Search results

1

A novel method of Mycobacterium tuberculosis complex strain differentiation using polymorphic GC-rich gene sequences

100%

Kotłowski R.

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2015

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vol. 62

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issue 2

317-322

EN

Tuberculosis is one of the leading infectious diseases. In this work, a new genotyping method of Mycobacterium tuberculosis (Mtb) complex strain is presented. 27 Mtb genomes were analyzed for the presence of length polymorphism within polymorphic GC-rich gene sequences. Four genes, Rv3345c, Rv3507, Rv0747 and Rv3511, showing variation in length depending on the Mtb strain were selected for designing primer sequences flanking variable regions for the PCR method. Identification of 16 genotypes among 27 analyzed genomes demonstrated usefulness of our genotyping method in differentiation of Mtb genomes based on sequence polymorphism in the four PGRS genes.

2

Application of the High Resolution Melting analysis for genetic mapping of Sequence Tagged Site markers in narrow-leafed lupin (Lupinus angustifolius L.)

100%

Kamel K., Kroc M., Święcicki W.

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2015

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vol. 62

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issue 3

533-540

EN

Sequence tagged site (STS) markers are valuable tools for genetic and physical mapping that can be successfully used in comparative analyses among related species. Current challenges for molecular markers genotyping in plants include the lack of fast, sensitive and inexpensive methods suitable for sequence variant detection. In contrast, high resolution melting (HRM) is a simple and high-throughput assay, which has been widely applied in sequence polymorphism identification as well as in the studies of genetic variability and genotyping. The present study is the first attempt to use the HRM analysis to genotype STS markers in narrow-leafed lupin (Lupinus angustifolius L.). The sensitivity and utility of this method was confirmed by the sequence polymorphism detection based on melting curve profiles in the parental genotypes and progeny of the narrow-leafed lupin mapping population. Application of different approaches, including amplicon size and a simulated heterozygote analysis, has allowed for successful genetic mapping of 16 new STS markers in the narrow-leafed lupin genome.

3

Association Analysis of GDF5 and Contributing Factors in Developmental Dysplasia of the Hip in Infants

88%

Harsanyi S., Zamborsky R., Krajciova L., Bohmer D., Kokavec M., Danisovic L.

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vol. 23(5)

335-339

EN

Background. Developmental dysplasia of the hip (DDH) is a developmental disorder which is reported to be associated with hip instability. When untreated, it can lead to irreversible joint damage. DDH is known to be a multifactorial disease involving genetic, mechanical and environmental factors. The greatest causative potential is attributed to the genetic component. Growth Differentiation Factor 5 (GDF5) is among the most studied genes associated with processes of regeneration and maintenance of joints. The aim of this work was to analyse the association of SNP rs143383 in the GDF5 gene and the occurrence of DDH, along with association with various contributing factors in the Caucasian population. Material and methods. A total of 118 samples were analysed for the presence of the mutation. DNA was isolated from all individuals from peripheral blood. SNP rs143383 in the GDF5 gene was genotyped using the TaqMan assay. A standard chi-square test was used to compare allele and genotype distributions in patients and healthy controls. Results. The association analysis of genotypes of DDH and rs143383 revealed a significant association. Also, the association of GDF5 and selected contributing factors was statistically significant in female gender (p=0.002), family history (p<0.001), count of pregnancy (p=0.009), laterality of hip involvement and initial US examination. Conclusions. 1. The results indicate an important effect of rs143383 polymorphism in the GDF5 gene on DDH development. 2. However, our results also suggest that rs143383 is not the only contributing factor in the genetic component of DDH.

4

Principles and applications of Ligation Mediated PCR methods for DNA-based typing of microbial organisms

88%

Krawczyk B., Kur J., Stojowska-Swędrzyńska K., Śpibida M.

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2016

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vol. 63

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issue 1

39-52

EN

A significant number of DNA-based techniques has been introduced into the field of microorganisms' characterization and taxonomy. These genomic fingerprinting methods were developed to detect DNA sequence polymorphisms by using general principles, such as restriction endonuclease analysis, molecular hybridization, and PCR amplification. In recent years, some alternative techniques based on ligation of oligonucleotide adapters before DNA amplification by PCR, known as Ligation-Mediated PCR methods (LM PCR), have been successfully applied for the typing of microorganisms below the species level. These molecular methods include: Amplified Fragment Length Polymorphism (AFLP), Amplification of DNA fragments Surrounding Rare Restriction Sites (ADSRRS), PCR Melting Profiles (PCR MP), Ligation Mediated PCR/Shifter (LM PCR/Shifter), Infrequent-Restriction-Site Amplification (IRS PCR), double digestion Ligation Mediated Suppression PCR (ddLMS PCR). These techniques are now applied more and more often because they involve less time, are comparably inexpensive, and require only standard lab equipment. Here, we present a general review of this group of methods showing their possibilities and limitations. We also identify questions and propose solutions which may be helpful in choosing a particular LM PCR method for the achievement of the required goal.

5

Fingerprinting of On-Farm Conserved Local Tunisian Orange Cultivars (Citrus sinensis (L.) Osbeck) Using Microsatellite Markers

75%

Abdelaali S. B., Debbabi O. S., Abdelaali N. B., Hajlaoui M. R., Mars M.

Acta Biologica Cracoviensia s. Botanica

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2018

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vol. 60

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issue 1

6

Host Range of Cyclospora Species: Zoonotic Implication

75%

Solarczyk P.

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vol. 60

13-20

EN

Cyclospora is an intracellular, gastrointestinal parasite found in birds and mammals worldwide. Limited accessibility of the protozoan for experimental use, scarcity, genome heterogeneity of the isolates and narrow panel of molecular markers hamper zoonotic investigations. One of the significant limitation in zoonotic studies is the lack of precise molecular tools that would be useful in linking animal vectors as a source of human infection. Strong and convincing evidence of zoonotic features will be achieved through proper typing of Cyclospora spp. taxonomic units (e.g. species or genotypes) in animal reservoirs. The most promising method that can be employ for zoonotic surveys is next-generation sequencing.

7

Polimorfi zm genetyczny wybranych alleli cytochromu CYP2D6 u pacjentów z kardiomiopatią rozstrzeniową i zapaleniem mięśnia sercowego

63%

Smolik S., Domal-Kwiatkowska D., Węglarz L.

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EN

Cytochrome P450 2D6 has been reported to possess variation in the encoding gene that aff ects enzymatic activity. Interindividual diff erences in CYP2D6 activity can produce adverse eff ects or lack of therapeutic eff ect under standard therapy. The aim of the study was to genotyope the chosen alleles of CYP2D6 among the patients with clinically confi rmed myocarditis or dilated cardiomyopathy. Tetra-primer PCR assays was used to detect mutations in CYP2D6 *3, *4 and *6 allelles among 53 patients. A multiplex long PCR was used to genotype CYP2D6*5 allele. Analysis showed the presence of one heterozygote for CYP2D6*3, two heterozygote for CYP2D6*6, ten heterozygote and two homozygote for CYP2D6*4 among the examined patients. One person with deletion of CYP2D6 locus was also detected. Presented methods will facilitate and accelerate the detailed pharmacogenomic analysis of CYP2D6.

PL

Cytochrom CYP2D6 ma różne warianty sekwencji kodującego go genu, wpływające na jego aktywność enzymatyczną. Międzyosobnicze różnice w aktywności izoenzymu CYP2D6 mogą prowadzić do działań niepożądanych lub braku skuteczności terapeutycznej standardowych dawek leku. Celem pracy było genotypowanie wybranych alleli CYP2D6 w grupie pacjentów z potwierdzonym klinicznie stanem zapalnym mięśnia sercowego lub kardiomiopatią rozstrzeniową. W pracy zastosowano reakcję PCR z użyciem czterech starterów w celu detekcji alleli 3*,4* i 6* CYP2D6 w grupie 53 pacjentów. Do wykrycia allelu CY2D6*5 zastosowano długołańcuchową reakcję PCR typu multipleks. Przeprowadzona analiza wykazała w badanej grupie pacjentów obecność jednej heterozygoty dla allelu CYP2D6*3, dwóch heterozygot dla allelu CYP2D*6, dziesięciu heterozygot i dwóch homozygot dla alellu CYP2D6*4. Znaleziono także jedną osobę z delecją locus CYP2D6. Przedstawione metody ułatwiają i przyspieszają dokładną analizę farmakogenetyczną izoformy CYP2D6.