Detection of beet necrotic yellow vein virus strains, variants and mixed infections by examining single-strand conformation polymorphisms of immunocapture RT-PCR products

Koenig, R.; Lüddecke, P.; Haeberlé, A. M.

doi:10.1099/0022-1317-76-8-2051

Cited by 115 publications

(52 citation statements)

References 10 publications

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“…About 30 different 20-mer oligonucleotide primers, originally obtained for other purposes, were annealed separately as random primers to plus-strand RNA from immunocaptured virus particles (to obtain cDNA to plusstrand RNA downstream of the known part of the sequence) or to RNA from denatured preparations of dsRNA (to obtain cDNA to minus-strand sequences upstream of the known sequence). The annealing was done under low stringency conditions and the annealing temperature lowered from 80 mC to room temperature over 1 h (Koenig et al, 1995). Under these conditions cDNA synthesis started at several sites, even when only five or six 3h-terminal nt of a given primer were complementary to a certain part of the RNA sequence.…”

Section: Resultsmentioning

confidence: 99%

“…RT-PCR products obtained by the immunocapture procedure or with denatured preparations of dsRNA (Koenig et al, 1995(Koenig et al, , 1996 were purified from agarose gels using the QIAquick Gel Extraction Kit and cloned into the pT7Blue T-vector (Novagen). Nucleotide sequences were determined by means of the Sequenase DNA sequencing Kit Version 2 (United States Biochemical) using [α-$&S]dATP in the labelling reaction.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Beet soil-borne virus RNA 2: similarities and dissimilarities to the coat protein gene-carrying RNAs of other furoviruses.

Koenig¹,

Commandeur²,

Loss³

et al. 1997

Journal of General Virology

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The complete sequence of the 3454 nt of RNA 2 of the Ahlum isolate of beet soil-borne furovirus (BSBV) has been determined starting with two short stretches of cloned cDNA. Unknown parts of the sequence were amplified by means of RT-PCR techniques using combinations of specific and random primers. BSBV RNA 2 is more similar in its genetic organization to potato mop top virus (PMTV) RNA 3 than to any other furoviral RNA, although it is more than 1100 nt longer. Its 3h-end, unlike that of PMTV RNA 3, has the potential to fold into a tRNA-like structure. It contains one large open

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Beet soil-borne virus RNA 2: similarities and dissimilarities to the coat protein gene-carrying RNAs of other furoviruses.

Koenig¹,

Commandeur²,

Loss³

et al. 1997

Journal of General Virology

View full text Add to dashboard Cite

show abstract

“…Among other applications, SSCP has been used for analysis of tumor-and disease-associated muta-tions, 10,22,24,27 studies of viroids and plant viruses, 23,32,39 evaluation of heterogeneity of hepatitis C virus isolates, 12,13,25,30,50 and detection of human papillomavirus variants. 2 Recently, it has also been used for studies of viral evolution and molecular epidemiology.…”

Section: Discussionmentioning

confidence: 99%

Application of Single-Strand Conformation Polymorphism to the Study of Bovine Viral Diarrhea Virus Isolates

Jones¹,

Weber²

2001

J VET Diagn Invest

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Abstract. Single-strand conformation polymorphism (SSCP) analysis of polymerase chain reaction (PCR) products is a genetic screening technique for rapid detection of nucleotide substitutions in PCR-amplified genomic DNA or cDNA. It is based on the observation that partially formamide-denatured double-stranded DNA migrates as 2 single-stranded DNA molecules when electrophoresed in nondenaturing polyacrylamide gels. The mobility depends on the 3-dimensional conformation of the strand under the conditions used. It is possible to discriminate between DNA strands differing in only 1 nucleotide. The method was applied to the analysis of Bovine Viral Diarrhea Virus (BVDV) isolates. Reference and Argentinian strains were assessed for variations in their 5Ј untranslated region (5Ј-UTR). The PCR products of the 5Ј-UTR ends were formamide denatured and compared by SSCP analysis in nondenaturing 15% polyacrylamide and 15% polyacrilamide-5% glycerol gels. The reference strains SD-1, Singer, and Oregon C24V had differences in electrophoretic patterns. Despite the high conservation among the 5Ј-UTR of pestiviruses, the method allowed discrimination among all 9 Argentinian isolates. The 5Ј-UTR of a fetal kidney-derived isolate (1R93) was PCR amplified and cloned in a plasmid vector; the SSCP analysis of 30 PCR products obtained by direct amplification over randomly selected clones produced 5 different banding patterns, indicating the existence of viral quasispecies. The results show that SSCP may be used to identify and differentiate among BVDV isolates.

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“…Additional gene segments can then be included in the analysis favored of population genetic studies and identification of species based on Single-Stranded Conformation Polymorphism (SSCP) analysis. The disadvantage of RFLP method is that mutations are recognized only when they occur in the sequence recognized by the restriction endonuclease, and that PCR products may need to be tested with many different restriction enzymes [11,12]. Because of this limitation, the SSCP technique is more appropriate for detecting point mutations and is more useful than PCR-RFLP to detect polymorphism [12].…”

Section: Introductionmentioning

confidence: 99%

Growth Parameters Evaluation and Identification of Growth Hormone Receptor Gene Polymorphisms in Various Strains of Rainbow Trout Oncorhynchus mykiss

Gorji¹,

Rahmani²

2016

J Aquac Res Development

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In the present study, polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and restriction fragment length polymorphism (RFLP) methods were compared to analyze the polymorphism of growth hormone receptor (GHR) gene in French, Iranian and Danish strains of Oncorhynchus mykiss. A monomorphic SSCP pattern of AA genotype in the French and Iranian strains and a dimorphic AA and AB genotype in the Danish strain were observed in 3' non-coding regions of GHR gene. In the Danish strain, the AB genotype polymorphism of the GHR gene with its very low frequency (5%) has no effect on the production trait. While, RFLP-Dde1 showed no polymorphism with genetic variation in the location of GHR. Moreover, comparing the condition factors (K) of three different rainbow trout strains showed a significant correlation between the French (1.312 ± 0.13), Iranian (1.245 ± 0.17) and Danish strains (0.763 ± 0.1), respectively (p<0.05). In particular, the French strain obtained a higher K compared to the two others. The length-weight relationship is shown by the following equations W= 0.013 × L 2.921 , W= 0.012 ×L 3.023 and W= 0.007 × L 3.176 for French, Iranian and Danish strains, respectively. With the mean (b= 2.921), the studied French strain exhibited a negative allometric growth b<3 while the Iranian (b=3.023) and the Danish (b=3.176) showed positive allometric growths. Regardless of the underlying mechanism(s) responsible for the different relationships, the results of this study suggested that the AA and AB genotypes polymorphism of the GHR gene are not associated with condition factor and environmental variables can influence condition factor and length-weight relationship of rainbow trout strains in this study.

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Detection of beet necrotic yellow vein virus strains, variants and mixed infections by examining single-strand conformation polymorphisms of immunocapture RT-PCR products

Cited by 115 publications

References 10 publications

Beet soil-borne virus RNA 2: similarities and dissimilarities to the coat protein gene-carrying RNAs of other furoviruses.

Beet soil-borne virus RNA 2: similarities and dissimilarities to the coat protein gene-carrying RNAs of other furoviruses.

Application of Single-Strand Conformation Polymorphism to the Study of Bovine Viral Diarrhea Virus Isolates

Growth Parameters Evaluation and Identification of Growth Hormone Receptor Gene Polymorphisms in Various Strains of Rainbow Trout Oncorhynchus mykiss

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