• Asian Pacific Journal of Cancer Prevention
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• v.16 no.17
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• pp.7589-7594
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• 2015

Background: MicroRNAs (miRNAs) are small non-coding RNA molecules, implicated in several activities like initiation, progression and prognosis of various cancers. Single nucleotide polymorphisms (SNPs) in miRNA genes can lead to alteration in mRNA expression, resulting in diverse functional consequences. The aim of our study was to investigate the association of miR-149C>T and miR-196a2C>T SNPs with susceptibility to development of oral squamous cell carcinoma (OSCC) in South Indian subjects. Materials and Methods: 100 OSCC patients and 102 healthy controls from the general population were recruited for the study. Genetic analysis was performed by polymerase chain reaction/restriction fragment length polymorphism (PCR/RFLP) as per a standard protocol. Results: The genotype frequencies in miR-196a2 polymorphism, of TT, CT and CC in the OSCC patients were 69%,10% and 22% respectively while for control group it was 80%, 15% and 5% respectively. The CC genotype of miR196a2 polymorphism was significantly associated with oral squamous cell carcinoma. The genotype frequencies in miR-149 polymorphisms of CC, CT and TT in the oral squamous cell carcinoma (OSCC) patients were 72%, 22% and 6% respectively and for control group 88%, 12% and 0% respectively. CT and TT genotypes of miR149 polymorphism were found to be significantly associated with OSCC (p = 0.05 and 0.07). Conclusions: Our study suggests that miR-196a2C>T and miR-149C>T polymorphisms may play crucial roles in the development of OSCC in South Indian subjects.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.9
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• pp.4057-4060
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• 2015

Cigarette smoke contains oxidants and free radicals which are carcinogens that can induce mutations in humans. Single nucleotide polymorphisms (SNPs) are the most frequent genetic alterations found in the human genome. In the present study, we have examined the ability of the murine double minute 2 (Mdm2) (rs769412) A>G polymorphism in cigarette smokers to predict risk of cancers. Our results showed that of smokers, 87% were found with AA genotype, 10% with heterozygous AG genotype, and 3% with GG genotype. The heterozygous AG genotype was observed in a lower percentage of smokers (10%) as compared to non-smokers (18%), whereas, homozygous AA genotype was observed in lower percentage of non-smokers (81%) as compared to the smokers (87%). The results from present study support the association with an allele and AG genotype in non-smokers. However, further studies are required to establish the role of Mdm2 (rs769412) C>T in cigarettes smokers and diseases.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.12
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• pp.1812-1819
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• 2007

Heart fatty acid-binding protein gene (H-FABP) is an important candidate gene for meat quality. One of the objectives of this study was to screen single nucleotide polymorphisms (SNP) of chicken H-FABP gene among 252 individuals that included 4 Chinese domestic chicken breeds (Fengkai Xinghua (T04), Huiyang Huxu (H), Qingyuan Ma (Q), Guangxi Xiayan (S1)), 2 breeds developed by the Institute of Animal Science, Guangdong Academy of Agricultural Sciences (Lingnan Huang (DC), dwarf chicken (E4)) and one introduced broiler (Abor Acre (AA)). Another objective of this study was to analyze the associations between polymorphisms of the H-FABP gene and fat deposition traits in chickens. PCR-SSCP was used to analyze SNPs in H-FABP and 4 SNPs (T260C, G675A, C783T and G2778A) were detected. Associations between polymorphic loci and intramuscular fat (IMF), abdominal fat weight (AFW) and abdominal fat percentage (AFP) were analyzed by ANCOVA method. The results showed that the T260C genotypes were significantly associated with IMF (p = 0.0233) and AFP (p = 0.0001); the G675A genotypes were significantly associated with AFW, AFP (p<0.01) and IMF (p<0.05); at the C783T locus, AFW and AFP differed highly between genotypes. However, the G2778A loci did not show any significant effect on fat deposition traits in this study. In addition, we found that there were some differences between AFP and definite haplotypes through a nonparametric statistical method, so the haplotypes based on the SNPs except G2778A loci were also significantly associated with IMF, AFW (g) (p<0.05) and AFP (%) (p<0.001). Significantly and suggestively dominant effects of H4H4 haplotype were observed for IMF and the H2H3 was dominant for AFW (g) and AFP (%). The results also revealed that H5H7 haplotype had a negative effect on IMF, while the H5H6 had a positive effect on AFW (g) and AFP (%).

• Parasites, Hosts and Diseases
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• v.47 no.2
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• pp.145-151
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• 2009

This study examined the association of cytokine gene polymorph isms with intrahepatic bile duct wall fibrosis in human clonorchiasis. A total of 240 residents in Heilongjiang, China underwent ultrasonography, blood sampling, and stool examination. Single nucleotide polymorphism (SNP) sites for $IFN-{\gamma}$ (+874 T/A), IL-10 (-1,082 G/A, -819 C/T, -592 C/A), $TNF-{\alpha}$ (-308 G/A), and $TGF-{\beta}1$ (codon 10 T/C, codon 25 G/C) genes were observed with the TaqMan allelic discrimination assay. No significant correlation was observed between individual cytokine gene polymorphisms and intrahepatic duct dilatation (IHDD). Among individuals with clonorchiasis of moderate intensity, the incidence of IHDD was high in those with $IFN-{\gamma}$ intermediate-producing genotype, +874AT (80.0%, P=0.177), and in those with $TNF-{\alpha}$ low-producing genotype, -308GG (63.0%, P=0.148). According to the combination of $IFN-{\gamma}$ and $TNF-{\alpha}$ genotypes, the risks for IHDD could be stratified into high (intermediate-producing $IFN-{\gamma}$ and low producing $TNF-{\alpha}$), moderate, and low (low-producing $IFN-{\gamma}$ and high producing $TNF-{\alpha}$) risk groups. The incidence of IHDD was significantly different among these groups (P=0.022): 88.9% (odds ratio, OR=24.0) in high, 56.5% (OR=3.9) in moderate, and 25.0% (OR=1) in low risk groups. SNP of $IFN-{\gamma}$ and $TNF-{\alpha}$ genes may contribute to the modulation of fibrosis in the intrahepatic bile duct wall in clonorchiasis patients.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.11
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• pp.5451-5454
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• 2012

Objective: The objective of this study was to evaluate the association of MDR1 gene polymorphisms with susceptibility to hepatocellular carcinoma (HCC). Methods: A total of 689 HCC patients and 680 cancer-free subjects were enrolled. Human MDR1 gene polymorphisms were investigated by created restriction site-polymerase chain reaction (CRS-PCR) and DNA sequencing methods. Multiple logistic regression models were applied to estimate the association between MDR1 gene polymorphisms and susceptibility to HCC. Results: We detected a novel c.4125A>C polymorphism and our findings suggested that this variant was significantly associated with susceptibility to HCC. A significantly increased susceptibility to HCC was noted in the homozygote comparison (CC versus AA: OR=1.621, 95% CI 1.143-2.300, ${\chi}^2$=7.4095, P=0.0065), recessive model (CC versus AC+AA: OR=1.625, 95% CI 1.167-2.264, ${\chi}^2$=8.3544, P=0.0039) and allele contrast (C versus A: OR=1.185, 95% CI 1.011-1.389, ${\chi}^2$=4.4046, P=0.0358). However, no significant increase was observed in the heterozygote comparison (AC versus AA: OR=0.995, 95% CI 0.794-1.248, ${\chi}^2$=0.0017, P=0.9672) and dominant model (CC+AC versus AA: OR=1.106, 95% CI 0.894-1.369, ${\chi}^2$=0.8560, P=0.3549). Conclusions: These findings suggest that the c.4125A>C polymorphism of the MDR1 gene might contribute to susceptibility to HCC in the Chinese population. Further work will be necessary to clarify the relationship between the c.4125A>C polymorphism and susceptibility to HCC on larger populations of diverse ethnicity.

• Biomedical Science Letters
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• v.4 no.2
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• pp.137-142
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• 1998

We examined mRNAs, isolated from the rat brain, to ascertain if there is any polymorphism for S-100 beta protein gene. As templates for polymerase chain reaction (PCR) the reverse-transcribed cDNA from the rat brain or phage DNAs isolated from the rat brain cDNA libraries were used. Although PCR products turned out to be exactly same as the expected size based on the previously reported mRNA sequence a single base substitution (CAT to CAC) was identified at nucleotide level. This change was considered as polymorphism since it did not cause any change of the primary structure for S-100 beta protein. This result should facilitate the understanding of the overall structure of the gene for S-100 beta protein.

• Food Science of Animal Resources
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• v.31 no.3
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• pp.356-365
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• 2011

We assessed the effects of single-nucleotide polymorphisms (SNPs) within the porcine fatty acid synthase (FASN) gene regarding meat quality and fatty acid composition in two pig populations: Korean native pigs (KNP) were crossed with Yorkshire (YS) $F_2$, and KNP were crossed with Landrace (LR) $F_2$. Direct DNA sequencing using eight KNP and eight YS pigs revealed two SNPs: c.265C>T (silent) in exon 4 and c.6545A>C (Asn${\rightarrow}$His) in exon 39. The frequency of the two SNPs was analyzed using the polymerase chain reaction-restriction fragment length polymorphism method in seven pig breeds and their association with meat quality traits and fatty acid composition was studied. In the $KNP{\times}YSF_2$ population, both SNPs were significantly associated with the level of monounsaturated fatty acids, including palmitoleic (C16:1) and oleic acid (C18:1) (p<0.005). c.6545A>C was associated with intramuscular fat content in both populations. Our results indicate that variations in c.265C>T and c.6545A>C of the pig FASN can be used to select animals with better fatty acid composition and meat quality. Moreover, KNP was a useful breed for identifying genetic factors affecting meat quality and fatty acid composition and for producing high quality pork.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.1
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• pp.58-62
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• 2019

Objective: The oxidized low density lipoprotein receptor 1 (OLR1) gene plays an important role in the degradation of oxidized low-density lipoprotein and adipocyte proliferation in mammals. For this reason, we aimed at investigating the association of OLR1 gene polymorphisms with carcass quality traits in Chinese Qinchuan cattle. Methods: The single nucleotide polymorphism (SNP) was identified in the 3' untranslated region of bovine OLR1 gene by DNA sequencing. In addition, the haplotype frequency and linkage disequilibrium estimates of three SNPs were evaluated in 520 individuals. Results: Results indicated that the studied three SNPs were within the range of moderate genetic diversity (0.25< polymorphism information content<0.5). Haplotype analysis of three SNPs showed that ten different haplotypes were identified, but only five haplotypes were listed as those with a frequency of <0.05 were excluded. The Hap3 ($-G_1T_2C_3-$) had the highest haplotype frequency (42.10%). Linkage disequilibrium analysis showed that the three SNPs had a low linkage ($r^2<0.001$). The T10588C and C10647T were significantly associated with backfat thickness and intramuscular fat content in Qinchuan cattle. Conclusion: Based on our results, we believe that the OLR1 gene could be a strong candidate gene for influencing carcass quality traits in Qinchuan cattle.

• Korean Journal of Plant Taxonomy
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• v.52 no.3
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• pp.156-172
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• 2022

Campsis grandiflora (Thunb.) K. Schum is an ornamental species with various useful biological effects. The chloroplast genome of C. grandiflora isolated in Korea is 154,293 bp long (GC ratio: 38.1%) and has four subregions: 84,121 bp of large single-copy (36.2%) and 18,521 bp of small single-copy (30.0%) regions are separated by 24,332 bp of inverted repeat (42.9%) regions including 132 genes (87 protein-coding genes, eight rRNAs, and 37 tRNAs). One single-nucleotide polymorphism and five insertion and deletion (INDEL) regions (40-bp in total) were identified, indicating a low level of intraspecific variation in the chloroplast genome. All five INDEL regions were linked to the repetitive sequences. Seventy-two normal simple sequence repeats (SSRs) and 47 extended SSRs were identified to develop molecular markers. The phylogenetic trees of 29 representative Bignoniaceae chloroplast genomes indicate that the tribe-level phylogenic relationship is congruent with the findings of previous studies.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.3
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• pp.889-896
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• 2015

Matrix metalloproteinase-2 (MMP2) is an endopeptidase, mainly responsible for degradation of extracellular matrix components, which plays an important role in cancer disease. A single nucleotide polymorphism (SNP) at -1306 disrupts a Sp1-type promoter site. The results from the published studies on the association between MMP2 -1306 C>T polymorphism and cancer risk are contradictory and inconclusive. In the present study, a meta-analysis was therefore performed to evaluate the strength of any association between the MMP2 -1306 C>T polymorphism and risk of cancer. We searched all eligible studies published on association between MMP2 -1306 C>T polymorphism and cancer risk in PubMed (Medline), EMBASE and Google Scholar online web databases until December 2013. Genotype distribution data were collected to calculate the pooled odds ratios (ORs) and 95% confidence intervals (95%CIs) to examine the strength of the association. A total of 8,590 cancer cases and 9,601 controls were included from twenty nine eligible case control studies. Overall pooled analysis suggested significantly reduced risk associated with heterozygous genotype (CT vs CC: OR=0.758, 95%CI=0.637 to 0.902, p=0.002) and dominant model (TT+CT vs CC: OR=0.816, 95%CI=0.678 to 0.982, p=0.032) genetic models. However, allelic (T vs C: OR=0.882, 95%CI=0.738 to 1.055, p=0.169), homozygous (TT vs CC: OR=1.185, 95%CI=0.825 to 1.700, p=0.358) and recessive (TT vs CC+CT: OR=1.268, 95%CI=0.897 to 1.793, p=0.179) models did not show any risk. No evidence of publication bias was detected during the analysis. The results of present meta-analysis suggest that the MMP2 -1306 C>T polymorphism is significantly associated with reduced risk of cancer. However, further studies with consideration of different populations will be required to evaluate this relationship in more detail.