Wyniki wyszukiwania - Biblioteka Nauki

1

Real-time PCR approach in dermatophyte detection and Trichophyton rubrum identification

100%

Kobylak N. , Bykowska B. , Nowicki R. , Brillowska-Dąbrowska A.

Acta Biochimica Polonica

|

2015

|

tom 62

|

nr 1

119-122

EN

Dermatophytes are keratinophilic molds that infect human hair, nails and skin. Diagnosis of dermatophytosis is based on morphological, serological and biochemical features. However, identification is difficult and laborious due to similarities between microorganisms. Thus, there is considerable interest to develop mycological diagnostic procedures based on molecular biology methods. In this study, fast, two-step DNA extraction method and real-time PCR was used for detection of dermatophytes DNA using pan-dermatophyte primers and identification of Trichophyton rubrum from pure cultures. The applied method allowed correct detection of all dermatophytes and correct identification of Trichophyton rubrum in less than 2 hours.

2

Comparason of extraction methods for PCR detection of Burkholderia cepacia complex (BCC) from cystic fibrosis patients

88%

Ergunay K. , Yurdakul P. , Sener B. , Ozcelik U. , Karabulut E. , Kiper N.

Open Medicine

|

2008

|

tom 3

|

nr 2

157-162

EN

Direct detection of Burkholderia cepacia complex (BCC) and its genomovars from sputum by molecular tests emerges as a method for rapid identification. In this study, four DNA extraction methods were evaluated for the identification for BCC from sputum of CF patients. Sputa from 28 CF patients were aliquoted and spiked with BCC reference strain. Boiling, phenol-chloroform, CTAB methods and a commercial spin column kit was used for DNA extraction. Total DNA yields were determined by spectrophotometry and single-round recA PCR was used for detection of BCC. No significant difference was observed in DNA yields from different extraction methods. Lower limit of detection for recA PCR was determined as 106 cfu/ml. Amplification was observed in 7/16 (43.7%) of sputa for boiling, 8/16 (50%) of sputa for CTAB and 13/16 (81.2%) of sputa for phenol-chloroform method and spin column kit in the assay sensitivity range determined in the study. Phenol-chloroform and commercial spin column kit were found to be better suited for DNA purification from sputum of CF patients for BCC identification. Diagnostic impact of single-round recA PCR directly from sputum was limited to chronically-infected patients.

3

Effects of agricultural land use change on fungal community composition

75%

Wu M. , Zhong G. , Meng D. , Wei W.

|

2015

|

tom 63

|

nr 3

EN

Anthropogenic disturbances, such as tillage, management practices, and fertilization, can influence soil microbial communities, but little is known about the effects of land use type on soil fungal communities. In this study, fungal abundance, diversity and community composition in soils were analyzed, to determine the impacts of different agricultural land use types, including old rice paddies (ORP), the long-term and (LTV), short-term (STV) cultivation of vegetables and Magnolia nursery plantations (MNP). Compared to the soils in ORP, the fungal abundance, determined by real-time quantitative polymerase chain reaction, was significantly higher in soils from LTV fields and lower in those from MNP; the copy numbers of the fungal ITS genes in the LTV soils were 30 times greater than in the MNP soils. The terminal restriction fragment length polymorphism (T-RFLP) results showed that the fungal community composition was obviously different in the different soils, based on land use type. Only three T-RFs were found in the soils from the LTV fields, followed by seven in the STV soils and nine in the MNP soils; the most (11) T-RFs were found in the ORP soils. Of the measured soil chemical properties, SOC, available P and NO₃⁻-N were the dominant factors that influenced the fungal communities based on the canonical correspondence analysis (CCA). The present study showed that conversion from paddy soil to vegetable cultivation changed soil properties, decreased soil fungal diversity, increased fungal abundance, and shifted fungal community composition.

4

An improved procedure of the metagenomic DNA extraction from saline soil, sediment and salt

75%

Kashi F. J.

International Letters of Natural Sciences

|

2016

|

tom 60

5

Sampling, metadata and DNA extraction - important steps in metagenomic studies

75%

Felczykowska A. , Krajewska A. , Zielińska S. , Łoś J.

Acta Biochimica Polonica

|

2015

|

tom 62

|

nr 1

151-160

EN

Metagenomic studies have become increasingly popular. They allow for the estimation of biodiversity in complex populations. This diversity presents an enormous but largely unexpected genetic and biological pool and can be exploited for the recovery of novel genes, entire metabolic pathways and their products. Generally metagenomic study is a genomic analysis of organisms by direct extraction and cloning of DNA from their natural environment. The most common problems of modern metagenomics are as follows: majority of the microorganisms present in the environment cannot be cultivated by standard techniques, DNA extraction methods are not very effective, isolated DNA is contaminated with various compounds, a choice for a screening method is not obvious.

6

Polymorphism of microsatellite loci - a tool in studying biodiversity of paddlefish aquaculture broodstock

75%

Kaczmarczyk D. , Kohlmann K. , Kersten P. , Luczynski M.

Environmental Biotechnology

|

2007

|

tom Vol. 3, No. 2

44-48

EN

American paddlefish (Polyodon spathula) is a new species in Polish aquaculture, its broodstocks are few and small, and it is possible that all mature fish originated from only a few spawners. Studies on polymorphism of highly variable microsatellite DNA allow revealing genetic characteristics of individual spawners as well as estimation of genetic variation within and divergence between broodstocks. This paper describes optimised protocols for isolation of DNA from fin tissues, amplification of nine microsatellite loci using PCR technique, and for fish genotyping using automatic capillary DNA sequencer. Our technique was tested towards the fin samples taken from all paddlefish reared in Poland and approaching their sexual maturity; the study included also samples taken from 47 fish of the Ukrainian breeding center (Gorny Tykich).

7

SNP-minisequencing as an excellent tool for analysing degraded DNA recovered from archival tissues

75%

Babol-Pokora K. , Berent J.

Acta Biochimica Polonica

|

2008

|

tom 55

|

nr 4

815-819

EN

SNP-minisequencing has become common in forensic genetics, especially for analysing degraded or low copy number DNA (LCN DNA). The aim of this study was to examine the usefulness of five SNP (single nucleotide polymorphism) markers for analyzing degraded and LCN DNA recovered from archival samples. DNA extractions of eight formalin-fixed paraffin-embedded (FFPE) tissues were performed and DNA fragments were amplified in one multiplex PCR (polymerase chain reaction). SNPs were identified in a minisequencing reaction and a gel electrophoresis in ABI Prism®377 Sequencer. The research confirmed the usefulness of SNP-minisequencing for analysing FFPE tissues.

8

Rapid and reliable detection of Echinococcus multilocularis from faeces using droplet digital PCR

75%

Bago F. , Hoelzl F. , Knauer F. , Kubber-Heiss A. , Smith S.

Acta Parasitologica

|

2021

|

tom 66

|

nr 2

9

Genotype characterisation of Blastocystis isolates from Polish patients - preliminary results

75%

Salamatin R. , Kaczmarek A. , Rozej-Bielicka W. , Cielecka D. , Janczak D. , Lewicki A. , Wesolowska M. , Mlocicki D. , Golab E.

|

tom 62

|

nr Suppl.

10

A new method of DNA extraction from the ethanol-fixed parasitic worms

75%

Tkach V. , Pawlowski J.

Acta Parasitologica

|

1999

|

tom 44

|

nr 2

EN

A protocol of the new method of DNA extraction from the ethanol fixed parasitic worms is described. The method is based on the use of the guanidine thiocyanate extraction buffer after evaporation of the ethanol from the tissues by drying. The method has been successfully used on several groups of parasitic Plathyhelminthes and provided higher DNA yield than a conventional phenol-chloroform extraction.

11

Development of a rapid, reliable and simple multiplex PCR assay for early detection of transgenic plant material

75%

Xu C. J. , Yang L. , Chen K. S.

Acta Physiologiae Plantarum

|

2005

|

tom 27

|

nr 3A

EN

Multiplex PCR is a variant of conventional PCR which includes two or more pairs of primers in a single reaction to amplify corresponding genes simultaneously. In this study, a reliable multiplex PCR analysis protocol was established for simple and fast detection of transgenes in plant materials. Two pairs of primers, corresponding to neomycin phosphotransferase gene and 1-aminocyclopropane-1-carboxylate synthase gene, were selected for target and resident gene respectively. The method bypasses routine DNA extraction, requires only very little amount of plant tissue and produces reliable results as shown by successful discrimination of transformed and non transformed tobacco, tomato and kumquat materials. The method facilitates early identification of transgenic buds when they are still quite small.

12

Molecular phylogenetics evidence for a novel lineage of amoebae within Discosea (Amoebozoa: Lobosa)

63%

Carsaro D. , Venditti D.

Acta Protozoologica

|

2013

|

tom 52

|

nr 4

13

Fast and easy method for total DNA extraction and gene amplification from larvae, spat and adult mussels Mytilus trossulus from the Baltic Sea

63%

Lasota R. , Pilczynska J. , Williams S. T. , Wolowicz M.

Oceanological and Hydrobiological Studies

|

2013

|

tom 42

|

nr 4

14

Prevalence and molecular characterization of bovine Cryptosporidium from dairy cows in Northern Thailand

63%

Inpankaew T. , Jiyipong T. , Sunanta C. , Kengradomkij C. , Pinyopanuwat N. , Jittapalapong S.

Acta Parasitologica

|

2017

|

tom 62

|

nr 4

15

Genetic diversity among Babesia rossi detected in naturally infected dogs in Abeokuta, Nigeria, based on 18S rRNA gene sequences

63%

Takeet M. I. , Oyewusi A. J. , Abakpa S. A. V. , Daramola O. O. , Peters S. O.

Acta Parasitologica

|

2017

|

tom 62

|

nr 1

16

PCR and real time PCR for the detection of Cryptosporidium parvum oocyst DNA

63%

Adamska M. , Leonska-Duniec A. , Maciejewska A. , Sawczuk M. , Skotarczyk B.

Folia Biologica

|

2011

|

tom 59

|

nr 3-4

17

Intra and inter species genetic variability of transferrin receptor gene regions in Trypanosoma evansi isolates of different livestock and geographical regions of India

63%

Sarkhel S. P. , Gupta S. K. , Kaushik J. , Singh J. , Saini V. K. , Kumar S. , Kumar R.

Acta Parasitologica

|

2017

|

tom 62

|

nr 1

18

Effect of extraction method and DNA quality on the reliability of molecular detection of Bradyrhizobium japonicum in soybean rhizosphere

63%

Baturo-Ciesniewska A. , Loddi G. , Prusinski J. , Lukanowski A.

Electronic Journal of Polish Agricultural Universities. Series Agronomy

|

2019

|

tom 22

|

nr 2

19

Potential refugia in Qinghai-Tibetan Plateau revealed by the phylogeographical study of Swertia tetraptera (Gentianaceae)

63%

Yang L.-C. , Zhou G.-Y. , Li C.-L. , Song W.-Z. , Chen G.-C.

Polish Journal of Ecology

|

2011

|

tom 59

|

nr 4

EN

We studied the phylogeography of Swertia tetraptera Maxim, which is an annual herbaceous plant endemic to the Qinghai-Tibetan Plateau (QTP), by sequencing one intergenic chloroplast spacer, trnL-trnF (773 bp). The sampling design included 35 populations and 399 individuals, and spanned the entire distribution of the species. Forty-four haplotypes were characterized, and one of them was widely distributed in all of the populations. The level of differentiation among the populations studied was relatively low (GST = 0.128). Estimates of NST -GST for populations of S. tetraptera indicated that no phylogeographical structure exists, which was supported by the distribution of haplotypes. The neutrality test, mismatch distribution and a ‘star-like’ genealogy all suggested that this species experienced population expansion. According to the number of rare haplotype and geological evidence, this study suggested that two potential refugia existed during the last glaciation: the first refugium was identified in a restricted semi-continuous area around the eastern margin of the plateau; the second refugium was located in the central of QTP. In fact, the findings of our study are somewhat similar as the third phylogeographical structure occurring in the QTP, that is, alpine plants have refugia not only in the edge area but also in the Plateau platform. However, the location of plateau edge and plateau platform refugia is very different among them due to the difference of species-specific characteristic such as distributional range and life history traits.

20

Evaluation of four commercial DNA extraction kits for the detection of Microsporidia and the importance of pretreatments in DNA isolation

63%

Cetinkaya U. , Charyyeva A. , Sivcan E. , Gurbuz E.

Acta Parasitologica

|

2018

|

tom 63

|

nr 2