• Asian Pacific Journal of Cancer Prevention
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• v.13 no.5
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• pp.1999-2002
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• 2012

Background: DNA polymerase is a single-copy gene that is considered to be part of the DNA repair machinery in mammalian cells. The encoded enzyme is a key to the base excision repair (BER) pathway. It is evident that pol beta has mutations in various cancer samples, but little is known about ovarian cancer. Aim: Identification of any variant form of $pol{\beta}$ cDNA in ovarian carcinoma and determination of association between the polymorphism and ovarian cancer risk in Indian patients. We used 152 samples to isolate and perform RT-PCR and sequencing. Results: A variant of polymerase beta (deletion of exon 4-6 and 11-13, comprising of amino acid 63-123, and 208-304) is detected in heterozygous condition. The product size of this variant is 532 bp while wild type pol beta is 1 kb. Our study of association between the variant and the endometrioid type shows that it is a statistically significant factor for ovarian cancer [OR=31.9 (4.12-246.25) with p<0.001]. The association between variant and stage IV patients further indicated risk (${\chi}^2$ value of 29.7, and OR value 6.77 with 95% CI values 3.3-13.86). The correlation study also confirms the association data (Pearson correlation values for variant/stage IV and variant/endometrioid of 0.44 and 0.39). Conclusion: Individuals from this part of India with this type of variant may be at risk of stage IV, endometrioid type ovarian carcinoma.

• Food Science of Animal Resources
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• v.25 no.3
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• pp.328-332
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• 2005

The effect of k-casein (k-CN) variant on milk production traits (milk yield, fat yield, protein yield, fat percentage and protein percentage) was estimated for 568 Holstein cows in the first lactation. The k-CN valiant were determined by PCR-RFLP (restriction fragment length polymorphism) technique at the DNA level. Single trait linear model was used for the statistical analysis of the data. Result of this study indicated that k-CN variant affected significantly milk yield (P<0.05) and protein yield (P<0.01). Animals with the BB variant produced 622kg milk more and had protein yield higher by 32kg compared with animals with the AA variant No associations between the k-CN variants and other milk production trait were found. Therefore, milk and protein yield may be improved through milk protein typing by increasing the frequencies of k-CN B variant in dairy cattle population. In cheese making, it will be also preferable to have milk with the B variant of k-CN, which gives higher yield having a better quality than the A variant milk.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.10
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• pp.4719-4722
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• 2016

Background: Glutathione S-transferase M1 (GSTM1) is involved in the detoxification of carcinogenic agents. DNA copy number variants of GSTM1 may be associated with cancer progression and may result in reduced survival time of various cancers. Determination of DNA copy number variants was here used to assess the association between GSTM1 copy number variant and pathological status and survival time of colorectal-cancer patients treated with 5-fluorouracil-based chemotherapy. Methods: One hundred thirteen Thai colorectal-cancer patients were investigated for GSTM1 copy number variant by real-time PCR. Relationships between gene copy number variants and clinico-pathological parameters were determined. Result: Associations were evident between GSTM1 copy number and stage of tumor (P = 0.026) and metastasis at diagnosis (P = 0.049), with odds ratio values of 0.2 and 0.3 respectively. Conclusions: GSTM1 copy number variant was here not related with reduced overall survival for the colorectal-cancer patients receiving 5-FU-based chemotherapy.

• BMB Reports
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• v.31 no.2
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• pp.149-155
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• 1998

The N199H variant of the EcoRI endonuclease has about twice the catalytic activity of the wild-type. A comparison of their biochemical characteristics, using synthetic oligonucleotides 5'-dAAAACTTAAGAAAAAAAAAAA-3' (KA) and 5'-dTTTTTGAATTCTTTTTTTTTT-3' (KT), helps to define the cleavage reaction pathway of these enzymes. Both EcoRI and EcoRI variant N199H were found to cleave singlestranded KA or KT about three times faster than the double-stranded forms, although the KT oligonucleotide was more susceptible. Using the ssDNA substrate in kinetic analyses, lower $K_m$ values were obtained for the N199H variant than for the wild-type at low (50 mM), as well as high (200 mM), sodium chloride concentrations. This difference between the endonucleases is attributed to a grealter accessibility for tbe substrate by the variant, and also a higher affinity for the DNA backbone. It also appears that the relative activities of the two enzymes, particularly at high ionic strength, are proportional to their populations in the monomeric enzyme form. That is, according to gel filtration data, half of the N199H molecules exist as monomers in 200 mM NaCl, whereas those of the wild-type are mainly dimeric. Consequently, the Asp199 residue of the EcoRI endonuclease may be implicated in the protein-protein interaction leading to dimerization, as well as in coupling to DNA substrates. In summary, it is proposed that active monomeric endonuclease molecules, derived from the dimeric enzyme, recognize and form a complex with a single stranded form of the DNA substrate, which then undergoes nucleophilic substitution and cleavage.

• Genomics & Informatics
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• v.19 no.4
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• pp.44.1-44.9
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• 2021

Autism is a complex neurodevelopmental disorder, the prevalence of which has increased drastically in India in recent years. Neuroligin is a type I transmembrane protein that plays a crucial role in synaptogenesis. Alterations in synaptic genes are most commonly implicated in autism and other cognitive disorders. The present study investigated the neuroligin 3 gene in the Indian autistic population by sequencing and in silico pathogenicity prediction of molecular changes. In total, 108 clinically described individuals with autism were included from the North Karnataka region of India, along with 150 age-, sex-, and ethnicity-matched healthy controls. Genomic DNA was extracted from peripheral blood, and exonic regions were sequenced. The functional and structural effects of variants of the neuroligin 3 protein were predicted. One coding sequence variant (a missense variant) and four non-coding variants (two 5'-untranslated region [UTR] variants and two 3'-UTR variants) were recorded. The novel missense variant was found in 25% of the autistic population. The C/C genotype of c.551T>C was significantly more common in autistic children than in controls (p = 0.001), and a significantly increased risk of autism (24.7-fold) was associated with this genotype (p = 0.001). The missense variant showed pathogenic effects and high evolutionary conservation over the functions of the neuroligin 3 protein. In the present study, we reported a novel missense variant, V184A, which causes abnormal neuroligin 3 and was found with high frequency in the Indian autistic population. Therefore, neuroligin is a candidate gene for future molecular investigations and functional analysis in the Indian autistic population.

• Journal of Ginseng Research
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• v.17 no.1
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• pp.39-44
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• 1993

In Korean ginseng, Panax ginseng C.A Meyer, it was difficult to isolate chloroplast DNA with classical methods, because of the high polysaccharide content of ginseng chloroplast The simple and efficient method of chloroplast DNA isolation from ginseng leaves has been developed by motificalion of recently advanced methods. Also, it can be successfully applied to ctDNA isolation of Chinese cabbage, radish, petunia tobacco as well as ginseng. Isolated chloroplast DNA from ginseng was digested with various restriction endonucleases. It was estimated that the molecular weight of Korean ginseng chloroplast DNA was about 142 kb. There was no difference in restriction endonuclease digestion patterns between two variants of Korean ginseng, which are Jakyung-Jong (violet-stem variant) and Hwang- sook-Jong (yellow-berry variant).

• Nuclear Engineering and Technology
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• v.56 no.6
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• pp.2421-2427
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• 2024

In this research, the Omicron variant of the SARS-CoV-2 virus was simulated and exposed to electron radiation with up to 20 keV energy. Absorbed energy was measured for spike protein, nucleocapsid protein, and envelope of the virus. Simulations were performed by Geant4-DNA in a water environment at temperature of 20 ℃ and pressure of 1 atm. Since the viral RNA is kept inside the nucleocapsid protein, damage to this area could destroy the viral RNA strand and create an inactive virus. Our findings showed that electron beams with an energy of 2.5 keV could cause a maximum absorption dose and consequently maximum damage to the nucleocapsid and effectively be used for inactivation virus.

• Korean Journal of Plant Taxonomy
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• v.44 no.4
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• pp.250-256
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• 2014

This study was carried out to understand the genetic relationship of three Aloe spp. cultivated in Korea, A. saponaria, A. vera and A. arborescens and a new variant in Korea based on three plastid (matK, trnL-F, rbcL) and one nuclear (ITS regions) DNA barcode markers. A total of 2,420 bp sequence was amplified. Two indels were detected in the trnL region, and also several species specific nucleotide loci were detected in all 29 parsimonious informative sites, and 148 variable sites were detected among four taxa studied while 170 variable and 75 parsimonious sites were detected when other Aloe spp. in worldwide were used. An UPGMA phenogram with 10,000 bootstrap replication showed that the new variant was closest to A. vera. The variant was not morphologically and genetically concurrent with any reported species so far. The clustering of Aloe species were broadly in agreement with previously reported results.

• Food Science of Animal Resources
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• v.26 no.1
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• pp.121-126
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• 2006

Major milk proteins have considerable variane which comes from substitution and deletions in their amino arid sequences. Variants in genes that code for milk proteins, such as ${\beta}$-lactoglobulin (${\beta}-LG$) have been established as genetic markers for milk production and milk protein composition in dairy cattle. The effect of ${\beta}-LG$ variant on milk production traits, such as milk yield. fat yield, protein yield, fat percentage and protein percentage, was estimated for 482 Holstein cows in the first lactation. The ${\beta}-LG$ variants were determined by PCR-RFLP technique at the DNA level. Single trait linear model was used for the statistical analysis of the data. Results of this study indicated that ${\beta}-LG$ variants affected significantly protein yield (p<0.05) and fat percentage (p<0.05). Animals with the AA variant produced 31kg of milk protein more than animals with the BB variant. On the contrary, cows with the BB variant had fat percentage higher by 0.35 and 0.32% compared with cows with the AA and AB variants, respectively. No associations between the ${\beta}-LG$ variants and milk yield, protein percentage and fat yield were found Therefore, milk production traits could be improved through ${\beta}-LG$ typing by increasing the frequency of A variant for protein yield or the frequency of B variant for fat content in Holstein dairy cattle population.

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1300-1302
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• 2013