• Asian-Australasian Journal of Animal Sciences
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• v.29 no.3
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• pp.315-320
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• 2016

Porcine beta-defensin-1 (PBD-1) gene plays an important role in the innate immunity of pigs. The peptide encoded by this gene is an antimicrobial peptide that has direct activity against a wide range of microbes. This peptide is involved in the co-creation of an antimicrobial barrier in the oral cavity of pigs. The objective of the present study was to detect polymorphisms, if any, in exon-1 and exon-2 regions of PBD-1 gene in Large White Yorkshire (LWY) and native Ankamali pigs of Kerala, India. Blood samples were collected from 100 pigs and genomic DNA was isolated using phenol chloroform method. The quantity of DNA was assessed in a spectrophotometer and quality by gel electrophoresis. Exon-1 and exon-2 regions of PBD-1 gene were amplified by polymerase chain reaction (PCR) and the products were subjected to single strand conformation polymorphism (SSCP) analysis. Subsequent silver staining of the polyacrylamide gels revealed three unique SSCP banding patterns in each of the two exons. The presence of single nucleotide polymorphisms (SNPs) was confirmed by nucleotide sequencing of the PCR products. A novel SNP was found in the 5'-UTR region of exon-1 and a SNP was detected in the mature peptide coding region of exon-2. In exon-1, the pooled population frequencies of GG, GT, and TT genotypes were 0.67, 0.30, and 0.03, respectively. GG genotype was predominant in both the breeds whereas TT genotype was not detected in LWY breed. Similarly, in exon-2, the pooled population frequencies of AA, AG, and GG genotypes were 0.50, 0.27, and 0.23, respectively. AA genotype was predominant in LWY pigs whereas GG genotype was predominant in native pigs. These results suggest that there exists a considerable genetic variation at PBD-1 locus and further association studies may help in development of a PCR based genotyping test to select pigs with better immunity.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.9
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• pp.1226-1230
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• 2005

The present investigation was undertaken to study the genetic polymorphism of the DRB3 exon 2 in 75 crossbred cattle by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique. Five genotypes i.e. HaeIII-a, HaeIII-b, HaeIII-e, HaeIII-ab and HaeIII-ae were observed when the 284 bp PCR products were digested with HaeIII restriction enzyme. The corresponding frequencies of these patterns were 0.53, 0.04, 0.01, 0.38 and 0.04, respectively. Digestion with RsaI restriction enzyme resolved 24 different restriction patterns. The frequencies of these patterns ranged from 0.013 (RsaI-f, RsaI-k and RsaI-c/n) to 0.120 (RsaI-n). The results revealed that the crossbred cows belonged to the RsaI patterns namely b, k, l, a/l, d/s, l/n, l/o and m/n, whose corresponding frequencies were 0.027, 0.013, 0.040, 0.027, 0.040, 0.067, 0.027 and 0.067, respectively. Digestion of the 284 bp PCR product of DRB3.2 gene with PstI in the crossbred cattle did not reveal any restriction site. These results suggested the absence of the recognition site in some of the animals. These results also revealed that the crossbred cows studied were in homozygous as well as heterozygous condition. On the basis of the above results it can be concluded that the DRB3.2 gene was found to be highly polymorphic in the crossbred cattle population.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.2
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• pp.165-170
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• 2006

Using the somatic cell hybrid panel (SCHP) and radiation hybrid (IMpRH) panel, porcine SOCS2 gene was mapped at SSC5 (1/2) q21-q24 and closely linked with SW1383 marker (47 cR in distance), while SOCS3 gene was assigned to SSC12p11-(2/3p13) and closely linked with SW2490 (43 cR). The reverse transcriptase-polymerase chain reaction (RT-PCR) was performed to detect the expression of these two genes in the different tissues and the results showed that both SOCS2 and SOCS3 genes were widely expressed in tissues investigated (heart, liver, spleen, lung, kidney skeletal muscle, fat and brain), although some tissues showed lower gene expression. Moreover, SOCS2 and SOCS3 genes had different expression levels at different stages, in different tissues and in different breeds. A G/A substitution, which can be recognized by restriction enzyme of Cfr421, was observed in 5' untranslated region (5'-UTR) of SOCS2 gene. The allele frequencies was investigated by PCR-restriction fragment length polymorphism (PCR-RFLP) method and it showed that the allele frequency among Dahuabai, Erhualian, Yushan, Qingping, Large white and Landrace tested were different. Association analysis in a cross experimental populations revealed no significant association between the SOCS2 gene polymorphism and the economic traits investigated. The full-length coding regions (CDs) of porcine SOCS3 gene was obtained by RT-PCR.

• Journal of Ginseng Research
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• v.43 no.3
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• pp.482-487
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• 2019

Background: The mixed-cultivation of different Panax ginseng cultivars can cause adverse effects on stability of yield and quality. K-1 is a superior cultivar with good root shape and stronger disease resistance. DNA markers mined from functional genes are clearly desirable for K-1, as they may associate with major traits and can be used for marker-assisted selection to maintain the high quality of Korean ginseng. Methods: Five genes encoding pathogenesis-related (PR) proteins of P. ginseng were amplified and compared for polymorphism mining. Primary, secondary, and tertiary structures of PR5 protein were analyzed by ExPASy-ProtParam, PSSpred, and I-TASSER methods, respectively. A coding single nucleotide polymorphism (SNP)-based specific primer was designed for K-1 by introducing a destabilizing mismatch within the 3' end. Allele-specific polymerase chain reaction (PCR) and real-time allele-specific PCR assays were conducted for molecular discrimination of K-1 from other cultivars and landraces. Results: A coding SNP leading to the modification of amino acid residue from aspartic acid to asparagine was exploited in PR5 gene of K-1 cultivar. Bioinformatics analysis showed that the modification of amino acid residue changed the secondary and tertiary structures of the PR5 protein. Primer KSR was designed for specific discrimination of K-1 from other ginseng cultivars and landraces. The developed real-time allele-specific PCR assay enabled easier automation and accurate genotyping of K-1 from a large number of ginseng samples. Conclusion: The SNP marker and the developed real-time allele-specific PCR assay will be useful not only for marker-assisted selection of K-1 cultivar but also for quality control in breeding and seed programs of P. ginseng.

• YAKHAK HOEJI
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• v.50 no.1
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• pp.26-32
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• 2006

Osteocalcin is a vitamin K dependent and bone specific protein which plays an important role in the regulation of bone and calcium metabolism. In this study, we evaluated the relationship between the C298T polymorphism in the osteocalcin gene and bone mineral density (BMD) in Korean young men and their interaction with physical activity. BMDs of the femoral neck and lumbar spine were measured using dual energy X-ray absorptiometry, and the C298T polymorphism in the osteocalcin gene determined using polymerase chain reaction (PCR)-HindIII restriction fragment length polymorphism (RFLP) method. We did not observe any significant differences in the femoral neck and lumbar spine BMDs across genotypes of this polymorphism in controls, athletes or combined groups, respectively (P>0.05). Therefore, our data suggest that the C298T polymorphism in the osteocalcin gene is not a suitable genetic marker for the susceptibility to BMD.

• Korean Journal of Biological Psychiatry
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• v.12 no.1
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• pp.62-67
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• 2005

Objective:There has been increasing evidence that neurodevelopmental dysfunction is involved in the pathophysiology of schizophrenia. Cadherin is known to be one of the important molecules in neurodevelopment. This study was performed to examine the relationship between T816C polymorphism of CDH2 gene and schizophrenia. Methods:Genoytypes of T816C polymorphism of CDH2 gene were analyzed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 156 Korea patents with schizophrenia and 170 controls. Results:No difference was found between the patients with schizophrenia and the controls in genotype and allele frequencies of T816C polymorphism of CDH2 gene. Conclusion:The results of this study do not support an association between T816C polymorphism of CDH2 gene and schizophrenia. However, it is necessary to investigate other polymorphic regions of CDH2 in schizophrenia.

• Environmental Mutagens and Carcinogens
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• v.23 no.1
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• pp.23-29
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• 2003

To determine the frequencies of the genotypes of estrogen metabolising enzyme (CYP17, CYP1A1, CYP1B1, and COMT) and to identify the high-risk genotypes of these metabolic enzymes to breast cancer in Korean, the author has analysed 115 breast cancer patients and corresponding age and sex matched heathy controls using polymerase chain reaction-restiction fragment length polymorphism (PCR-RFLP). A2/A2 genotype in CYP17 polymorphism, m2/m2 genotype in CYP1A1 polymorphism, and Val/Val genotype in CYP1B1 had 0.95, 1.40 and 0.76 relive risks to breast cancer comparing with reference genotypes of each polymorphism, respectively. Among the genotypes of COMT enzyme polymorphism, L/H and L/L genotypes had 0.97 and 1.54 relative risks to breast cancer, respectively. According to the number of high risk genotype, the patients with one or two putative high risk genotypes had 0.95 and 1.94 relative risks to breast cancer, respectively. This study have demonstrated the unique frequency of genotypes of estrogen metabolizing enzyme in Korean healthy women, which will provide the basic data and insights to study the estrogen related conditions in Korean women including breast and endometrial cancers. And it also indicates that the well-known high risk genotypes of estrogen metabolizing enzymes are not significantly associated with the development of breast cancer in Korean women.

• Parasites, Hosts and Diseases
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• v.34 no.1
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• pp.15-20
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• 1996

Cysts of Entamoebn histoIMtica are still found from humans in Korea, but notall of the cysts are known as pathogenic. The non-pathogenic strain is regarded as a differenL species, E. nispnr. In this study, Korean isolates of conventional E. histolvticn were subjected for the differentiation by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis. Human stools were screened by routine microscopic examination, and cyst or trophozoite positive stools were inoculated into Robinson media. The cultivated trophozoites were prepared for DNA extraction, and the DNAs were used for PCR with common primers of Pl gene. The PCR products were divested with 3 restriction enzymes and RFLP was observed. Also anti-sense primers containing the cleavage site of each restriction eWe were designed for differentiation only by PCR. The PCR products of Korean isolates 59,512, YS-6, and YS-27 were spliced by Taq I and Xmnl but not byAccl, and the isolates S1, S3, S11, S15, S16, S17, S20, YS- l7, and YS-44 were spliced by Acc I but not by Taq I and Xmn I. These RFLP pattern correlated well with PCR products by the species specific primers. The findings confirm that the Korean isolates 59,512, YS-6, and YS-27 are E. histolwtico and others are E. dispar. In Korea, most of the asymptomatic cyst carriers are infected by E. dispar, not by E. histolytica. Key words: Entcmoebc histolytica, Entcmoebn dispar Korean isolates, polymerase chain reaction (PCR), restriction fragment length polymorphism (RFLP)

• Clinical and Experimental Reproductive Medicine
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• v.31 no.1
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• pp.51-57
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• 2004

Objective: To investigate whether polymorphism of gene encoding COMT is associated with the risk of endometriosis in Korean women. Methods: We investigated 136 patients with histopathologically confirmed endometriosis rAFS stage III/IV and 251 control group women who were surgically proven to have no endometriosis. Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) of PCR products were done to determine each participant's COMT genotype. Results: The distribution according to NIaIII genetic polymorphisms of COMT were as follows. $COMT^{HH}$, $COMT^{HL}$, and $COMT^{LL}$ genotypes were 56.6% (77 women), 34.6% (47 women) and 8.8% (12 women) in the study group and 50.6% (127 women), 39.4% (99 women) and 10.0% (25 women) in the control group. There was no significant difference between the study group and the control group. Conclusion: The results suggest that COMT genetic polymorphism may not be associated with the development of endometriosis in Korean women.

• Journal of Acupuncture Research
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• v.24 no.3
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• pp.197-205
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• 2007

Objectives : Tumor necrosis factor-${\alpha}$(TNF ${\alpha}$) is a proinflammatory cytokine involved in the pathogenesis of rheumatoid arthritis. This study was designed to investigate the relation between TNF-${\alpha}$ gene polymorphism and rheumatoid arthritis in Korean population. Methods : This study was carried out on 103 rheumatoid arthritis patients who fulfilled the American College of Rheumatology 1987 revised criteria for rheumatoid arthritis and 208 healthy control subjects. Blood samples from all subjects were obtained for DNA extraction. The extracted DNA was amplified by polymerse chain reaction(PCR). PCR products were visualized by 2% agarose gel electrophoresis. We investigated the genotyping of TNF-${\alpha}$ by using Pyrosequencing. Results: The genotypes of TNF-${\alpha}$ gene were GG, AG and AA. While the distribution of TNF-${\alpha}$ polymorphism in control subjects was 92.31%, 7.21%, 0.48% respectively, in rheumatoid arthritis patients was 93.20%, 6.80%, 0.00%(GG, AG, AA). There was no statistical significant allelic frequency difference between control and rheumatoid arthritis groups. Conclusions : We concluded that there was no significant association between TNF-${\alpha}$ gene polymorphism and rheumatoid arthritis. However, the findings of this study need to be confirmed in more patients and further studies.