scholarly journals A Study on Keratin-Associated Protein (KAP) 3.2 Gene and Its Polymorphism in Sandyno Breed of Sheep

2020 ◽  
pp. 40-45
Author(s):  
R. Bharathesree ◽  
R. Saravanan ◽  
M. Jeyakumar ◽  
N. Murali
Keyword(s):  
Gene Locus ◽  
Pcr Amplification ◽  
Staining Technique ◽  
Single Strand Conformation Polymorphism ◽  
Effective Number ◽  
Specific Primer ◽  
Hardy Weinberg Equilibrium ◽  
Its Polymorphism ◽  
Silver Staining Technique ◽  
Conformation Polymorphism

The current study investigates the polymorphic patterns of keratin-associated protein (KAP) 3.2 gene in Sandyno breed of sheep. Genomic DNA was isolated from blood samples of 51 numbers of Sandyno breed. Ovine specific primer associated PCR amplification of KAP 3.2 gene revealed product at 393 bp and genotyped by PCR-SSCP (Single Strand Conformation Polymorphism) method and visualized under silver staining technique. KAP 3.2 gene locus revealed 3 genotypes, viz. AA, AB and BB with a frequency of 0.84, 0.16 and 0 in Sandyno breed with allele frequencies of A(0.92) and B(0.08). Regarding population genetic indices, the effective number of alleles (Ne) for KAP 3.2 in Sandyno breed of sheep was found to be 1.1716. The PIC values was 0.1356 and FIS values was negative (– 0.0864) in this breed. The result revealed that the selected population of Sandyno breed of sheep was in Hardy-Weinberg equilibrium without any significant deviation from the population mean and was monomorphic for KAP 3.2 gene.

Use of Single-Strand Conformation Polymorphism of Amplified 16S rDNA for Grouping of Bacteria Isolated from Foods

2008 ◽  
Vol 71 (4) ◽  
pp. 839-844 ◽  
Author(s):  
HAJIME TAKAHASHI ◽  
BON KIMURA ◽  
YUICHIRO TANAKA ◽  
MAYUMI MORI ◽  
ASAMI YOKOI ◽  
...  
Keyword(s):  
16S Rdna ◽  
Pcr Amplification ◽  
Single Strand Conformation Polymorphism ◽  
Food Samples ◽  
Single Strand ◽  
Bacterial Strains ◽  
16S Rdna Sequence ◽  
Grouping Method ◽  
Speed And Accuracy ◽  
Conformation Polymorphism

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.

Polymorphism of Keratin - Associated Protein (KAP) 6.1 gene and its association with wool traits of Sandyno and Nilagiri breeds of sheep

2019 ◽  
Author(s):  
R. Bharathesree ◽  
N. Murali ◽  
R. Saravanan ◽  
R. Anilkumar
Keyword(s):  
Genomic Dna ◽  
Gene Locus ◽  
Genetic Selection ◽  
Effective Number ◽  
Heterozygous Genotype ◽  
Specific Primers ◽  
Hardy Weinberg Equilibrium ◽  
Polymorphic Variants ◽  
High Degree ◽  
Selection Of

Polymorphic variants of keratin-associated protein (KAP) 6.1 gene with wool traits of Sandyno and Nilagiri breeds of sheep were investigated in this study. Genomic DNA was isolated from blood samples of 125 Sandyno, Nilagiri and Dorset x Nilagiri breeds of sheep along with 76 numbers of wool samples. A 528 bp segment was amplified by PCR using ovine specific primers for KAP 6.1 gene. SSCP analysis of KAP 6.1 gene in Dorset x Nilagiri crossbred sheep resulted in two genotypes for the A/B with no polymorphism. KAP 6.1 gene locus revealed allele frequencies of A, B, C, D and E in Sandyno sheep were 0.67, 0.23, 0.04, 0.01 and 0.04 and in Nilagiri were 0.75, 0.06, 0.11, 0.04 and 0.04 respectively. KAP 6.1 gene revealed departure from Hardy-Weinberg equilibrium. KAP 6.1 genes were found to have high degree of homozygosity (0.6667) in Nilagiri sheep. The effective number of alleles (Ne) for KAP 6.1 gene was 1.1690 and 1.7006 respectively in Sandyno and Nilagiri breeds of sheep. The PIC values for KAP 6.1 gene was 0.1341 and 0.3909 in Sandyno and Nilagiri breeds of sheep respectively. FIS values for KAP 6.1 gene was positive (0.1909) in Nilagiri breed and it was negative (– 0.0110) in Sandyno breed. Least squares analysis of variance showed significant (P less than 0.05) effect between genotypes and between sexes for wool traits like GFW (kg), CWY (%) and FD (µ). Significant (P less than 0.05) effect of breed (Sandyno and Nilagiri) was observed for all the wool traits (GFW, CWY, FD, SL and Medullation %). Significant (p less than 0.05) higher CWY production was recorded for AC genotype (62.00 ± 1.73 %) while low value was recorded for BB genotype (56.25 ± 1.74 %). FD was found to be high in genotype AC (24.29 ± 1.17 µ) than in AA genotype (23.24 ± 0.49 µ). The homozygote AA was found to have more Medullation (%) and SL. Genotypes BB had higher GFW and lower CWY. The heterozygous genotype AC yielded more FD and CWY with lower most Medullation (%) and SL values. From the study, it may be concluded that KAP 6.1 gene might be a potential molecular marker for genetic selection of wool traits in Sandyno and Nilagiri breeds of sheep.

Simultaneous Identification of Seven Foodborne Pathogens and Escherichia coli (Pathogenic and Nonpathogenic) Using Capillary Electrophoresis–Based Single-Strand Conformation Polymorphism Coupled with Multiplex PCR

2009 ◽  
Vol 72 (6) ◽  
pp. 1262-1266 ◽  
Author(s):  
MI-HWA OH ◽  
SE-HEE PAEK ◽  
GI WON SHIN ◽  
HAE-YEONG KIM ◽  
GYOO YEOL JUNG ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Capillary Electrophoresis ◽  
Multiplex Pcr ◽  
Simultaneous Detection ◽  
Pcr Amplification ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Rrna Gene ◽  
Optimal Separation ◽  
Conformation Polymorphism

The objective of this study was to develop a novel technique for parallel analysis of eight important foodborne microbes using capillary electrophoresis–based single-strand conformation polymorphism (CE-SSCP) coupled with multiplex PCR. Specific primers for multiplex PCR amplification of the 16S rRNA gene were designed, corresponding to eight species of bacteria, including Escherichia coli, Clostridium perfringens, Campylobacter jejuni, Salmonella enterica, Listeria monocytogenes, Vibrio parahaemolyticus, Staphylococcus aureus, and Bacillus cereus, for the species-specific identification and optimal separation of their PCR products in subsequent analysis by CE-SSCP. Multiplex PCR conditions including annealing temperature, extension time, the number of PCR cycles, and primer concentrations were then optimized for simultaneous detection of all target foodborne bacteria. The diagnostic system using CE-SSCP combined with multiplex PCR developed here can be used for rapid investigation of causative agents of foodborne illness. The simplicity and high sensitivity of the method may lead to improved management of safety and illness related to food.

The microbial signature of drinking waters: myth or reality?

2006 ◽  
Vol 53 (1) ◽  
pp. 259-266 ◽  
Author(s):  
J. Harmand ◽  
L. Paulou ◽  
J. Desmoutiers ◽  
L Garrelly ◽  
P. Dabert ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Principal Component ◽  
Single Strand Conformation Polymorphism ◽  
Matlab Toolbox ◽  
Microbial Ecosystems ◽  
Drinking Waters ◽  
Processing Abilities ◽  
Typing Technique ◽  
Conformation Polymorphism ◽  
Genetic Analyzer

This paper presents a new software developed for analyzing single strand conformation polymorphism (SSCP) electrophoresis patterns delivered by the genetic analyzer ABI310 (Applied Biosystems). SSCP is a molecular typing technique based on the PCR amplification of microbial 16S rDNA and used for the monitoring of complex microbial ecosystems dynamics. The software – a home-made MATLAB toolbox called MODIMECO – developed for the analysis of SSCP patterns is presented. MODIMECO includes a number of basic signal processing abilities as well as largely used statistical tools such as the well known principal component analysis. The use of the SSCP for assessing the hypothesis of the existence of a microbial signature of drinking waters illustrates the typical advantages of using such software tools. Results are discussed and conclusions drawn.

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