Journal articles: 'SSCP [Single Strand Conformation Polymorphism ]'

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Maréchal, V. "SSCP (single strand conformation polymorphism)." EMC - Biologie médicale 3, no. 1 (2008): 1–5. http://dx.doi.org/10.1016/s2211-9698(08)71401-8.

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AL-ADHAMI, BATOL H., FLORENCE HUBY-CHILTON, BURTON W. BLAIS, AMALIA MARTINEZ-PEREZ, NEIL B. CHILTON, and ALVIN A. GAJADHAR. "Rapid Discrimination of Salmonella Isolates by Single-Strand Conformation Polymorphism Analysis." Journal of Food Protection 71, no. 10 (2008): 1960–66. http://dx.doi.org/10.4315/0362-028x-71.10.1960.

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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.

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Satoh, T., M. Kobayashi, M. Kaneda, M. Tanihiro, K. Okada, and K. Ueda. "Genotypical classification of neutrophil Fc gamma receptor III by polymerase chain reaction-single-strand conformation polymorphism." Blood 83, no. 11 (1994): 3312–15. http://dx.doi.org/10.1182/blood.v83.11.3312.3312.

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Abstract We classified the genotype of neutrophil Fc gamma receptor III (FcRIII) (CD16) with a new method. Genomic DNA from mononuclear cells of 39 unrelated healthy donors (13 NA1/NA1, 13 NA2/NA2, and 13 NA1/NA2 typed serologically) were subjected to polymerase chain reaction (PCR) to amplify the polymorphic third exon of the FcRIII genes. The PCR products were heat denatured, electrophoresed, and visualized by silver staining. Allelic differences were detected by distinctive electrophoretic patterns of each single strand, depending on their sequence specific conformations (single-strand conformation polymorphism [SSCP]). The genotypes of neutrophil FcRIII determined by this method were consistent with the phenotypes of NA antigens determined by serologic examinations. These results indicate that the PCR-SSCP system is a very useful tool for genotyping of the neutrophil FcRIII.

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Satoh, T., M. Kobayashi, M. Kaneda, M. Tanihiro, K. Okada, and K. Ueda. "Genotypical classification of neutrophil Fc gamma receptor III by polymerase chain reaction-single-strand conformation polymorphism." Blood 83, no. 11 (1994): 3312–15. http://dx.doi.org/10.1182/blood.v83.11.3312.bloodjournal83113312.

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We classified the genotype of neutrophil Fc gamma receptor III (FcRIII) (CD16) with a new method. Genomic DNA from mononuclear cells of 39 unrelated healthy donors (13 NA1/NA1, 13 NA2/NA2, and 13 NA1/NA2 typed serologically) were subjected to polymerase chain reaction (PCR) to amplify the polymorphic third exon of the FcRIII genes. The PCR products were heat denatured, electrophoresed, and visualized by silver staining. Allelic differences were detected by distinctive electrophoretic patterns of each single strand, depending on their sequence specific conformations (single-strand conformation polymorphism [SSCP]). The genotypes of neutrophil FcRIII determined by this method were consistent with the phenotypes of NA antigens determined by serologic examinations. These results indicate that the PCR-SSCP system is a very useful tool for genotyping of the neutrophil FcRIII.

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Iizuka, M., K. Hayashi, and T. Sekiya. "Single-strand conformation polymorphism (SSCP) at the D8S86 locus." Nucleic Acids Research 19, no. 22 (1991): 6346. http://dx.doi.org/10.1093/nar/19.22.6346.

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Lizuka, M., K. Hayashi, and T. Sekiya. "Single-strand conformation polymorphism (SSCP) at the D8S86 locus." Nucleic Acids Research 20, no. 2 (1992): 388. http://dx.doi.org/10.1093/nar/20.2.388.

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MUGGIA, Lucia, and Martin GRUBE. "Fungal composition of lichen thalli assessed by single strand conformation polymorphism." Lichenologist 42, no. 4 (2010): 461–73. http://dx.doi.org/10.1017/s0024282909990752.

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AbstractFungi that are unrelated to the mycobiont species frequently colonize lichens. Some of these fungal colonists are described lichenicolous fungi, lichen parasites and pathogens that produce recognizable morphological characters, while others apparently produce no noticeable structures. Here we apply the single strand conformation polymorphism (SSCP) technique to directly assess the abundance of different fungi in lichens. Twenty-eight lichen thalli were chosen, some with and some without externally visible symptoms of parasite infection, and these were subjected to total DNA extraction. PCR was conducted with fungal-specific primers for the ITS region of ribosomal DNA. Single strands of the products were separated on native acrylamide gels. The majority of lichen specimens, both infected and those without symptoms, displayed more than one band in the stained gels. In one case, 14 bands were detected using SSCP. Some of these bands apparently represent other neighbouring lichens in the habitat, but many are apparently non-lichen-forming. Since few lichen-associated fungi have been cultured and sequenced, it is difficult to know if SSCP bands represent obligate lichenicolous fungi, other asymptomatic lichen parasites, or fungi not obligately associated with lichens, but our results indicate that large numbers of non-lichen-forming fungi commonly co-occur with lichens in nature. For specimens of the filamentous lichens Cystocoleus ebeneus and Racodium rupestre we used cloned sequences to compare the number of sequences obtained by the SSCP method to the number obtained by direct sequencing of thallus extracts, and we generally found that more sequences could be detected by SSCP than could be seen by direct sequencing.

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Markoff, Arseni, Alex Savov, Vladimir Vladimirov, Nadia Bogdanova, Ivo Kremensky, and Varban Ganev. "Optimization of single-strand conformation polymorphism analysis in the presence of polyethylene glycol." Clinical Chemistry 43, no. 1 (1997): 30–33. http://dx.doi.org/10.1093/clinchem/43.1.30.

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Abstract We report optimization of single-strand conformation polymorphism (SSCP) analysis in the presence of polyethylene glycol. The protocol developed separates single-strand conformers in a much shorter time (1–3 h) than conventional SSCP protocols and broadens the applicability of SSCP analysis from 150 to as much as 500 bp of DNA by different percentages of GC content present. We conclude that addition of polyethylene glycol helps improve the differential separation of conformers and, in combination with high-resolution polyacrylamide gel electrophoresis, offers an alternative to previous SSCP analysis protocols. This protocol should be very useful for clinical applications in routine detection of mutations as well as for research purposes.

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Isam, Zahraa, Rabab Omran Al-jelawi-, and Ammad Hassan Mahmood. "DETECTION SINGLE NUCLEOTIDE POLYMORPHISMS IN UROMODULIN PROMOTER REGION ASSOCIATED WITH RENAL DISEASES USING SINGLE-STRAND CONFORMATION POLYMORPHISM-POLYMERASE CHAIN POLYMORPHISMS TECHNIQUE." Asian Journal of Pharmaceutical and Clinical Research 11, no. 1 (2018): 205. http://dx.doi.org/10.22159/ajpcr.2017.v11i1.22063.

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Objective: The uromodulin, a glycoprotein, expressed and secreted by epithelial kidney cells lining the thick ascending limb of the Henle’s loop. It is encoded by the UMOD gene in humans. Our objective was to analyze single nucleotide polymorphisms (SNPs) in the UMOD promoter region in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD).Methods: The blood samples were collected from 100 patients with CKD (50) and ESRD (50), who admitted at Merjan Teaching Hospital in Babylon Province, Iraq (February-July 2016). In addition, 50 blood samples of healthy control. The SNPs of UMOD promoter region was investigated using single-strand conformation polymorphism-polymerase chain polymorphisms (SSCP-PCR) and DNA sequencing techniques.Results: UOMD promoter region polymorphisms using PCR-SSCP and sequencing DNA appeared three different conformational haplotypes, including A\G 49 haplotype (5 bands), A\G 49 and C\A 247 haplotype (5 bands), and C\G 45 and A\G 49 haplotype (6 bands) distributed among CKD and ESRD cases, due to the presence of three SNPs. There was no association between band numbers of PCR-SSCP with ESRD and CKD compared with a control group.Conclusion: SSCP-PCR is a good screening method to detect genetic variations in an uromodulin promoter region.

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Isam, Zahraa, Rabab Omran Al-jelawi-, and Ammad Hassan Mahmood. "DETECTION SINGLE NUCLEOTIDE POLYMORPHISMS IN UROMODULIN PROMOTER REGION ASSOCIATED WITH RENAL DISEASES USING SINGLE-STRAND CONFORMATION POLYMORPHISM-POLYMERASE CHAIN POLYMORPHISMS TECHNIQUE." Asian Journal of Pharmaceutical and Clinical Research 11, no. 1 (2018): 205. http://dx.doi.org/10.22159/ajpcr.2018.v11i1.22063.

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Objective: The uromodulin, a glycoprotein, expressed and secreted by epithelial kidney cells lining the thick ascending limb of the Henle’s loop. It is encoded by the UMOD gene in humans. Our objective was to analyze single nucleotide polymorphisms (SNPs) in the UMOD promoter region in patients with chronic kidney disease (CKD) and end-stage renal disease (ESRD).Methods: The blood samples were collected from 100 patients with CKD (50) and ESRD (50), who admitted at Merjan Teaching Hospital in Babylon Province, Iraq (February-July 2016). In addition, 50 blood samples of healthy control. The SNPs of UMOD promoter region was investigated using single-strand conformation polymorphism-polymerase chain polymorphisms (SSCP-PCR) and DNA sequencing techniques.Results: UOMD promoter region polymorphisms using PCR-SSCP and sequencing DNA appeared three different conformational haplotypes, including A\G 49 haplotype (5 bands), A\G 49 and C\A 247 haplotype (5 bands), and C\G 45 and A\G 49 haplotype (6 bands) distributed among CKD and ESRD cases, due to the presence of three SNPs. There was no association between band numbers of PCR-SSCP with ESRD and CKD compared with a control group.Conclusion: SSCP-PCR is a good screening method to detect genetic variations in an uromodulin promoter region.

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Bahrami, A., S. R. Miraei-Ashtiani, H. Mehrabani-Yeganeh, H. Banani-Rad, and Sh Behzadi. "The association between polymorphism of the GH1 gene and changes in protein structure and carcass traits in Mehraban sheep (Ovis aries)." Animal Production Science 55, no. 5 (2015): 661. http://dx.doi.org/10.1071/an13446.

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The present study indicates an association between carcass traits and genetic polymorphism and changes in the protein structure of the growth hormone 1 (GH1) gene in Mehraban sheep. Polymorphism of the GH1 gene was detected by polymerase chain reaction–single strand conformation polymorphism (PCR–SSCP) and DNA sequencing methods in 463 individuals. Two different structures in the GH1 protein and six single nucleotide polymorphisms were identified. The association of these SSCP patterns and protein structures with carcass traits was analysed. The SSCP patterns were shown to be associated with carcass traits. Individuals with AB SSCP pattern and Type B protein structure had significantly higher fat-tail weight and volume (P < 0.05) than did those individuals with CC SSCP pattern and Type A protein structure. Moreover, CC SSCP pattern and Type A protein structure contributed to low concentration of blood triglycerides (P = 0.004). The results confirmed the importance of GH1 as a candidate gene for marker-assisted selection for carcass-trait variations in sheep.

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Liu, Li-Herng Eric, Wesley Gladwell, and Christina T. Teng. "Detection of exon polymorphisms in the human lactoferrin gene." Biochemistry and Cell Biology 80, no. 1 (2002): 17–22. http://dx.doi.org/10.1139/o01-207.

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We previously demonstrated that lactoferrin gene polymorphisms occur in cancer cells of patients with leukemia and breast cancer. In this study, we established a non-radioactive polymerase chain reactionsingle strand conformation polymorphism (PCRSSCP) analysis, one of the most sensitive and simplest methods to detect polymorphisms and mutations of the human lactoferrin gene. We optimized the PCR conditions for nine different DNA templates and 16 pairs of exon primers for SSCP analysis. The DNA templates used in the analyses were prepared from a cosmid clone (CT61) that contains the human lactoferrin gene, human placental tissue, leukocytes from 10 normal volunteers, leukemic cells of two patients, and previously established three breast and two leukemic cell lines. With the appropriate exon-primer sets, PCR products from exon 1 to exon 16 of the lactoferrin gene were generated from the DNA templates and analyzed by SSCP. Compared with the homogenous cloned DNA, lactoferrin gene polymorphisms were detected within exons 2, 5, 7, 9, 13, 14, and 15 of the normal placental and leukocyte DNA. In addition, abnormal migration patterns of the lactoferrin gene in cancer cells were detected in exons 4, 5, 13, 14, and 15. The PCRSSCP band migration patterns can be attributed either to gene polymorphism in normal cells or to DNA mutations in cancer cells and the employed method cannot distinguish between them. Nonetheless, the present analysis suggests that genetic polymorphisms of the lactoferrin gene exist in selected exons and additional mutations of the lactoferrin gene do occur in the cancer cells.Key words: lactoferrin, polymorphisms, human lactoferrin, single-strand conformation polymorphism (SSCP).

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Tisza, Ákos, Ádám Csikós, Ádám Simon, Gabriella Gulyás, András Jávor, and Levente Czeglédi. "Identification of poultry species using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) methods." Food Control 59 (January 2016): 430–38. http://dx.doi.org/10.1016/j.foodcont.2015.06.006.

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Magome, H., N. Yoshikawa, and T. Takahashi. "Single-Strand Conformation Polymorphism Analysis of Apple Stem Grooving Capillovirus Sequence Variants." Phytopathology® 89, no. 2 (1999): 136–40. http://dx.doi.org/10.1094/phyto.1999.89.2.136.

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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.

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Xie, Jiahua, Todd C. Wehner, and Mark A. Conkling. "PCR-based Single-strand Conformation Polymorphism (SSCP) Analysis to Clone Nine Aquaporin Genes in Cucumber." Journal of the American Society for Horticultural Science 127, no. 6 (2002): 925–30. http://dx.doi.org/10.21273/jashs.127.6.925.

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Combining the use of PCR and single-strand conformation polymorphisms (SSCP), nine sequences from the cucumber genome were successfully identified and cloned that encoded two well-conserved asparagine-proline-alanine (NPA) domain homologues to aquaporin genes. The sensitivity and detection efficiency of SSCP and restriction enzyme analysis for detecting DNA sequence variation were evaluated using similar-sized DNA fragments. The SSCP analysis was more sensitive and efficient for discriminating different clones than restriction enzyme analysis, although some sequence variation inside similar-sized DNA fragments could be identified by restriction analysis. Consideration of the results of SSCP analysis with DNA sequence information indicated that one or two base pair changes in the amplified regions could be detected. Moreover, the SSCP analysis results of genomic DNA PCR products that were amplified by degenerate primers can provide rough information about the number of member genes. If the SSCP bands of a cloned fragment (such as CRB7) did not have the corresponding bands from genomic DNA PCR products, that fragment might be a misamplified product. The PCR-based SSCP method with degenerate oligonucleotide primers should facilitate the cloning of member genes.

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Pieneman, W. C., P. H. Reitsma, and E. Briët. "Double Strand Conformation Polymorphism (DSCP) Detects Two Point Mutations at Codon 280 (AAC→ATC) and at Codon 431 (TAC→AAC) of the Blood Coagulation Factor VIII Gene." Thrombosis and Haemostasis 69, no. 05 (1993): 473–75. http://dx.doi.org/10.1055/s-0038-1651635.

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SummaryHemophilia A is a hereditary, X-linked, bleeding disorder that is caused by a defect in the factor VIII gene. Here, we report two novel point mutations in the factor VIII gene that result in an aberrant electrophoretic mobility of double strand PCR fragments (double strand conformation polymorphism, DSCP). In exon 9 a TAC→AAC mutation at codon 431, replacing Tyr by Asn, was observed in a family (A211) with moderately severe hemophilia A. A family with mild hemophilia A revealed an A→T mutation in codon 280 (exon 7) that results in the replacement of Asn by Ile. One of these two mutations was not detected in an analysis based on single strand conformation polymorphisms (SSCP).At present we have no explanation for the effect of the nucleotide changes on the electrophoretic mobility of double strand DNA. Although DSCP is not able to detect all mutations the combination of DSCP analysis with SSCP analysis increases the sensitivity in a screening for factor VIII mutations.

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Makino, R., H. Yazyu, Y. Kishimoto, T. Sekiya, and K. Hayashi. "F-SSCP: fluorescence-based polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) analysis." Genome Research 2, no. 1 (1992): 10–13. http://dx.doi.org/10.1101/gr.2.1.10.

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Tsai, M. Y., P. Suess, K. Schwichtenberg, et al. "Determination of apolipoprotein E genotypes by single-strand conformational polymorphism." Clinical Chemistry 39, no. 10 (1993): 2121–24. http://dx.doi.org/10.1093/clinchem/39.10.2121.

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Abstract We used single-strand conformational polymorphism (SSCP) to determine apolipoprotein E (Apo E) genotypes in 47 individuals. A 295-base-pair (bp) DNA fragment coding for amino acid residues 80-178 of the Apo E protein gave distinct patterns for the three alleles. When we used SSCP to determine the Apo E polymorphism of five individuals whose phenotyping results differed from those of genotyping, the SSCP results agreed with the genotyping results obtained by the PCR-based amplification refractory mutation system (ARMS). Because most of the reported rare alleles of the Apo E gene involve mutations of amino acid residues in positions 120-160, our SSCP method is useful for determining rare as well as common alleles.

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Maekawa, Masato, Kayoko Sudo, Dilip Chandra Dey, Kazuo Kotani, and Takashi Kanno. "Effect of electrophoretic conditions on single strand conformation polymorphism (SSCP) pattern." SEIBUTSU BUTSURI KAGAKU 38, no. 2 (1994): 95–101. http://dx.doi.org/10.2198/sbk.38.95.

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Mora, B., F. Petronzelli, R. Grillo, P. Ferrante, and M. C. Mazzilli. "SINGLE-STRAND CONFORMATION POLYMORPHISM (SSCP) ANALYSIS OF HLA-DRB1*1101-06." International Journal of Immunogenetics 23, no. 5 (1996): 345–52. http://dx.doi.org/10.1111/j.1744-313x.1996.tb00007.x.

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Mohabeer, Ajay J., Alan L. Hiti, and John W. Martin. "Non-radioactive single strand conformation polymorphism (SSCP) using the Pharmacia ‘PhastSystem’." Nucleic Acids Research 19, no. 11 (1991): 3154. http://dx.doi.org/10.1093/nar/19.11.3154.

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Spagnolo, Dominic V., Gavin R. Turbett, Brett Dix, and Barry Iacopetta. "Polymerase Chain Reaction and Single-Strand Conformation Polymorphism Analysis (PCR–SSCP)." Advances in Anatomic Pathology 1, no. 2 (1994): 61–77. http://dx.doi.org/10.1097/00125480-199409000-00001.

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Gasser, Robin B., Min Hu, Neil B. Chilton, et al. "Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation." Nature Protocols 1, no. 6 (2006): 3121–28. http://dx.doi.org/10.1038/nprot.2006.485.

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Santos, Marcelo A. C. G. dos, Elisangela Pereira de S. Quedas, Rodrigo de Almeida Toledo, Delmar M. Lourenço-Júnior, and Sergio Pereira de A. Toledo. "Screening of RET gene mutations in multiple endocrine neoplasia type-2 using Conformation Sensitive Gel Electrophoresis (CSGE)." Arquivos Brasileiros de Endocrinologia & Metabologia 51, no. 9 (2007): 1468–76. http://dx.doi.org/10.1590/s0004-27302007000900009.

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Multiple endocrine neoplasia type 2 (MEN2) is an autosomal dominant inherited tumor syndrome caused by RET proto-oncogene germline mutations (RET). Here we tested the Conformation Sensitive Gel Electrophoresis (CSGE) as a screening method for RET hot-spot mutations. Seven MEN2 families were studied by direct sequencing analysis, CSGE and Single Strand Conformational Polymorphism (SSCP). Using CSGE/SSCP, we were able to detect four out of five types of RET mutations verified by sequencing analysis: Cys620Arg, Cys634Arg, Cys634Tyr, and Met918Thr, furthermore a missense substitution at codon 648 (Val648Ile). RET polymorphisms 691 and 769 were also verified. Data obtained using CSGE/SSCP were fully concordant. We conclude that CSGE showed to be a sensitive, fast, low-cost, and simple procedure to detect RET mutations in codons which are reported as the most prevalent RET variants (~ 95%) in large MEN2 series. As to the Val804Met mutation, this method still needs to be optimized.

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HUBY-CHILTON, FLORENCE, JOHANNA MURPHY, NEIL B. CHILTON, ALVIN A. GAJADHAR, and BURTON W. BLAIS. "Detection of Prohibited Animal Products in Livestock Feeds by Single-Strand Conformation Polymorphism Analysis†‡." Journal of Food Protection 73, no. 1 (2010): 119–24. http://dx.doi.org/10.4315/0362-028x-73.1.119.

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Single-strand conformation polymorphism (SSCP) analysis of amplicons produced from a mitochondrial DNA region between the tRNALys and ATPase8 genes was applied for the detection of animal product within livestock feeds. Identification of prohibited animal (cattle, elk, sheep, deer, and goat) and nonprohibited animal (pig and horse) products from North America was possible based on the differential display of the single-stranded DNA fragments for the different animal species on SSCP gels. This method allowed specific detection and identification of mixed genomic DNA from different animal species. Trace amounts of cattle-derived materials were also detected in pig meat and bone meal and in grain-based feeds fortified with 10, 5, 1, or 0% porcine meat and bone meal. This study demonstrates the applicability of SSCP analyses to successfully identify the origin of animal species derived materials potentially present in animal feeds.

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Welsh, Judith A., Katariina Castrén, and Kirsi H. Vähäkangas. "Single-strand conformation polymorphism analysis to detect p53 mutations: characterization and development of controls." Clinical Chemistry 43, no. 12 (1997): 2251–55. http://dx.doi.org/10.1093/clinchem/43.12.2251.

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Abstract Single-strand conformation polymorphism (SSCP) analysis is widely used to prescreen mutations in p53 gene. However, standardization of SSCP to detect p53 mutations has rarely been pursued so far. We have developed complete conditions for a temperature-controlled nonradioactive SSCP for mutation detection in amplified p53 exons 4-8, where mutations frequently occur in human tumors. Easily obtainable and clearly distinguishable positive controls were developed by replacing the regular 5′ primers in amplification with primers that include one to three mutated sites. Careful purification of the amplified products by gel electrophoresis appeared to be essential. The efficiency of the method was studied by using previously sequenced samples with p53 mutations and the various positive controls. The use of two temperatures (exon 4: 4 °C and 15 °C; other exons: 4 °C and 20 °C) in combination with other optimized conditions resulted in 98% efficiency in mutation detection, which was considered sufficient for routine screening.

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Wang, Qi-Ming, Juan Li, Shi-An Wang, and Feng-Yan Bai. "Rapid Differentiation of Phenotypically Similar Yeast Species by Single-Strand Conformation Polymorphism Analysis of Ribosomal DNA." Applied and Environmental Microbiology 74, no. 9 (2008): 2604–11. http://dx.doi.org/10.1128/aem.02223-07.

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ABSTRACT Single-strand conformation polymorphism (SSCP) analysis of ribosomal DNA (rDNA) was investigated for rapid differentiation of phenotypically similar yeast species. Sensitive tests indicated that some yeast strains with one, most strains with two, and all strains with three or more nucleotide differences in the internal transcribed spacer 1 (ITS1) or ITS2 region could be distinguished by PCR SSCP analysis. The discriminative power of SSCP in yeast species differentiation was demonstrated by comparative studies of representative groups of yeast species from ascomycetes and basidiomycetes, including Saccharomyces species, medically important Candida species, and phylloplane basidiomycetous yeast species. Though the species within each group selected are closely related and have relatively similar rDNA sequences, they were clearly differentiated by PCR-SSCP analysis of the ITS1 region, given the amplified fragments were less than 350 bp in sizes. By using SSCP analysis for rapid screening of yeast strains with different rDNA sequences, species diversity existing in a large collection of yeast strains from natural sources was effectively and thoroughly investigated with substantially reduced time and cost in subsequent DNA sequencing.

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TAKAHASHI, HAJIME, MIKI SATO, BON KIMURA, TATSUYA ISHIKAWA, and TATEO FUJII. "Evaluation of PCR–Single-Strand Conformational Polymorphism Analysis for Identification of Gram-Negative Histamine-Producing Bacteria Isolated from Fish." Journal of Food Protection 70, no. 5 (2007): 1200–1205. http://dx.doi.org/10.4315/0362-028x-70.5.1200.

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In this study, the previously established PCR–single-strand conformation polymorphism (SSCP) system for detecting and identifying gram-negative histamine-producing bacteria was evaluated. This system can detect and identify histamine-producing bacteria directly from seafood by the use of sequence polymorphisms of the histidine decarboxylase gene (hdc). First, we isolated 81 histamine-producing strains of bacteria from fish samples and analyzed the hdc gene by the PCR-SSCP system. The 22 newly obtained SSCP banding patterns were added to our database, and the utility of our modified database was tested in a second experiment consisting of 18 strains of histamine-producing bacteria isolated from 25 fish samples. Approximately 80% of the histamine-producing strains corresponded to those in the new database. Use of the database for PCR-SSCP analysis, including the band patterns newly added in this study, for the hdc gene makes it possible to more accurately identify histamine producers.

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Schwieger, Frank, and Christoph C. Tebbe. "A New Approach To Utilize PCR–Single-Strand-Conformation Polymorphism for 16S rRNA Gene-Based Microbial Community Analysis." Applied and Environmental Microbiology 64, no. 12 (1998): 4870–76. http://dx.doi.org/10.1128/aem.64.12.4870-4876.1998.

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ABSTRACT Single-strand-conformation polymorphism (SSCP) of DNA, a method widely used in mutation analysis, was adapted to the analysis and differentiation of cultivated pure-culture soil microorganisms and noncultivated rhizosphere microbial communities. A fragment (approximately 400 bp) of the bacterial 16S rRNA gene (V-4 and V-5 regions) was amplified by PCR with universal primers, with one primer phosphorylated at the 5′ end. The phosphorylated strands of the PCR products were selectively digested with lambda exonuclease, and the remaining strands were separated by electrophoresis with an MDE polyacrylamide gel, a matrix specifically optimized for SSCP purposes. By this means, reannealing and heteroduplex formation of DNA strands during electrophoresis could be excluded, and the number of bands per organism was reduced. PCR products from 10 of 11 different bacterial type strains tested could be differentiated from each other. With template mixtures consisting of pure-culture DNAs from 5 and 10 bacterial strains, most of the single strains could be detected from such model communities after PCR and SSCP analyses. Purified bands amplified from pure cultures and model communities extracted from gels could be reamplified by PCR, but by this process, additional products were also generated, as detected by further SSCP analysis. Profiles generated with DNAs of rhizosphere bacterial communities, directly extracted from two different plant species grown in the same field site, could be clearly distinguished. This study demonstrates the potential of the selected PCR–single-stranded DNA approach for microbial community analysis.

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Zhi-Qiang, Chen, Deng Xue-Mei, Zhou Jun, Li Ning, and Wu Chang-Xin. "An association between tyrosinase gene single nucleotide polymorphisms and melanin distribution in chicken." Chinese Journal of Agricultural Biotechnology 2, no. 3 (2005): 167–71. http://dx.doi.org/10.1079/cjb200576.

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AbstractTyrosinase (TYR) is a key enzyme of melanin biosynthesis. Single-strand conformation polymorphism (SSCP) analysis was applied to detect the single nucleotide polymorphisms (SNPs) in the upstream regulating region from -641 to -2125 bp of the TYR gene. Three SNPs were found in this region. Correlations were obtained between genotypes of the SNP sites and pigment traits in chicken parental and F2 generations of the Chinese Agricultural University (CAU) resource population. The chi-square test indicated that these mutations were significantly related to shank and body skin colours.

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Nakabayashi, Y., and K. Nishigaki. "Single-Strand Conformation Polymorphism (SSCP) Can Be Explained by Semistable Conformation Dynamics of Single-Stranded DNA." Journal of Biochemistry 120, no. 2 (1996): 320–25. http://dx.doi.org/10.1093/oxfordjournals.jbchem.a021416.

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Li, Ximei, Daojun Yuan, Hantao Wang, et al. "Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP." Genome 55, no. 6 (2012): 459–70. http://dx.doi.org/10.1139/g2012-032.

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Simple sequence repeat (SSR) markers are widely used in plant genetics and breeding. However, there are many SSR markers that do not reveal polymorphism in cotton. Traditional SSR genotyping methods only provide information on product sizes. This leaves many marker polymorphism undetected, thus, lowering the utility of SSRs. In the present study, monomorphic SSRs between two mapping parents, ‘Emian22’ and 3-79, were subjected to single-strand conformation polymorphism (SSCP) analysis to reveal polymorphism. Of the 4194 monomorphic SSR primer pairs, 158 pairs (3.77%) showed polymorphism and revealed 174 polymorphic loci. Sequence analysis showed that the differences in PCR products between the mapping parents were solely due to base transition or transversion, which was in agreement with SSCP principles. SSCP also revealed SSRs with motifs of AT/TA and GAA/CTT were more polymorphic in dinucleotides and trinucleotides, respectively. Genetic mapping integrated 160 loci into our interspecific BC1 linkage map, 5 of which associated with QTLs related to cotton fiber quality. The technique discussed in the present study enables us to detect polymorphism of monomorphic SSRs, and increase the utilization efficiency of the existing SSR primers.

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Wang, W., K. Okazaki, T. Kishida, M. Fukuda, and Y. Tamaki. "Subtyping of D20S85 STR alleles by single-strand conformation polymorphism (SSCP) analysis." Forensic Science International 86, no. 3 (1997): 187–92. http://dx.doi.org/10.1016/s0379-0738(97)02130-0.

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Palacio, Ana, and Núria Duran-Vila. "Single-strand conformation polymorphism (SSCP) analysis as a tool for viroid characterisation." Journal of Virological Methods 77, no. 1 (1999): 27–36. http://dx.doi.org/10.1016/s0166-0934(98)00121-9.

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Beier, David R. "Single-strand conformation polymorphism (SSCP) analysis as a tool for genetic mapping." Mammalian Genome 4, no. 11 (1993): 627–31. http://dx.doi.org/10.1007/bf00360898.

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BØGH, H. O., X. Q. ZHU, B. Z. QIAN, and R. B. GASSER. "Scanning for nucleotide variations in mitochondrial DNA fragments of Schistosoma japonicum by single-strand conformation polymorphism." Parasitology 118, no. 1 (1999): 73–82. http://dx.doi.org/10.1017/s0031182098003527.

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In this study, we employed a mutation scanning approach for the direct visual display of genetic variability in mitochondrial DNA (mtDNA) fragments within and among populations of Schistosoma japonicum from the People's Republic of China. Fragments of the NADH dehydrogenase 1 gene (ND1) and the cytochrome c oxidase subunit I (COI) were individually amplified from parasite DNA by polymerase chain reaction (PCR), denatured and subjected to single-strand conformation polymorphism (SSCP) analysis. Using ND1 and COI fragments, individuals representing different genotypes could be readily identified based on characteristic and reproducible SSCP profiles. The results demonstrated the usefulness of SSCP for the direct visual display of low-level sequence variation in mtDNA of S. japonicum prior to DNA sequence analysis. This approach has important implications for studying the genetic structure and biology of S. japonicum populations, and for analysing the inheritance of mitochondrial DNA.

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Bandyopadhyay, S., A. K. Bera, S. Sikdar, et al. "Intra-species variability in ITS-1 sequences of Haemonchus contortus isolated from goats in West Bengal, India." Journal of Helminthology 85, no. 2 (2010): 204–9. http://dx.doi.org/10.1017/s0022149x10000465.

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AbstractThis study evaluated the existence of different genotypes of Haemonchus contortus prevailing among goats in West Bengal, India. These parasites were isolated from the abomasum of goat intestine and the molecular characterization was performed by comparing variation of nucleotide sequences of the internal transcribed spacer 1 (ITS-1) gene region. Single-strand conformation polymorphism (SSCP) analysis of ITS-1 amplified product showed the presence of three distinct conformations both in male and female parasites. The sequence analysis of conformations showed two single nucleotide polymorphisms (SNP) in male parasites at nucleotide positions 106 and 107 and one SNP was detected in female parasites at nucleotide position 157. These nucleotide variations in different isolates did not alter the interior loop structure of the predicted secondary RNA, therefore we believe these variations may not be responsible for any evolutionary changes among conformations.

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Jin, Y., HC Dietz, A. Nurden, and PF Bray. "Single-strand conformation polymorphism analysis is a rapid and effective method for the identification of mutations and polymorphisms in the gene for glycoprotein IIIa." Blood 82, no. 8 (1993): 2281–88. http://dx.doi.org/10.1182/blood.v82.8.2281.2281.

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Abstract Glanzmann thrombasthenia (GT) is the most common inherited disorder of platelets. Most of the molecular defects previously identified in GT have been caused by point (or other small) mutations in the genes for glycoprotein (GP) IIb or GPIIIa. We have used single-strand conformation polymorphism (SSCP) analysis to rapidly identify single- base changes in the GPIIIa gene. Using genomic DNA from normal individuals and patients with GT, each GPIIIa exon and a short stretch of flanking intronic sequence was amplified, heat-denatured, and separated in nondenaturing acrylamide gels. Only those fragments with an abnormal migration pattern were isolated and the nucleotide sequence determined. Using SSCP, we detected the polymorphism in the HPA-1 (P1A) system and all three known silent polymorphisms in the GPIIIa gene. Screening 14 GPIIIa exons from 5 patients with GT, one mutant allele was identified. The nucleotide sequence of the abnormal 240-bp SSCP fragment was determined and a G-->A substitution in the splice donor site of exon iv was identified. Analysis of platelet RNA resulting from this mutation showed two mRNA species: one contained a deletion of exon iv, whereas the other had a 27-bp addition to exon iv due to the use of a cryptic splice site in the downstream intron. Single-base substitutions are the most common mutation in GT and often result in abnormal mRNA splicing. SSCP is a rapid and sensitive technique for identifying mutations or polymorphisms in the GPIIIa gene.

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Jin, Y., HC Dietz, A. Nurden, and PF Bray. "Single-strand conformation polymorphism analysis is a rapid and effective method for the identification of mutations and polymorphisms in the gene for glycoprotein IIIa." Blood 82, no. 8 (1993): 2281–88. http://dx.doi.org/10.1182/blood.v82.8.2281.bloodjournal8282281.

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Glanzmann thrombasthenia (GT) is the most common inherited disorder of platelets. Most of the molecular defects previously identified in GT have been caused by point (or other small) mutations in the genes for glycoprotein (GP) IIb or GPIIIa. We have used single-strand conformation polymorphism (SSCP) analysis to rapidly identify single- base changes in the GPIIIa gene. Using genomic DNA from normal individuals and patients with GT, each GPIIIa exon and a short stretch of flanking intronic sequence was amplified, heat-denatured, and separated in nondenaturing acrylamide gels. Only those fragments with an abnormal migration pattern were isolated and the nucleotide sequence determined. Using SSCP, we detected the polymorphism in the HPA-1 (P1A) system and all three known silent polymorphisms in the GPIIIa gene. Screening 14 GPIIIa exons from 5 patients with GT, one mutant allele was identified. The nucleotide sequence of the abnormal 240-bp SSCP fragment was determined and a G-->A substitution in the splice donor site of exon iv was identified. Analysis of platelet RNA resulting from this mutation showed two mRNA species: one contained a deletion of exon iv, whereas the other had a 27-bp addition to exon iv due to the use of a cryptic splice site in the downstream intron. Single-base substitutions are the most common mutation in GT and often result in abnormal mRNA splicing. SSCP is a rapid and sensitive technique for identifying mutations or polymorphisms in the GPIIIa gene.

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TAKAHASHI, HAJIME, BON KIMURA, YUICHIRO TANAKA, MAYUMI MORI, ASAMI YOKOI, and TATEO FUJII. "Use of Single-Strand Conformation Polymorphism of Amplified 16S rDNA for Grouping of Bacteria Isolated from Foods." Journal of Food Protection 71, no. 4 (2008): 839–44. http://dx.doi.org/10.4315/0362-028x-71.4.839.

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The grouping method for isolated strains from foods using single-strand conformation polymorphism (SSCP) after PCR amplification of a portion of 16S rDNA was developed. This method was able to group the strains from various food samples based on 16S rDNA sequence. As 97.8% of the isolated strains from various foods were grouped correctly, use of the PCRSSCP method enables the prompt and labor-saving analysis of microbial population of food-derived bacterial strains. Advantages in speed and accuracy of bacterial population identification by the PCR-SSCP method have practical application for food suppliers and testing laboratories.

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Urmila Pannu, Hemlata Chouhan. "Identification of Polymorphism in LEP Gene by Single Strand Conformation Polymorphism (SSCP) in Rathi Cattle." International Journal of Current Microbiology and Applied Sciences 10, no. 2 (2021): 1834–40. http://dx.doi.org/10.20546/ijcmas.2021.1002.217.

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Mohammed, Amera, Tahreer Al-Thuwaini, and Mohammed Al-Shuhaib. "Single nucleotide polymorphism rs7908486 of the tcf7l2 gene is highly associated with obesity in the Iraqi population." Archives of Biological Sciences, no. 00 (2020): 56. http://dx.doi.org/10.2298/abs201213056m.

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This study was conducted to assess the possible association between polymorphisms of the transcription factor 7-like 2 (TCF7L2) gene and obese Iraqi adults. DNA was obtained from 158 obese subjects and 142 controls. Two specific PCR fragments were designed to incorporate two highly frequent single nucleotide polymorphism (SNP)s within TCF7L2, rs11196208 and rs7908486. Both amplified loci were genotyped by PCR-single-strand conformation polymorphism (SSCP) followed by sequencing. Logistic regression analysis was performed to detect the association between both genetic variants and obesity. Concerning rs11196208-based amplicons, PCR-SSCP genotyping showed homogeneous banding patterns for all investigated samples. In contrast with rs11196208, three SSCP banding patterns in the rs7908486-based amplicons, GG, AG and AA, were observed. Individuals with the AA genotype showed significantly higher (P<0.05) body mass index (BMI), waist circumference (WC), fasting blood glucose (FBG), and insulin values than those with either AG or GG genotypes. Association analysis revealed that individuals with the A allele exhibited a greater risk of obesity than individuals with the B allele. Data indicate that rs7908486 SNP exerted a tight association with obesity. The study suggests implementing TCF7L2 rs7908486-based genotyping in the early detection of obesity.

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Vera-Otarola, Jorge, María Inés Barría, Ursula León, Pilar Carvallo, Alejandro Soza, and Marcelo López-Lastra. "Is Single-Strand Conformation Polymorphism Analysis of the Full 5′ Untranslated Region an Adequate Approach To Study Hepatitis C Virus Quasispecies Distribution?" Journal of Virology 83, no. 17 (2009): 9018–21. http://dx.doi.org/10.1128/jvi.00971-09.

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ABSTRACT Single-strand conformation polymorphism (SSCP) analysis is used by many laboratories to study the quasispecies distribution of the hepatitis C virus (HCV). Here we question the validity of this experimental approach, as conclusions are drawn from the analysis of the migration patterns of two ssDNA molecules and not from RNA. Using previously characterized mutants of the HCV 5′ untranslated regions, we show that contrary to what has been predicted, SSCP migration patterns of DNA amplicons with differences in their nucleotide sequences generated from the full 5′ UTR of HCV are not necessarily unique.

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Wilton, S. "Rapid identification of ApoE alleles by multiple-single-strand conformation polymorphism (SSCP) analysis." Trends in Genetics 11, no. 9 (1995): 341. http://dx.doi.org/10.1016/s0168-9525(00)89102-7.

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de Albuquerque, Dulcinéia Martins, and Sandra Cecı́lia Botelho Costa. "Genotyping of human cytomegalovirus using non-radioactive single-strand conformation polymorphism (SSCP) analysis." Journal of Virological Methods 110, no. 1 (2003): 25–28. http://dx.doi.org/10.1016/s0166-0934(03)00094-6.

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David, Dezso, Humberto A. V. Rosa, Susan Pemberton, Maria J. Diniz, Manuel Campos, and João Lavinha. "Single-strand conformation polymorphism (SSCP) analysis of the molecular pathology of hemophilia B." Human Mutation 2, no. 5 (1993): 355–61. http://dx.doi.org/10.1002/humu.1380020506.

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Speldooren, Valérie, Beate Heym, Roger Labia та Marie-Hélène Nicolas-Chanoine. "Discriminatory Detection of Inhibitor-Resistant β-Lactamases in Escherichia coli by Single-Strand Conformation Polymorphism-PCR". Antimicrobial Agents and Chemotherapy 42, № 4 (1998): 879–84. http://dx.doi.org/10.1128/aac.42.4.879.

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ABSTRACT Plasmid-mediated mechanisms, comprising TEM hyperproduction, TEM derivative production, and OXA production, lead to amoxicillin-clavulanic acid resistance in enterobacteria. The ability of the single-strand conformation polymorphism (SSCP)-PCR method to differentiate the genes encoding inhibitor-resistant β-lactamases was evaluated with three bla TEM primer pairs. Thebla TEM genes, which were known to be different on the basis of their nucleotide sequences (bla TEM-1A, bla TEM-1B,bla TEM-2, bla TEM-30,bla TEM-32, andbla TEM-35), were identified as different by their electrophoretic mobilities. Thebla TEM-33, bla TEM-34,bla TEM-36, bla TEM-37,bla TEM-38, andbla TEM-39 genes, whose sequence differences have been established by oligotyping, displayed different SSCP profiles for different fragments, suggesting genetic differences in addition to those defined by oligotyping. Confirmed by sequencing, these additional genetic events concerned silent mutations at certain positions and, notably, a G→T transversion at position 1 of the −10 consensus sequence in bla TEM-34,bla TEM-36, bla TEM-37, and bla TEM-39. Applied to eight clinical isolates of Escherichia coli resistant to amoxicillin-clavulanic acid, the SSCP method detected TEM-1 in three strains and TEM-30, TEM-32, and TEM-35 in three other strains, respectively. A novel TEM derivative (TEM-58) was detected in another strain, and the deduced amino acid sequence showed two substitutions: Arg244Ser, which is known to confer amoxicillin-clavulanic acid resistance in TEM-30, and Val261Ile, which has not been described previously. The eighth strain produced an OXA β-lactamase. Given the discriminatory power and the applicability of SSCP-PCR, this method can be proposed as a means of following the evolution of the frequencies of the different inhibitor-resistant β-lactamases.

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Aryani, Ni Luh Tati, and Sri Suratmi. "PENERAPAN TEKNIK ANALISIS DNA DENGAN PCR-SSCP (Single-Strand Conformation Polymorphism ) PADA UDANG WINDU, Penaeus monodon." Buletin Teknik Litkayasa Akuakultur 7, no. 2 (2016): 135. http://dx.doi.org/10.15578/blta.7.2.2008.135-140.

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SSCP (Single Strand Conformation Polymorphism) merupakan suatu metode analisis molekuler yang bertujuan untuk melihat perbedaan jumlah basa antar fragmen, dengan menggunakan gel poliakrilamid, yang masing-masing dapat memisahkan 6-8 basa Template DNA pada poliakrilamid gel di fragmentasi dengan elektroforesis terkontrol yang disebut GenePhor. GenePhor merupakan horizontal elektroforesis kering, dengan suhu yang dapat diatur sedemikian rupa, sehingga dapat memisahkan DNA pada tegangan tinggi tanpa menimbulkan panas yang berlebihan pada poliakrilamid gel. Metode staining menggunakan silver staining kit. Hasil dari SSCP sangat dipengaruhi dan ditentukan oleh konsentrasi DNA sampel serta proses ekstraksi, amplifikasi, purifikasi dan restriksi, dan optimasi dalam pelaksanaan staining. Teknik ini merupakan salah satu teknik analisis polimorfisme dan banyak diterapkan pada bidang akuakultur (ikan, udang) untuk genotyping dengan hasil cukup akurat.

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Snyder, Tara Morcone, and Linda B. McGown. "Multiplex Single Strand Conformation Polymorphism Analysis by Capillary Electrophoresis with On-the-Fly Fluorescence Lifetime Detection." Applied Spectroscopy 59, no. 3 (2005): 335–39. http://dx.doi.org/10.1366/0003702053585417.

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This paper describes the use of on-the-fly fluorescence lifetime detection (OFLD) for multiplex single strand conformation polymorphism (SSCP) analysis by capillary electrophoresis (CE). The dye labels studied for multiplex SSCP-OFLD-CE analyses included RG, NBD, and BODIPY-FL. The dyes were first investigated for a model system of “Wild Type” and “Mutant” 43-base fragments designed to vary by a single A/T substitution. Two dye pairs, BODIPY-FL/RG and BODIPY-FL/NBD, were then used to detect the G20210A mutation in the human prothrombin gene. Mobility correction was required for the BODIPY-FL/RG system. Three “blind” analyses were performed of three mixtures that combined a control fragment (wild type-BODIPY-FL) with two “unknown” fragments selected among four possibilities (wild type or mutant labeled with NBD or RG). In each multiplex analysis, the “origin” of the unknown fragments was correctly identified on the basis of fluorescence lifetime of the dye label and the presence or absence of the mutation was correctly determined on the basis of conformation-induced differences in migration time.

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Antolin, Michael F., Christopher F. Bosio, Julie Cotton, William Sweeney, Michael R. Strand, and William C. Black. "Intensive Linkage Mapping in a Wasp (Bracon hebetor) and a Mosquito (Aedes aegypti) With Single-Strand Conformation Polymorphism Analysis of Random Amplified Polymorphic DNA Markers." Genetics 143, no. 4 (1996): 1727–38. http://dx.doi.org/10.1093/genetics/143.4.1727.

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Abstract The use of random amplified polymorphic DNA from the polymerase chain reaction (RAPD-PCR) allows efficient construction of saturated linkage maps. However, when analyzed by agarose gel electrophoresis, most RAPD-PCR markers segregate as dominant alleles, reducing the amount of linkage information obtained. We describe the use of single strand conformation polymorphism (SSCP) analysis of RAPD markers to generate linkage maps in a haplodiploid parasitic wasp Bracon (Habrobracon) hebetor and a diploid mosquito, Aedes aegypti. RAPD-SSCP analysis revealed segregation of codominant alleles at markers that appeared to segregate as dominant (band presence/band absence) markers or appeared invariant on agarose gels. Our SSCP protocol uses silver staining to detect DNA fractionated on large thin polyacrylamide gels and reveals more polymorphic markers than agarose gel electrophoresis. In B. hebetor, 79 markers were mapped with 12 RAPD primers in six weeks; in A. aegypti, 94 markers were mapped with 10 RAPD primers in five weeks. Forty-five percent of markers segregated as codominant loci in B. hebetor, while 11% segregated as codominant loci in A. aegypti. SSCP analysis of RAPD-PCR markers offers a rapid and inexpensive means of constructing intensive linkage maps of many species.

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Journal articles on the topic 'SSCP [Single Strand Conformation Polymorphism ]'

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