scholarly journals Screening of the FcεRI-β-Gene in a Swiss Population of Asthmatic Children: No Association with E237G and Identification of New Sequence Variations

1998 ◽  
Vol 14 (3) ◽  
pp. 177-186 ◽  
Author(s):  
M. Rohrbach ◽  
R. Kraemer ◽  
S. Liechti-Gallati
Keyword(s):  
Candidate Gene ◽  
Single Strand Conformation Polymorphism ◽  
Sequence Variant ◽  
Missense Mutations ◽  
Asthmatic Children ◽  
Sequence Variations ◽  
Swiss Population ◽  
High Affinity Receptor ◽  
Conformation Polymorphism ◽  
Exon Amplification

Background: The gene of the beta subunit of the high affinity receptor for IgE (FcεRI-β) encoded on chromosome 11q13 has recently been identified as a candidate gene for asthma and atopy. Two coding variations, E237G and I181L have been described as being associated with asthma and atopy. Our aim was to investigate a Swiss population of atopic and asthmatic children for variations in this gene.Methods: We screened all 7 exons of the FcεRI-β- gene in 224 atopic/asthmatic, 68 relatives and 159 control subjects using exon amplification by PCR and single strand conformation polymorphism (SSCP) analysis followed by fluorescence based DNA sequencing.Results: The sequence variant E237G was found in 3.7% in atopics and in 2.6% in the control population. None of the samples carried the I181L mutation. In addition, we characterised nine novel mutations (1 nonsense mutation, 2 missense mutations, mutation, 2 silent mutations, 4 intronic mutations).Conclusions: Our results suggest that the E237G does not have a primary effect on the development of atopy and asthma, and thus excludes the FcεRI-β locus from being a candidate gene directly involved in these diseases.

scholarly journals Sequence Variations in the Bovine Growth Hormone Gene Characterized by Single-Strand Conformation Polymorphism (SSCP) Analysis and Their Association with Milk Production Traits in Holsteins

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1809-1816 ◽  
Author(s):  
Jianbo Yao ◽  
Samuel E Aggrey ◽  
David Zadworny ◽  
J Flan Hayes ◽  
Urs Kühnlein
Keyword(s):  
Growth Hormone ◽  
Milk Production ◽  
Milk Yield ◽  
Single Strand Conformation Polymorphism ◽  
Sscp Analysis ◽  
Bovine Growth Hormone ◽  
Production Traits ◽  
Milk Production Traits ◽  
Sequence Variations ◽  
Conformation Polymorphism

Sequence variations in the bovine growth hormone (GH) gene were investigated by single strand conformation polymorphism (SSCP) analysis of seven amplified fragments covering almost the entire gene (2.7 kb). SSCPs were detected in four of these fragments and a total of six polymorphisms were found in a sample of 128 Holstein bulls. Two polymorphisms, a T→C transition in the third intron (designated GH4.1) and an A→C transversion in the fifth exon (designated GH6.2), were shown to be associated with milk production traits. GH4.1c/GH4.1c bulls had higher milk yield than GH4.1c/GH4.1t (P ≤ 0.005) and GH4.1t/GH4.1t (P ≤ 0.0022) bulls. GH4.1c/GH4.1c bulls had higher kg fat (P ≤ 0.0076) and protein (P ≤ 0.0018) than GH4.1c/GH4.1t bulls. Similar effects on milk production traits with the GH6.2 polymorphism were observed with the GH6.2a allele being the favorable allele. The average effects of the gene substitution for GH4.1 and GH6.2 are similar, with ±300 kg for milk yield, ±8 kg for fat content and ±7 kg for protein content per lactation. The positive association of GH4.1c and GH6.2a with milk production traits may be useful for improving milk performance in dairy cattle.

scholarly journals Molecular study of eight Japanese cases of glucose-6-phosphate dehydrogenase deficiency by nonradioisotopic single-strand conformation polymorphism analysis [see comments]

Blood ◽  
1994 ◽  
Vol 83 (11) ◽  
pp. 3363-3368 ◽  
Author(s):  
A Hirono ◽  
S Miwa ◽  
H Fujii ◽  
F Ishida ◽  
K Yamada ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Japanese Patients ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Sscp Analysis ◽  
Polymorphism Analysis ◽  
Missense Mutations ◽  
G6pd Gene ◽  
Glucose 6 Phosphate Dehydrogenase ◽  
Conformation Polymorphism

Abstract Using a newly developed nonradioisotopic method of polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) analysis combined with the direct sequencing using the fluorescence-labeled terminator, we identified seven missense mutations, 527 A-->G, 1003 G-- >A, 1159 C--eT, 1160 G-->A, 1229 G-->A, 1246 G-->A, and 1361 G-->A, in eight Japanese patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency. Except for the 527 A-->G, each mutation has been reported to cause variants G6PD Chatham, G6PD Guadalajara, G6PD Beverly Hills, G6PD “Japan”, G6PD Tokyo, and G6PD Andalus, respectively. In addition, a single base deletion in intron 5 was found in the patients with G6PD Guadalajara or G6PD Andalus. The variant with unique 527 A-->G was characterized and designated as G6PD Shinshu. We also characterized G6PD “Japan” and found that the variant had the striking resemblance with G6PD Riverside, bearing a missense mutation in the same codon, but causing a different amino acid substitution. Our modified PCR-SSCP analysis using minigel and ethidium bromide staining could detect six of the eight diverse mutations in the G6PD gene. Because it is easy and requires no special apparatus, this modified method will be useful for screening mutations in the G6PD gene.

scholarly journals High sensitivity of the single-strand conformation polymorphism method for detecting sequence variations in the low-density lipoprotein receptor gene validated by DNA sequencing

1996 ◽  
Vol 42 (8) ◽  
pp. 1140-1146 ◽  
Author(s):  
H K Jensen ◽  
L G Jensen ◽  
P S Hansen ◽  
O Faergeman ◽  
N Gregersen
Keyword(s):  
Dna Sequencing ◽  
Receptor Gene ◽  
Ldl Receptor ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Sscp Analysis ◽  
Oligonucleotide Primer ◽  
In Vitro Mutagenesis ◽  
Sequence Variations ◽  
Conformation Polymorphism

Abstract We designed oligonucleotide primer pairs to amplify the promoter region, the translated exon sequences, and the flanking intron sequences of all 18 exons of the LDL receptor gene to compare the ability of the PCR single-strand conformation polymorphism (PCR-SSCP) method with semiautomated solid-phase genomic DNA sequencing to detect sequence variations. In 20 apparently unrelated Danish patients with a clinical diagnosis of heterozygous familial hypercholesterolemia (FH), we identified 13 different mutations in the LDL receptor gene: two silent (C331C, N494 N); five missense (W66G, E119K, T383P, W556S, T7051); one nonsense (W23X); three splice-site (313 + 1G-->A, 1061-8T-->C, 1846-1G-->A); and two frameshift (335del10, 1650delG) mutations. Four of these mutations, N494 N, T383P, 1061-8T-->C, and W556S, have not been reported earlier. The pathogenicity of the T383P, 1061-8T-->C, and W556S mutations remains to be established by in vitro mutagenesis and transfection studies. One patient had three mutations (335del10, 1061-8T-->C, and T705I) on the same allele. Further, nine well-known polymorphisms were detectable with this methodological setup. Direct DNA sequencing of the PCR products used for the SSCP analysis did not reveal any sequence variations not detected by the PCR-SSCP method. In two patients we did not detect any mutation by either method. We conclude that the PCR-SSCP analysis, performed as described here, is as sensitive and efficient as DNA sequencing in the ability to identify the sequence variations in the LDL receptor gene of the patients with heterozygous FH of this study.

Two Novel Missense Mutations in the Peripherin/RDS Gene in two Unrelated French Patients with Autosomal Dominant Retinitis Pigmentosa

1998 ◽  
Vol 8 (2) ◽  
pp. 98-101 ◽  
Author(s):  
E.H. Souied ◽  
J.-M. Rozet ◽  
S. Gerber ◽  
J.-L. Dufier ◽  
G. Soubrane ◽  
...  
Keyword(s):  
Retinitis Pigmentosa ◽  
Autosomal Dominant ◽  
Single Strand Conformation Polymorphism ◽  
Base Substitution ◽  
Missense Mutations ◽  
Direct Sequence ◽  
Sequence Analyses ◽  
Autosomal Dominant Retinitis Pigmentosa ◽  
Direct Sequence Analysis ◽  
Conformation Polymorphism

Purpose To report the identification of two novel RDS mutations in the peripherin/RDS gene of two unrelated French patients affected by autosomal dominant retinitis pigmentosa (ADRP). Methods Fifty-eight unrelated patients affected by ADRP were analyzed. Our diagnostic criteria for RP were bilateral fundus involvement, concentric depression of the visual field and severe involvement on electroretinogram. Transmission of the trait was unambiguous. Our strategy was to analyze the coding sequence of the gene using a combination of single-strand conformation polymorphism (SSCP) and direct sequence analysis of the exons of the gene. Exons that displayed conformational polymorphisms were sequenced on an automated DNA sequencer. Results The sequence analyses revealed two previously unreported missense mutations: Cys165Tyr and Phe211Leu in exons 1 and 2, respectively. None of the 70 controls analyzed carried these base changes. Cosegregation of the base substitution with the disease could be tested in both families presenting the Cys165Tyr and Phe211Leu mutations. Conclusions Several lines of evidence support the idea that these base substitutions are disease-causing mutations. To the best of our knowledge, no peripherin/RDS gene analysis has been previously reported in ADRP in France.

scholarly journals Single-Strand Conformation Polymorphism Analysis of Apple Stem Grooving Capillovirus Sequence Variants

1999 ◽  
Vol 89 (2) ◽  
pp. 136-140 ◽  
Author(s):  
H. Magome ◽  
N. Yoshikawa ◽  
T. Takahashi
Keyword(s):  
Chenopodium Quinoa ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Sscp Analysis ◽  
Polymorphism Analysis ◽  
Sequence Variant ◽  
Sequence Variants ◽  
Individual Tree ◽  
Apple Stem ◽  
Conformation Polymorphism

In an earlier study, we demonstrated that isolates of apple stem grooving capillovirus (ASGV) from fruit trees comprise at least two to four sequence variants that differ considerably from each other in nucleotide sequence. In order to characterize the population of sequence variants within a single tree, we applied a combination of an immunocapture reverse transcription-polymerase chain reaction (IC-RT-PCR) and a single-strand conformation polymorphism (SSCP) analysis of a nested asymmetric PCR product. In the SSCP analysis of the PCR products from ASGV-infected apple, Japanese pear, or European pear trees, two to four bands were detected in samples from all trees, indicating that ASGV exists as a mixture of sequence variants. The composition of sequence variants (the number of bands and their relative quantity) differed among leaf samples from different branches, showing that each sequence variant is distributed unevenly within an individual tree. The SSCP analysis of isolates after serial passage in Chenopodium quinoa plants indicated that passages changed the composition of sequence variants originally contained in ASGV isolates; i.e., some sequence variants dominated and others decreased to undetectable levels.

Rapid Discrimination of Salmonella Isolates by Single-Strand Conformation Polymorphism Analysis

2008 ◽  
Vol 71 (10) ◽  
pp. 1960-1966 ◽  
Author(s):  
BATOL H. AL-ADHAMI ◽  
FLORENCE HUBY-CHILTON ◽  
BURTON W. BLAIS ◽  
AMALIA MARTINEZ-PEREZ ◽  
NEIL B. CHILTON ◽  
...  
Keyword(s):  
Target Genes ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Food Microbiology ◽  
Sscp Analysis ◽  
Polymorphism Analysis ◽  
Banding Patterns ◽  
Sequence Variations ◽  
Rapid Discrimination ◽  
Conformation Polymorphism

A molecular typing technique was developed for the differentiation of Salmonella isolates based on single-strand conformation polymorphism (SSCP) analysis of amplicons generated by PCR. Amplicons from parts of the fimA (both the 5′ and 3′ ends), mdh, invA, and atpD genes were generated separately from a panel of Salmonella strains representing Salmonella bongori, and four subspecies and 17 serovars of Salmonella enterica. These amplicons were subjected to SSCP analysis for differentiation of the salmonellae on the basis of different conformational forms arising due to nucleotide sequence variations in the target genes. Several distinct SSCP banding patterns (a maximum of 14 each for atpD and fimA 3′ end) were observed with this panel of Salmonella strains for amplicons generated from each target gene. The best discrimination of Salmonella subspecies and serovar was achieved from the SSCP analysis of a combination of at least three gene targets: atpD, invA, and either mdh or fimA 3′ end. This demonstrates the applicability of SSCP analysis as an important additional method to classical typing approaches for the differentiation of foodborne Salmonella isolates. SSCP is simple to perform and should be readily transferable to food microbiology laboratories with basic PCR capability.

scholarly journals Molecular study of eight Japanese cases of glucose-6-phosphate dehydrogenase deficiency by nonradioisotopic single-strand conformation polymorphism analysis [see comments]

Blood ◽  
1994 ◽  
Vol 83 (11) ◽  
pp. 3363-3368
Author(s):  
A Hirono ◽  
S Miwa ◽  
H Fujii ◽  
F Ishida ◽  
K Yamada ◽  
...  
Keyword(s):  
Direct Sequencing ◽  
Japanese Patients ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Sscp Analysis ◽  
Polymorphism Analysis ◽  
Missense Mutations ◽  
G6pd Gene ◽  
Glucose 6 Phosphate Dehydrogenase ◽  
Conformation Polymorphism

Using a newly developed nonradioisotopic method of polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) analysis combined with the direct sequencing using the fluorescence-labeled terminator, we identified seven missense mutations, 527 A-->G, 1003 G-- >A, 1159 C--eT, 1160 G-->A, 1229 G-->A, 1246 G-->A, and 1361 G-->A, in eight Japanese patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency. Except for the 527 A-->G, each mutation has been reported to cause variants G6PD Chatham, G6PD Guadalajara, G6PD Beverly Hills, G6PD “Japan”, G6PD Tokyo, and G6PD Andalus, respectively. In addition, a single base deletion in intron 5 was found in the patients with G6PD Guadalajara or G6PD Andalus. The variant with unique 527 A-->G was characterized and designated as G6PD Shinshu. We also characterized G6PD “Japan” and found that the variant had the striking resemblance with G6PD Riverside, bearing a missense mutation in the same codon, but causing a different amino acid substitution. Our modified PCR-SSCP analysis using minigel and ethidium bromide staining could detect six of the eight diverse mutations in the G6PD gene. Because it is easy and requires no special apparatus, this modified method will be useful for screening mutations in the G6PD gene.

scholarly journals Application of biological and single-strand conformation polymorphism assays for characterizing potential mild isolates of Citrus tristeza virus for cross protection

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Sagheer Atta ◽  
Ummad ud din Umar ◽  
Muhammad Amjad Bashir ◽  
Abdul Hannan ◽  
Ateeq ur Rehman ◽  
...  
Keyword(s):  
Citrus Tristeza Virus ◽  
Single Strand Conformation Polymorphism ◽  
Biological Indicator ◽  
Cross Protection ◽  
Single Strand ◽  
Sequence Variant ◽  
Viral Pathogen ◽  
Tristeza Virus ◽  
Conformation Polymorphism ◽  
Citrus Tristeza

Abstract Citrus tristeza virus (CTV) by killing millions of citrus cultivars grown on sour orange rootstock worldwide has become one of the most dangerous viral pathogen. Characterization of 12 CTV isolates was analyzed by biological indexing. Infected samples of citrus were collected from citrus growing areas of Pakistan and CTV was detected by symptoms on indicator plants and confirmed by direct tissue blot immunoassay (DTBIA). CTV positive samples were graft inoculated on six biological indicator hosts in the study. A standardized protocol was deployed to study biological characteristics of these isolates. All biological indicators induced mild and from mild to moderate reactions against all of the CTV isolates tested. About two isolates produced stem-pitting symptoms from moderate to severe on Mexican lime. CTV strains were further characterized and confirmed by the analysis of p25 gene of CTV isolates using single-strand conformation polymorphism (SSCP) assay. SSCP analysis revealed that most isolates confined only one predominant sequence variant. SSCP profiles of PCR amplified products from CTV isolates showed bands patterns corresponding to mild and sever strain. Three isolates (4MF, 8KBS and 10GS) from different regions and cultivars were identified as potential source of mild strains for cross protection. These results are the best base for mild strain cross protection (MSCP) in the country.

Screening for mutations in factor VIII gene using the single-strand conformation polymorphism

1995 ◽  
Vol 5 (4) ◽  
pp. 357-359
Author(s):  
Khédoudja Nafa ◽  
Farida Meriane ◽  
Thouraya Chellali ◽  
Mohamed Benabadji ◽  
Abderrezak Reghis ◽  
...  
Keyword(s):  
Factor Viii ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Factor Viii Gene ◽  
Conformation Polymorphism
Sign in / Sign up

Export Citation Format

Share Document