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1

Genotyping by sequencing of Acanthamoeba and Naegleria isolates from the thermal pool distributed throughout Turkey

100%

Degerli S., Degerli N., Camur D., Dogan O., Ilter H.

Acta Parasitologica

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2020

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tom 65

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nr 1

2

rDNA-based genotyping of clinical isolates of Candida albicans

86%

Nawrot U., Pajaczkowska M., Wlodarczyk K., Mecler I.

Polish Journal of Microbiology

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2010

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tom 59

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nr 3

The study presents an analysis of the restriction pattern of rDNA fragments of 95 C. albicans isolates previously classified on the basis of the presence of the intron in rDNA into genotypes A (62 isolates), B (28), and C (5). Most isolates (61) with genotype A were classified as "subtype a" and one as "subtype d" (Karahan and Akar; 2005). No differences were observed in the restriction patterns of the tested genotype B isolates. Similarly, most genotype C strains (4/5) showed the same restriction pattern. The results indicate low subtyping variations of the analyzed isolates, which is in contrast to published data obtained from a Turkish collection of yeasts.

3

Sensitivity and specificity of high-resolution melting analysis in screening unknown SNPs and genotyping a known mutation

86%

Ye M. H., Chen J. L., Zhao G. P., Zheng M. Q., Wen J.

Animal Science Papers and Reports

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2010

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tom 28

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nr 2

High-resolution melting analysis (HRMA) was used to screen potential SNPs in the exons of chicken CAPN1 (μ-calpain/large subunit) gene. A total of 312 DNA samples from Beijing-you chickens were used for detection. Twelve pairs of primer were designed to amplify twelve different exons and SNPs were detected in five of them. HRMA was also compared with PCR-SSCP analysis for genotyping of a known SNP site in the chicken adipocyte fatty acid binding protein gene (A-FABP). Amplicons of 275-bp fragment, bracketing the polymorphic site, were grouped by PCR-SSCP into three genotypem designated as CC, TT and CT. Small amplicons (56 bp) within the 275-bp fragments were designed to maximize the Tm difference between homozygotes and to genotype all possible three genotypes after a single melting analysis successfully. Results from different methods were cross-validated and sequencing results from randomly selected heterozygotes and homozygotes confirmed the specificity of HRM technique. The full consistency proved that HRMA was a useful tool for rapid, close-tube genotyping of polymorphic sites. It has great potential for SNPs detection and scanning especially on a large scale.

4

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Genetic comparison of Campylobacter jejuni isolated from different cattle farms

86%

Bednarski M., Wieliczko A., Mazurkiewicz M.

Polish Journal of Veterinary Sciences

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2011

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tom 14

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nr 2

To compare the genotypes of Campylobacter jejuni, isolates of cattle origin were collected from 9 Polish farms and genotyped by ERIC-PCR. We identified 28 genotypes among the 43 C. jejuni isolates, and demonstrated high genomic diversity. The highest level of diversity was observed in strains isolated from stanchion-barn animals in opposition to those from the loose-housing system.

5

Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

86%

Su Y., Hu D., Zheng H.

Dendrobiology

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2016

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tom 76

Compared to angiosperms, conifers represent more complex genomes with larger giga-genome size. To detect large-scale single nucleotide polymorphisms (SNPs), whole genome sequencing of a conifer population is still unaffordable. In this work, we report the use of DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), an ecological and economic important conifer in China. SLAF libraries of 18 parent clones of a Chinese fir 2.5 generation seed orchard were sequenced and a total of 117,924 SLAFs were developed. We detected 147,376 SNPs from these SLAFs; 146,231 of them represented simple nucleotide change in A/G, C/T, A/C, A/T, C/G or G/T. The most frequent SNPs occurred in C/T (34.3%), while the majority of SNPs (68.2%) belonged to transition events (A/G and C/T). Notably, all the sequenced samples had high portion (78.2–80.9%) of common SNPs indicating that the Chinese fir genomes tended to change its nucleotides at common loci. 48,406 informative SNPs were then successfully utilized to genotype the tested samples (n = 18) followed by a phylogenetic tree to clarify their genetic relationship. Furthermore, a set of very high linkage disequilibrium (0.51–1.00) were identified from these informative SNPs. In brief, our work demonstrated that SLAF-seq is an alternative and cost-effectively high-throughput approach for large-scale SNP exploitation in Chinese fir. While the obtained SNPs offer useful marker resource for further genetic and genomic studies and will be helpful for Chinese fir breeding programs.

6

Report of fatal mixed infection with Cryptosporidium parvum and Giardia intestinalis in neonatal calves

86%

Matsuura Y., Matsubayashi M., Nukata S., Shibahara T., Ayukawa O., Kondo Y., Matsuo T., Uni S., Furuya M., Tani H., Tsuji N., Sasai K.

Acta Parasitologica

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2017

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tom 62

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nr 1

7

Phylogenetic analysis of genetically distinct Enterocytozoon bieneusi infecting renal transplant recipients

86%

Khanduja S., Ghoshal U., Ghoshal U. C.

Acta Parasitologica

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2017

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tom 62

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nr 1

8

The effect of DNA labeling with the fluorescent dyes R110 and R6G on genotype analysis using capillary electrophoresis

86%

Khan H. A.

Cellular and Molecular Biology Letters

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2005

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tom 10

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nr 2

9

Genotyping of the Echinococcus granulosus in paraffin-embedded human tissue samples from Iran

72%

Mirahmadi H., Behravan M., Raz A., Tasa D., Namaei M. H., Solgi R.

Acta Parasitologica

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2021

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tom 66

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nr 2

10

Genotyping of Anaplasma phagocytophilum strains from Poland for selected genes

72%

Rymaszewska A.

Folia Biologica

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2014

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tom 62

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nr 1

11

Molecular characterization of Polish Prototheca zopfii mastitis isolates and first isolation of Prototheca blaschkeae in Poland

72%

Jagielski T., Lassa H., Ahrholdt J., Roesler U., Malinowski E.

Polish Journal of Veterinary Sciences

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2010

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tom 13

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nr 4

Bovine mastitits caused by the colorless, yeast-like alga Prototheca zopfii is a serious and complex condition that results in heavy economic losses in the dairy industry, both through a substantial reduction in milk production and culling of infected animals. Based on the 18S rDNA sequence analysis, genotype-specific PCR assays have recently been developed to differentiate within the species P. zopfii three distinct P. zopfii genotypes (1-3), of which P. zopfii genotype 3 has been considered a new species P. blaschkeae sp. nov. The purpose of this study was to employ the newly-devised molecular approach for the detection of the two P. zopfii genotypes and P. blaschkeae sp. nov. among bovine mastitis isolates from Poland. This study is the first to provide molecular characterization of Polish P. zopfii mastitis isolates. It also gives the first description of bovine mammary protothecosis due to P. blaschkeae in Poland, as evidenced by genotypical, microbiological, and electron microscopy findings.

12

Actin gene-based molecular typing of Trichomonas vaginalis clinical isolates from the North of Iran

72%

Hezarjaribi H. Z., Taghavi M., Saravi K. H., Faridnia R., Kalani H., Mardani A., Jorjani O., Hosseinikhah Z., Esboei B. R., Gholami M., Fakhar M.

Acta Parasitologica

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2020

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tom 65

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nr 4

13

High-throughput phenotyping and genotyping in comparative QTL analysis of early short-time drought tolerance in Polish fodder and malting spring barleys

72%

Wojcik-Jagla M., Rapacz M., Tyrka M., Koscielniak J., Crissy K., Zmuda K.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

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2013

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tom 94

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nr 3

14

First detection and molecular characterization of Echinococcus equinus in a mule in Turkey

72%

Simsek S., Cevik A.

Acta Parasitologica

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2014

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tom 59

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nr 4

Cystic echinococcosis is a zoonotic disease with a cosmopolital distribution. It is caused by the larval stages (metacestodes) of the parasite Echinococcus granulosus which infects different animal species. In this report, we present a case of E. granulosus infection in a mule and molecular characterization of the cyst. For this purpose parasite material was collected from the liver of a necropsied mule. DNA was isolated and PCR amplification of mitochondrial 12S rRNA as well as partial sequencing of mitochondrial cytochrome c oxidase subunit 1 (mt-CO1) genes were performed. Six unilocular cysts, filled with clear fluid were found in the liver and spleen. All cysts were found to be fertile. The 12S rRNA-PCR did not yield any band while mt-CO1-PCR yielded a 446 bp sized amplification product. Sequence corresponding to mt-CO1 gene was identical to a sequence reported for E. equinus (formerly G4) (Genbank accession number: KC953029). This is the first record of E. equinus as a cause of cystic echinococcosis in a mule in Turkey.

15

Genotyping of Acanthamoeba spp. from water sources from Northwestern Iran

72%

Haniloo A., Pezeshki A., Mahmmodzadeh A., Kadkhodamohammadi E.

Acta Parasitologica

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2017

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tom 62

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nr 4

16

Characterization of Klebsiella pneumoniae strains isolated from urinary tract infection: Detection of ESBL characteristics, antibiotic susceptibility and RAPD genotyping

72%

Aladag M. O., Uysal A., Dundar N., Durak Y., Gunes E.

Polish Journal of Microbiology

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2013

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tom 62

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nr 4

In this study, a hundred Klebsiella pneumoniae strains isolated from urinary tract infections were evaluated in terms of genotyping, susceptibility to certain antibiotics and detection of extended spectrum of beta lactamase (ESBL) production. The random amplified polymorphic DNA (RAPD-PCR) method was used to identify the genetic differentiation of K pneumoniae isolates. A total of 26 different DNA bands ranging between 334 bp and 28033 bp were detected among the strains. It was found that 100 K. pneumoniae strains revealed 11 different RAPD profiles. Antibiotic susceptibility tests were conducted using a disc diffusion method against 16 antibiotics. Fifty-five different resistance profiles were determined among the strains. ESBL-productions of the strains were determined by the double disc synergy test (DDST) and ESBL E-test methods. ESBL production rates among the strains were found to be 55% by E-test method and 45% by DDST method. While ESBL-producing K. pneumoniae strains showed the greatest resistance to penicillin G (100%), followed by piperacillin (92.7%) and erythromycin (85.4%), the resistance rates of non ESBLproducing strains to those antibiotics were determined as 97.8%, 88.8% and 88.8%, respectively. Both groups of strains showed the highest sensitivity to meropenem. Based on the results obtained from the study, it was concluded that the detection of ESBL-producing strains by the E-test method was more sensitive than by the DDST method. Phenotypic and genotypic identification methods should be used together to detect ESBL presence. The RAPD-PCR method alone will not be adequate in the genotyping of the strains and alternative DNA-based methods should be used.

17

Rep-PCR - a variant to RAPD or an independent technique of bacteria genotyping? A comparison of the typing properties of rep-PCR with other recognised methods of genotyping of microorganisms

72%

Baldy-Chudzik K.

Acta Microbiologica Polonica

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2001

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tom 50

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nr 3-4

189-204

18

Extended multiple-locus variable-number tandem-repeat analysis of Bacillus anthracis strains isolated in Poland

72%

Gierczynski R., Jakubczak A., Jagielski M.

Polish Journal of Microbiology

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2009

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tom 58

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nr 1

3-7

Twenty-one variable-number tandem-repeat (VNTR) marker loci were used for extended multiple locus VNTR analysis (MLVA) of 14 laboratory strains of Bacillus anthracis isolated in Poland and vaccine strain Sterne 34F2A. The extended MLVA (MLVA-21) distinguished six genotypes clustered in three main branches. Monomorphic branch 1 consisted of the vaccine strain and six isolates from distinct samples of a cow died from anthrax. This group also encompassed three haemolytic isolates of B. anthracis. Branches 2 and 3 were heterogeneous and consisted of five and three isolates of the phylogenetic lineages B2 and A1, respectively. MLVA-21 supported thesis on the anthrax agent heterogeneity in Poland. This study brought an additional evidence that haemolytic B. anthracis strains isolated in Poland are closely related to the vaccine strain Steme 34F2 and may together constitute the same sensu stricto strain. No epidemiological link could be however traced between both the vaccine and the haemolytic strains.

19

Genotyping of Giardia duodenalis human isolates using PCR-RFLP in Zabol City, East of Iran

72%

Abedi M., Dabirzadeh M., Ghasemian M.

Annals of Parasitology

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2016

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tom 62

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nr Suppl.

20

Genotyping and virulence analysis of Toxoplasma gondii isolates from a dead human fetus and dead pigs in Jiangsu province, Eastern China

72%

Hou Z., Zhou Y., Liu D., Su S., Zhao Z., Xu J., Tao J.

Acta Parasitologica

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2018

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tom 63

|

nr 2

Ograniczanie wyników

Genotyping by sequencing of Acanthamoeba and Naegleria isolates from the thermal pool distributed throughout Turkey

rDNA-based genotyping of clinical isolates of Candida albicans

Sensitivity and specificity of high-resolution melting analysis in screening unknown SNPs and genotyping a known mutation

Genetic comparison of Campylobacter jejuni isolated from different cattle farms

Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

Report of fatal mixed infection with Cryptosporidium parvum and Giardia intestinalis in neonatal calves

Phylogenetic analysis of genetically distinct Enterocytozoon bieneusi infecting renal transplant recipients

The effect of DNA labeling with the fluorescent dyes R110 and R6G on genotype analysis using capillary electrophoresis

Genotyping of the Echinococcus granulosus in paraffin-embedded human tissue samples from Iran

Genotyping of Anaplasma phagocytophilum strains from Poland for selected genes

Molecular characterization of Polish Prototheca zopfii mastitis isolates and first isolation of Prototheca blaschkeae in Poland

Actin gene-based molecular typing of Trichomonas vaginalis clinical isolates from the North of Iran

High-throughput phenotyping and genotyping in comparative QTL analysis of early short-time drought tolerance in Polish fodder and malting spring barleys

First detection and molecular characterization of Echinococcus equinus in a mule in Turkey