• Parasites, Hosts and Diseases
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• 제52권5호
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• pp.557-564
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• 2014

The vir genes are antigenic genes and are considered to be possible vaccine targets. Since India is highly endemic to Plasmodium vivax, we sequenced 5 different vir genes and investigated DNA sequence variations in 93 single-clonal P. vivax isolates. High variability was observed in all the 5 vir genes; the vir 1/9 gene was highly diverged across Indian populations. The patterns of genetic diversity do not follow geographical locations, as geographically distant populations were found to be genetically similar. The results in general present complex genetic diversity patterns in India, requiring further in-depth population genetic and functional studies.

• ALGAE
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• 제30권4호
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• pp.275-280
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• 2015

Coolia santacroce is a newly described epibenthic dinoflagellate species collected from the U.S. Virgin Islands. The original description indicates this species is unique from others in the Coolia monotis complex due to the relative size of the apical pore complex, broad range of pore sizes, and ribosomal DNA. The original description was done based on the isolation and cultivation of one isolate of the organism. In this study, we report three more isolates of Coolia santacroce collected from the Bahamas. Morphological observations were made using scanning electron microscopy that do not correspond to those from the original description, indicating the variability of the morphological features. However, analysis of the D1 / D2 regions of the large subunit rDNA places the three strains in a strongly supported monophyletic clade with the type specimen.

• Genomics & Informatics
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• 제9권4호
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• pp.189-193
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• 2011

Simple sequence repeats (SSRs) are ubiquitous short tandem duplications found within eukaryotic genomes. Their length variability and abundance throughout the genome has led them to be widely used as molecular markers for crop-breeding programs, facilitating the use of marker-assisted selection as well as estimation of genetic population structure. Here, we report a software application, "SSR-Primer Generator " for SSR discovery, SSR-primer design, and homology-based search of in silico amplicons from a DNA sequence dataset. On submission of multiple FASTA-format DNA sequences, those analyses are batch processed in a Java runtime environment (JRE) platform, in a pipeline, and the resulting data are visualized in HTML tabular format. This application will be a useful tool for reducing the time and costs associated with the development and application of SSR markers.

• Journal of Microbiology and Biotechnology
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• 제8권5호
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• pp.490-496
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• 1998

Random amplified polymorphic DNA (RAPD) markers were used to survey genetic variability among 34 Botrytis cinerea isolates from nine different host plants in Korea. For RAPD analysis, 115 arbitrary decamer primers were initially screened for polymorphic major DNA bands with 11 representative B. cinerea isolates. Eleven primers that initially detected polymorphisms were tested a second time with additional 23 isolates of B. cinerea as well as one isolate of Botrytis squamosa as an outgroup. The RAPD analyses revealed that all isolates except one showed different molecular phenotypes. Dendrograms obtained from dissimilarity matrices using the unweighted paired group method of arithmetic means (UPGMA) showed the 36.4% to 90.0% similarity among all B. cinerea isolates. The B. squamosa isolate showed the least similarity to all B. cinerea isolates. The cluster analyses indicated no correlation among all the characteristics examined including molecular phenotypes, host and geographic origins, year of isolation, or pathogenicity. The RAPD data suggest that a high level of genetic variation exists among Korean populations of B. cinerea and it seems to be caused by heterokaryosis among preexisting molecular phenotypes.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.51-56
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• 2005

There are many sources of systematic variations in cDNA microarray experiments which affect the measured gene expression levels like differences in labeling efficiency between the two fluorescent dyes. Print-tip lowess normalization is used in situations where dye biases can depend on spot overall intensity and/or spatial location within the array. However, print-tip lowess normalization performs poorly in situation where error variability for each gene is heterogeneous over intensity ranges. We proposed the new print-tip normalization methods based on support vector machine regression(SVMR) and support vector machine quantile regression(SVMQR). SVMQR was derived by employing the basic principle of support vector machine (SVM) for the estimation of the linear and nonlinear quantile regressions. We applied our proposed methods to previous cDNA micro array data of apolipoprotein-AI-knockout (apoAI-KO) mice, diet-induced obese mice, and genistein-fed obese mice. From our statistical analysis, we found that the proposed methods perform better than the existing print-tip lowess normalization method.

• Asian-Australasian Journal of Animal Sciences
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• 제20권10호
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• pp.1478-1484
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• 2007

To determine the origin and genetic diversity of Red Chittagong (RC) cattle in Bangladesh, we analyzed mitochondrial DNA displacement loop (D-loop) sequences of 48 samples along with 22 previously published sequences from Bos indicus and Bos taurus breeds. Twenty five haplotypes were identified in RC cattle that were defined by 44 polymorphic sites and nucleotide diversity was $0.0055{\pm}0.0026$. The estimated sequence divergence times between RC and other zebu cattle breeds studied ranged between 22,700-26,900 years before present (YBP) which, it is suggested, predate domestication of RC cattle. Furthermore, it is assumed that introgressions have occurred in this breed mainly from Indian zebu breeds in the recent millennia. The phylogenetic studies showed RC cattle clustered with Bos indicus lineage with two distinct haplogroups representing high genetic variability of this breed. These findings can be used for designing proper breeding and conservation strategies for RC cattle in Bangladesh.

• 한국수산과학회지
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• 제41권6호
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• pp.466-470
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• 2008

Microsatellite DNA markers were used to investigate the genetic diversity and population structure of Pacific abalone Haliotis discus hannai collected from six locations (Uljin, Ulsan, Daechon, Taean, Wando, and Yosu) where hatchery-produced abalone have been released intensively. There was no distinguishable difference in the observed and expected heterozygosities between the six populations and a cultured population. However, there was a difference in the number of alleles per locus: 12.8 for the cultured population and 13.8 to 15.8 for the six populations. The proportion of stocked abalone ranged from 41.1 to 92.7% for wild-caught populations with a decreasing tendency of alleles per locus for an increasing proportion of stocked abalone. A departure from Hardy-Weinberg equilibrium (HWE) assessed using the Markov chain procedure (P<0.05) was observed in the six populations and cultured population at loci Hdh145 and Hdh5l2. The pairwise Fst test (P<0.05) showed a significant difference between the Uljin and Ulsan populations and four remaining populations (Wando, Daechon, Yosu, and the cultured population), among which the Wando population differed less than the other three populations (Daechon, Yosu, and the cultured population).

• Clinical and Experimental Reproductive Medicine
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• 제49권3호
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• pp.196-201
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• 2022

Objective: This prospective consecutive study investigated the variation in sperm DNA fragmentation (SDF) in multiple semen samples from patients with cancer. Methods: Eighty-one patients with various cancers underwent multiple semen collections on 3 consecutive days for sperm cryopreservation prior to cancer treatment. A commercial Halosperm kit was used to measure SDF. Within- and between-subject coefficients of variation were estimated via random-effects analysis of variance to assess the consistency of semen parameters and SDF. Intraclass correlation coefficients (ICCs) were calculated to assess the magnitude of the between-subject component of variance relative to the total variance. Results: The volume of semen in the day-2 and day-3 samples was significantly lower compared with the day-1 sample. Most parameters showed high ICC values, suggesting that within-subject fluctuations were small relative to the between-subject variability. The highest ICC values were identified for the SDF (ICC, 0.68; 95% confidence interval [CI], 0.45-0.84) and semen volume (ICC, 0.67; 95% CI, 0.45-0.84). Conclusion: Our findings showed that repeated ejaculates from patients with cancer had stable SDF levels.

• Journal of Nutrition and Health
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• 제44권5호
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• pp.366-377
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• 2011

Glutathione S-transferase (GST) is a multigene family of phase II detoxifying enzymes that metabolize a wide range of exogenous and endogenous electrophilic compounds. GSTM1 and GSTT1 gene polymorphisms may account for inter-individual variability in coping with oxidative stress. We investigated the relationships between the level of lymphocyte DNA and antioxidative parameters and the effect on GST genotypes. GSTM1 and GSTT1 were characterized in 301 young healthy Korean adults and compared with oxidative stress parameters such as the level of lymphocyte DNA, plasma antioxidant vitamins, and erythrocyte antioxidant enzymes in smokers and non smokers. GST genotype, degree of DNA damage in lymphocytes, erythrocyte activities of superoxide dismutase, catalase, and glutathione peroxidase (GSH-Px), and plasma concentrations of total radical-trapping antioxidant potential (TRAP), vitamin C, ${\alpha}$- and ${\gamma}$-tocopherol, ${\alpha}$- and ${\beta}$-carotene, and cryptoxanthin were analyzed. Lymphocyte DNA damage assessed by the comet assay was higher in smokers than that in non-smokers, but the levels of plasma vitamin C, ${\beta}$-carotene, TRAP, erythrocyte catalase, and GSH-Px were lower than those of non-smokers (p < 0.05). Lymphocyte DNA damage was higher in subjects with the GSTM1- or GSTT1-present genotype than those with the GSTM1-present or GSTT1- genotype. No difference in erythrocyte antioxidant enzyme activities, plasma TRAP, or vitamin levels was observed in subjects with the GSTM1 or GSTT1 genotypes, except ${\beta}$-carotene. Significant negative correlations were observed between lymphocyte DNA damage and plasma levels of TRAP and erythrocyte activities of catalase and GSH-Px after adjusting for smoking pack-years. Negative correlations were observed between plasma vitamin C and lymphocyte DNA damage only in individuals with the GSTM1-present or GSTT1- genotype. The interesting finding was the significant positive correlations between lymphocyte DNA damage and plasma levels of ${\alpha}$-carotene, ${\beta}$-carotene, and cryptoxanthin. In conclusion, the GSTM1- and GSTT1-present genotypes as well as smoking aggravated antioxidant status through lymphocyte DNA damage. This finding confirms that GST polymorphisms could be important determinants of antioxidant status in young smoking and non-smoking adults. Consequently, the protective effect of supplemental antioxidants on DNA damage in individuals carrying the GSTM1- or GSTT1-present genotypes might show significantly higher values than expected.

• 한국수산과학회지
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• 제30권1호
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• pp.88-94
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• 1997

황해 서식 대하(P. chinenesis) 각 개체군의 유전 구조를 파악하기 위하여 미토콘드리아 DNA(mtDNA)를 추출한 후 BamHI등 15종의 제한효소를 이용한 제한효소 절편 다형 현상 (Restriction Fragment Length Polymer-phisms; RFLPs)을 분석하였으며 보리새우 (P. japonicus)와의 염기 치환 정도를 비교하기 위하여 일본 나가사키 1 집단의 절편 양상도 함께 분석하였다. 한국의 대천, 진도, 나로도 집단과 중국의 발해, 청도 집단 등 5개 집단을 분석한 결과, 대하에서는 3종의 haplotype이 발견되었으나 5개 집단 모두가 하나의 haplotype에 의해 지배되고 있는 것으로 나타났다. 나타난 변이는 2종류로 Cla I과 Pvu II 인식부위가 부가된 변이가 청도와 나로도 집단에서 출현하였을 뿐 전 집단에 대한 나머지 13종의 제한 효소 절편 양상은 모두 동일한 것으로 나타났다. 이와 같은 결과에서 보면 황해산 대하의 각 집단 사이에는 활발한 유전자 교류가 있는 것으로 판단되며, 3개 계군에 대한 지금까지의 구분은 재검토되어야 할 것으로 판단된다. 대하와 보리새우의 mtDNA 공통절편을 이용한 p 값에 의한 염기치환은 $13.7\%$ 정도인 것으로 나타났으며, 제한 효소별 절편의 크기를 비교한 결과 대하의 mtDNA의 크기는 평균 16.44kb였고 보리새우는 약 16.31kb였다.