH
- Financing, Organized MeSH
- Immunohistochemistry methods utilization MeSH
- Microsatellite Instability drug effects MeSH
- DNA Mutational Analysis methods utilization MeSH
- Polymerase Chain Reaction methods utilization MeSH
- Loss of Heterozygosity physiology immunology MeSH
The results in this study suggest that microsatellite polymorphism within the transmembrane region of MIC-A gene is associated with genetic susceptibility to adult-onset of type 1 diabetes mellitus (T1DM), MIC-A5.1 allele, corrected P = 0.001, whereas it is not associated with latent autoimmune diabetes in adults (LADA) in Czech population. According to our findings, we can hypothesize that adult-onset T1DM and LADA may have partly different immunogenetic aetiopathogenesis
- MeSH
- Diabetes Mellitus, Type 1 genetics MeSH
- Adult MeSH
- Financing, Organized MeSH
- Genetic Predisposition to Disease genetics MeSH
- Humans MeSH
- Histocompatibility Antigens Class I genetics MeSH
- Microsatellite Repeats genetics MeSH
- Polymorphism, Genetic genetics MeSH
- Check Tag
- Adult MeSH
- Humans MeSH
- Male MeSH
- Female MeSH
- Geographicals
- Czech Republic MeSH
[2] s. : il. ; 30 cm
- MeSH
- Base Pair Mismatch MeSH
- Colorectal Neoplasms, Hereditary Nonpolyposis diagnosis genetics physiopathology MeSH
- Genetic Predisposition to Disease MeSH
- Genetic Testing MeSH
- Immunohistochemistry methods utilization MeSH
- Microsatellite Instability MeSH
- Neoplasm Proteins analysis MeSH
- DNA Mismatch Repair MeSH
- Conspectus
- Biochemie. Molekulární biologie. Biofyzika
- NML Fields
- onkologie
- gastroenterologie
- biologie
- NML Publication type
- informační publikace
Bones are a valuable source of DNA in forensic, anthropological, and archaeological investigations. There are a number of scenarios in which the only samples available for testing are highly degraded and/or skeletonized. Often it is necessary to perform more than one type of marker analysis on such samples in order to compile sufficient data for identification. Lineage markers, such as Y-STRs and mitochondrial DNA (mtDNA), represent important systems to complement autosomal DNA markers and anthropological metadata in making associations between unidentified remains and living relatives or for characterization of the remains for historical and archaeological studies. In this comparative study, Y-STR typing with both Yfiler™ and Yfiler™ Plus (Thermo Fisher Scientific, Waltham, MA, USA) was performed on a variety of human skeletal remains, including samples from the American Civil War (1861-1865), the late nineteenth century gold rush era in Deadwood, SD, USA (1874-1877), the Seven Years' War (1756-1763), a seventeenth-century archaeological site in Raspenava, Bohemia (Czech Republic), and World War II (1939-1945). The skeletal remains used for this study were recovered from a wide range of environmental conditions and were extracted using several common methods. Regardless of the DNA extraction method used and the age/condition of the remains, 22 out of 24 bone samples yielded a greater number of alleles using the Yfiler™ Plus kit compared to the Yfiler™ kit using the same quantity of input DNA. There was no discernable correlation with the degradation index values for these samples. Overall, the efficacy of the Yfiler™ Plus assay was demonstrated on degraded DNA from skeletal remains. Yfiler™ Plus increases the discriminatory power over the previous generation multiplex due to the larger set of Y-STR markers available for analysis and buffer modifications with the newer version kit. Increased haplotype resolution is provided to infer or refute putative genetic relationships.
- MeSH
- Alleles MeSH
- DNA Fingerprinting instrumentation MeSH
- Bone and Bones chemistry MeSH
- Humans MeSH
- Chromosomes, Human, Y MeSH
- Microsatellite Repeats * MeSH
- DNA Degradation, Necrotic MeSH
- Disaster Victims MeSH
- Polymerase Chain Reaction MeSH
- Body Remains * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Comparative Study MeSH
- MeSH
- Base Pair Mismatch * genetics MeSH
- Colorectal Neoplasms, Hereditary Nonpolyposis genetics MeSH
- DNA-Binding Proteins MeSH
- Adult MeSH
- MutS Homolog 2 Protein MeSH
- Immunohistochemistry MeSH
- Cohort Studies MeSH
- Colorectal Neoplasms * genetics MeSH
- Middle Aged MeSH
- Humans MeSH
- Microsatellite Instability * MeSH
- Mismatch Repair Endonuclease PMS2 MeSH
- MutL Protein Homolog 1 MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
