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Tytuł:
Application of polymerase chain reaction-restriction fragment length polymorphism (RFLP-PCR) in the analysis of single nucleotide polymorphisms (SNPs)
Autorzy:
Tarach, Piotr
Powiązania:
https://bibliotekanauki.pl/articles/1830648.pdf
Data publikacji:
2021-09-29
Wydawca:
Uniwersytet Łódzki. Wydawnictwo Uniwersytetu Łódzkiego
Tematy:
nucleotide polymorphisms
DNA analysis
polymerase chain reaction
Opis:
Polymerase chain reaction-restriction fragment length polymorphism (RFLP-PCR) is a technique used to identify single nucleotide polymorphisms (SNPs) based on the recognition of restriction sites by restriction enzymes. RFLP-PCR is an easy-to-perform and inexpensive tool for initial analysis of SNPs potentially associated with some monogenic diseases, as well as in genotyping, genetic mapping, lineage screening, forensics and ancient DNA analysis. The RFLP-PCR method employs four steps: (1) isolation of genetic material and PCR; (2) restriction digestion of amplicons; (3) electrophoresis of digested fragments; and (4) visualisation. Despite its obsolescence and the presence of high-throughput DNA analysis techniques, it is still applied in the analysis of SNPs associated with disease entities and in the analysis of genetic variation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RFLP-PCR is a low-cost and low-throughput research method allowing for the analysis of SNPs in the absence of specialised equipment, and it is useful when there is a limited budget.
Źródło:
Acta Universitatis Lodziensis. Folia Biologica et Oecologica; 2021, 17; 48-53
1730-2366
2083-8484
Pojawia się w:
Acta Universitatis Lodziensis. Folia Biologica et Oecologica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Cacao swollen shoot virus detection and DNA barcoding of its vectors and putative vectors in Theobroma cacao L. by using polymerase chain reaction
Autorzy:
Obok, E.E.
Aikpokpodion, P.O.
Ani, O.C.
Allainguillaume, J.
Wetten, A.
Powiązania:
https://bibliotekanauki.pl/articles/2096411.pdf
Data publikacji:
2021
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
Cacao swollen shoot virus
COI – cytochrome c oxidase subunit I
DNA barcoding
Jack Beardsley
mealybug
PCR – polymerase chain reaction
Theobroma cacao
Opis:
Cacao swollen shoot virus (CSSV) is an endemic pathogen causing significant economic losses to cacao (Theobroma cacao L.) production in West Africa. There is limited updated report on the occurrence, spread, genetic diversity and species of CSSV and its mealybug vectors, especially in Nigeria. Nigeria is presently lagging behind in the search for resistance to CSSV and its vectors in T. cacao L. The present study aimed to map and screen for the presence of CSSV and its natural vectors – female mealybugs (Pseudococcidae: Hemiptera) in cacao plantations in Nigeria. Symptomatic and asymptomatic cacao leaves and whole female mealybug samples were collected from major cacao-growing areas in Nigeria – Abia, Akwa Ibom, Cross River, Edo, Ondo and Oyo States. A total of 2568 cacao leaves from 1052 cacao trees were screened with polymerase chain reaction (PCR) using an open reading frame 1 (ORF 1) CSSV-specific primer pair. PCR screening of the mealybug species was performed using the cytochrome c oxidase subunit I (COI) gene. A combination of scanning electron microscopy (SEM) and histology for morphological identification and DNA barcoding enabled to characterise the female mealybug species. The results revealed that CSSV and its mealybug vectors are present in the major cacao-growing areas in Nigeria. Although CSSV and its vectors have been previously reported in Cross River, Ondo and Oyo States, our results present the first documented evidence of CSSV emergence and its mealybug vectors in Abia, Akwa Ibom and Edo States. We also present the first report of Pseudococcus jackbeardsleyi (Gimpel and Miller) mealybug species on cacao in Nigeria. In conclusion, it is pertinent to re-establish coordinated routine survey and monitoring of CSSV and its mealybug vector presence in T. cacao L. in Nigeria.
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2021, 102, 3; 229-244
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Enhancement of fungal DNA templates and PCR amplification yield by three types of nanoparticles
Autorzy:
Al-Dhabaan, F.A.
Yousef, H.
Shoala, T.
Shaheen, J.
El Sawi, Y.
Farag, T.
Powiązania:
https://bibliotekanauki.pl/articles/65369.pdf
Data publikacji:
2018
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
plant pathology
detection
identification
plant pathogen
toxigenic fungi
improvement
specificity
efficiency
polymerase chain reaction
Alternaria alternata
DNA extraction
nanoparticle
Rhizoctonia solani
nanobiotechnology
Opis:
Nanodiagonastic methods in plant pathology are used for enhancing detection and identification of different plant pathogens and toxigenic fungi. Improvement of the specificity and efficiency of the polymerase chain reaction (PCR) by using some nanoparticles is emerging as a new area of research. In the current research, silver, zinc, and gold nanoparticles were used to increase the yield of DNA for two plant pathogenic fungi including soil-borne fungus Rhizoctonia solani and toxigenic fungus Alternaria alternata. Gold nanoparticles combined with zinc and silver nanoparticles enhanced both DNA yield and PCR products compared to DNA extraction methods with ALB buffer, sodium dodecyl sulfate, ALBfree from protinase K, ZnNPs and AgNPs. Also, by using ZnNPs and AgNPs the DNA yield was enhanced and the sensitivity of random amplified polymorphic DNA (RAPD) PCR products was increased. Application of nanomaterials in the PCR reaction could increase or decrease the PCR product according to the type of applied nanometal and the type of DNA template. Additions of AuNPs to PCR mix increased both sensitivity and specificity for PCR products of the tested fungi. Thus, the use of these highly stable, commercially available and inexpensive inorganic nano reagents open new opportunities for improving the specificity and sensitivity of PCR amplicon, which is the most important standard method in molecular plant pathology and mycotoxicology.
Źródło:
Journal of Plant Protection Research; 2018, 58, 1
1427-4345
Pojawia się w:
Journal of Plant Protection Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
In vitro and molecular characterization using ISSR markers of Glycyrrhiza glabra L.
Autorzy:
El-Hameid, A.A.
El-Kheir, Z.A.
Abdel-Hady, M.
Helmy, W.
Powiązania:
https://bibliotekanauki.pl/articles/80908.pdf
Data publikacji:
2018
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
licorice
Glycyrrhiza glabra
callus induction
genomic DNA
ISSR marker
molecular characteristics
polymerase chain reaction
kinetin
Murashige medium
Skoog's medium
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2018, 99, 4
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A simple method for extracting DNA from rhododendron plants infected with Phytophthora spp. for use in PCR
Autorzy:
Trzewik, A.
Nowak, K.J.
Orlikowska, T.
Powiązania:
https://bibliotekanauki.pl/articles/66480.pdf
Data publikacji:
2016
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
simple method
DNA extraction
rhododendron
leaf
plant infection
Phytophthora
polymerase chain reaction
detection
real-time PCR method
Opis:
Among the numerous protocols that describe the extraction of DNA, those relating to the isolation of DNA from infected plants, are rare. This study describes a rapid and reliable method of extracting a high quality and quantity of DNA from rhododendron leaves artificially infected with Phytophthora cactorum, P. cambivora, P. cinnamomi, P. citrophthora, and P. plurivora. The use of the modified Doyle and Doyle protocol (1987) allowed us to obtain high quantity and quality DNA (18.26 μg from 100 mg of the fresh weight of infected leaves at the ratios of A260/280 and A260/230 – 1.83 and 1.72, respectively), suitable for conventional polymerase chain reaction (PCR) and real-time PCR amplifications.
Źródło:
Journal of Plant Protection Research; 2016, 56, 1
1427-4345
Pojawia się w:
Journal of Plant Protection Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Detection of Giardia intestinalis DNA in environmental water and soil samples collected from the Pomerania Province and the Warmia-Masuria Province, Poland using real-time PCR and nested–PCR
Autorzy:
Lass, A.
Szostakowska, B.
Powiązania:
https://bibliotekanauki.pl/articles/6172.pdf
Data publikacji:
2016
Wydawca:
Polskie Towarzystwo Parazytologiczne
Tematy:
detection
Giardia intestinalis
DNA
environmental water
soil sample
Pomeranian region
Warmia-Mazury region
Polska
real-time PCR method
nested polymerase chain reaction
Źródło:
Annals of Parasitology; 2016, 62, Suppl.
0043-5163
Pojawia się w:
Annals of Parasitology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Epi-genes potentiate plant biodiversity
Autorzy:
Szopa, J.
Powiązania:
https://bibliotekanauki.pl/articles/951285.pdf
Data publikacji:
2015
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
biodiversity
oligonucleotide
DNA methylation
gene expression
protein
methylase
polymerase
RNA polymerase
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2015, 96, 1
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Evaluation of methods for Erwinia amylovora detection
Autorzy:
Kaluzna, M.
Pulawska, J.
Mikicinski, A.
Powiązania:
https://bibliotekanauki.pl/articles/1986.pdf
Data publikacji:
2013
Wydawca:
Instytut Ogrodnictwa
Tematy:
Erwinia amylovora
fire blight
real-time polymerase chain reaction
LAMP technique
DNA sequence
detection method
disease control
Źródło:
Journal of Horticultural Research; 2013, 21, 2
2300-5009
Pojawia się w:
Journal of Horticultural Research
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
The expression of UVR3 and two putative photolyases, PHR2 and At4g25290, is regulated by light
Autorzy:
Sztatelman, O.
Labuz, J.
Banas, A.K.
Powiązania:
https://bibliotekanauki.pl/articles/80793.pdf
Data publikacji:
2013
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
conference
DNA strand
RNA polymerase
DNA polymerase
replication
transcription
light regulation
putative photolyase
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Virulence and antibiotic resistance of Escherichia coli isolated from rooks
Autorzy:
Kmet, V.
Drugdova, Z.
Kmetova, M.
Stanko, M.
Powiązania:
https://bibliotekanauki.pl/articles/51141.pdf
Data publikacji:
2013
Wydawca:
Instytut Medycyny Wsi
Tematy:
virulence
antibiotic resistance
Escherichia coli
isolation
rook
polymerase chain reaction
DNA microarray
Opis:
With regard to antibiotic resistance studies in various model animals in the urban environment, the presented study focused on the rook, many behavioural and ecological aspects of which are important from an epidemiological point of view. A total of 130 Escherichia coli strains isolated from rook faeces during a two-year period (2011–2012) were investigated for antibiotic resistance and virulence. Resistance to ampicillin (60%) and streptomycin (40%) were the most frequent, followed by resistance to fluoroquinolones (ciprofloxacin-22% and enrofloxacin-24%), tetracycline (18%), cotrimoxazol (17%) and florfenicol (14%). Ceftiofur resistance occured in 10.7 % of strains and cefquinom resistance in 1.5 % of strains. Twenty-five E.coli strains with a higher level of MICs of cephalosporins (over 2mg/L of ceftazidime and ceftriaxon) and fluoroquinolones were selected for detection of betalactamase genes (CTX-M, CMY), plasmid-mediated quinolone resistance qnrS, integrase 1, and for APEC (avian pathogenic E.coli) virulence factors (iutA, cvaC, iss, tsh, ibeA, papC, kpsII). Genes of CTX-M1, CMY-2, integrase 1, papC, cvaC, iutA were detected in one strain of E.coli, and qnrS, integrase 1, iss, cvaC, tsh were detected in another E.coli. DNA microarray revealed the absence of verotoxin and enterotoxin genes and pathogenicity islands. The results show that rooks can serve as a reservoir of antibiotic-resistant E. coli with avian pathogenic virulence factors for the human population, and potentially transmit such E.coli over long distances.
Źródło:
Annals of Agricultural and Environmental Medicine; 2013, 20, 2
1232-1966
Pojawia się w:
Annals of Agricultural and Environmental Medicine
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Description of DNA analysis techniques and their application in oat (Avena L.) genome research
Charakterystyka technik analiz DNA oraz ich wykorzystanie w badaniach owsa (Avena L.)
Autorzy:
Okon, S.
Kowalczyk, K.
Powiązania:
https://bibliotekanauki.pl/articles/26845.pdf
Data publikacji:
2012
Wydawca:
Polskie Towarzystwo Botaniczne
Tematy:
DNA analysis technique
application
oat
Avena
genome
molecular marker
crossbreeding efficiency
genetic map
hexaploid
diploid
plant species
crown rust
powdery mildew
plant resistance
DNA marker
polymerase chain reaction
Opis:
DNA markers are used not only to estimate genetic similarity and distance but also to select and identify desirable forms, to assess the adjustment of breeding material, to confirm crossbreeding efficiency, to determine seed purity, and to identify the genes which determine important functional traits. In the case of oat, DNA markers were used to construct and increase the density of genetic maps both in hexaploid and diploid species. The development of markers for some important traits provides a fast selection of genotypes containing dwarf genes as well as the resistance genes to crown rust and powdery mildew. Numerous analyses of genetic similarity between different species belonging to the genus Avena which are currently carried out may contribute to explaining the process of evolution within this genus and may also explain the development of particular species of oat.
Markery DNA znalazły zastosowanie nie tylko w ocenie podobieństwa lub dystansu genetycznego, ale również w selekcji i identyfikacji pożądanych form, ocenie wyrównania materiałów hodowlanych, potwierdzaniu skuteczności krzyżowań, ocenie czystości materiału siewnego czy też do identyfikacji genów, warunkujących ważne cechy użytkowe. U owsa posłużyły one między innymi do konstrukcji i zagęszczenia map genetycznych zarówno gatunków heksaploidalnych jak i diploidalnych. Opracowanie markerów dla niektórych cech użytkowych pozwala na szybką selekcję genotypów zawierających geny karłowatości, odporności na rdzę koronową czy mączniaka prawdziwego. Natomiast prowadzone liczne analizy podobieństwa genetycznego różnych gatunków z rodzaju Avena mogą przyczynić się do wyjaśnienia ewolucji w obrębie tego rodzaju jak również mogą wyjaśnić powstawanie poszczególnych gatunków owsa.
Źródło:
Acta Agrobotanica; 2012, 65, 1
0065-0951
2300-357X
Pojawia się w:
Acta Agrobotanica
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Segmented hybridization probes: modulating target affinity and base pairing selectivity
Autorzy:
Egetenmeyer, S.
Geiger, E.
Richert, C.
Powiązania:
https://bibliotekanauki.pl/articles/81071.pdf
Data publikacji:
2012
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
oligonucleotide
DNA
RNA
hybridization
base pairing
molecular biology
polymerase chain reaction
Źródło:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2012, 93, 3
0860-7796
Pojawia się w:
BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
A comparison of PCR-based markers for the molecular identification of Sphagnum species of the section Acutifolia
Autorzy:
Sawicki, J.
Szczecinska, M.
Powiązania:
https://bibliotekanauki.pl/articles/57748.pdf
Data publikacji:
2011
Wydawca:
Polskie Towarzystwo Botaniczne
Tematy:
Acutifolia
random amplified polymorphic DNA
Sphagnum
genetic similarity
molecular identification
molecular marker
polymerase chain reaction
genetic relationship
species identification
peat moss
chloroplast
nuclear genome
Opis:
RAPDs, ISJs, ISSRs, ITS and katGs were applied to determine genetic relationships between common Sphagnum species of the section Acutifolia. Twenty populations were genotyped using ten ISJ primers, 12 pairs of katG primers, 10 ISSR and 10 RAPD primers, and a restriction analysis of ITS1 and ITS2. ISSR and katG markers revealed the greatest number of species-specific bands. An analysis of ITS1 and ITS2 regions with restriction enzymes also proved to be a highly effective tool for species identification.
Źródło:
Acta Societatis Botanicorum Poloniae; 2011, 80, 3
0001-6977
2083-9480
Pojawia się w:
Acta Societatis Botanicorum Poloniae
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Application of DNA markers against illegal logging as a new tool for the Forest Guard Service
Autorzy:
Nowakowska, J.A.
Powiązania:
https://bibliotekanauki.pl/articles/38611.pdf
Data publikacji:
2011
Wydawca:
Instytut Badawczy Leśnictwa
Tematy:
application
DNA marker
DNA structure
wood
molecular identification
Forest Guard Service
tree species
determination
DNA profile
polymerase chain reaction
Opis:
DNA markers are currently the most precise tool for forest tree species identification and can be used for comparative analyses of plant material. Molecular diagnosis of evidence and reference material is based on comparing the structure of DNA markers duplicated in the PCR reaction and estimation of the DNA profiles obtained in studied wood samples. For this purpose, the microsatellite DNA markers are the most suitable tool because of their high polymorphism and accurate detection of structural changes in the genome. The analysis of tree stump DNA profiles let avoid timely collection of data such as tree age, diameter, height and thickness, although such a piece of information may advantageous in wood identification process. For each examined tree species, i.e. Pinus sylvestris L., Picea abies (L.) Karst., Quercus robur L. and Q. petraea (Matt.) Liebl., Fagus sylvatica L., Betula pendula L., and Alnus glutinosa L., wood identification was possible via the DNA profiles established on a basis of minimum 4 microsatellite nuclear DNA loci, and at least one cytoplasmatic (mitochondrial or chloroplast) DNA marker. Determination of the DNA profiles provided fast and reliable comparison of genetic similarity between material of evidence (wood, needles, leaves, seeds) and material of reference (tree stumps) in the forest. This was done with high probability (approximately 98– 99%).
Źródło:
Folia Forestalia Polonica. Series A . Forestry; 2011, 53, 2
0071-6677
Pojawia się w:
Folia Forestalia Polonica. Series A . Forestry
Dostawca treści:
Biblioteka Nauki
Artykuł
Tytuł:
Comparison between two approaches to modeling microsatellite DNA repeats: infinite dimensional model and its n-dimensional
Autorzy:
Białka, M.
Powiązania:
https://bibliotekanauki.pl/articles/229939.pdf
Data publikacji:
2011
Wydawca:
Polska Akademia Nauk. Czytelnia Czasopism PAN
Tematy:
infinite-dimensional systems
asymptotic stability
chain systems
microsatellites DNA repeats
polymerase slippage
Opis:
Two approaches to modeling microsatellite DNA repeats are considered. The former is an infinite dimensional system based on the theory of branching random walks which dynamic properties are characterized using Laplace transforms and Laplace asymptotic techniques. The latter is an n-dimensional approximation where microsatellite DNA repeats model is the example of a chain system. Both models were the subject of many numerical calculations using the MATLAB software. The results allow us to evaluate the asymptotic behavior and determine the effect of the system parameters on the run of the solution and the state variables.
Źródło:
Archives of Control Sciences; 2011, 21, 4; 419-441
1230-2384
Pojawia się w:
Archives of Control Sciences
Dostawca treści:
Biblioteka Nauki
Artykuł

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