• Korean Journal of Head & Neck Oncology
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• v.24 no.1
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• pp.33-42
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• 2008

Head and neck squamous cell carcinoma(HNSCC) is notorious for its poor outcome and increasing incidence. But, the studies of cytogenetic analysis in HNSCC are relatively rare, because of difficulties in culturing solid tumor cells and complexity in chromosomal DNA abberations associated with the lesions. The purpose of this study is to evaluate the location of chromosomal aberrations in Korean HNSCC cell lines (SNU-1041, 1066, and 1076) with comparative genomic hybridization(CGH) and array based CGH(array-CGH). Chromosomal gains of 3q23-q27, 5p13-p15.3, 7p21-pter, 8q11.2-q12, 8q21.1-qter, 9q22-q34, 16q22-q24, and 20q11.2-qter, as well as chromosomal losses on 3p10-p14 were found in all 3 SNU cell lines. Losses on 3p15- p23, 4q22-q27, 4q31.3-qter, 6q14-q15, 7q31-q34, 8p12-pter, 18q21-q23, and 21q11.2-q12 were observed in 2 of 3 cell lines. In array-CGH, many genes were altered including gains of PIK3CA, MYC, EVI1, MAD1L1 genes and losses of SERPIN genes. These aberrations of gene and chromosome coincide with other results of study, generally. These data about the patterns of chromosomal aberrations could be a basic step for understanding more detailed genetic events in the carcinogenesis and also provide information for diagosis and treatment in HNSCC.

• The Journal of the Korea Contents Association
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• v.9 no.4
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• pp.19-26
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• 2009

The microwave exposure device for microwave breast cancer detection consists of RF transceiver and several antennas. The microwave information of object acquired from the microwave exposure device can be calculated permittivity and conductivity by using the inverse scattered analysis. In this paper, we have developed the software for detecting breast cancers based on microwave tomography, by which users not only can check out the existence of breast cancers through the permittivity and conductivity information analysis of the object's internal, but also can analysis easily information for distribution of breast cancers. The developed software provides the function for visualizing the captured permittivity and conductivity information as 2D or 3D color images on which users can easily detect the existence of breast cancers. For more detailed analysis of tomography images, the proposed software also has provided the functions for displaying their cutting profiles as well as position and size information of special area in them.

• Journal of Plant Biotechnology
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• v.45 no.3
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• pp.171-182
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• 2018

Papaya (Carica papaya L.) is one of the crops widely planted in tropical and subtropical areas. The papaya fruit has low calories and are plentiful in vitamins A and C and in minerals. A major problem in papaya production is a plant disease caused by the papaya ringspot virus (PRSV). The first PRSV-resistant GM papaya expressing a PRSV coat protein gene was developed by USA scientists in 1992. The first commercial GM papaya cultivars derived from the event was approved by the US government in 1997. Development of transgenic papayas has been focused on vaccine production and limited agricultural traits, including insect and pathogen resistance, long shelf life, and aluminum and herbicide tolerance. Approximately 17 countries, including the USA and China, produced transgenic papayas and/or commercialized them, which provoked studies on biosafety assessment and development of GM-detection technologies. For the biosafety assessment of potential effects on human health, effects of long-term feeding to model animals have been studied in terms of toxicity and allergenicity. Studies on environmental safety assessment include influence on soil-microbial biodiversity and transfer to soil bacteria of GM selection markers. Many countries, such as Korea, the European Union, and Japan, that have strict regulations for GM crops have serious concerns about unintended introduction of GM cultivars and food commodities using unauthorized GM crops. Transgene- and/or GM event-specific molecular markers and technologies for genomics-based detection of unauthorized GM papaya have been developed and have resulted in the robust detection of GM papayas.

• Korean Journal of Microbiology
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• v.42 no.2
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• pp.89-94
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• 2006

The purpose of this study is to develop the strain-specific PCR primers for the identification of prevotella inter-media ATCC 49046 which is frequently used in the pathogenesis studies of periodontitis. The Hind III-digested genomic DNA of P. intermedia ATCC 49046 were cloned by random cloning method. The specificity of cloned DNA fragments were determined by Southern blot analysis. The nucleotide sequence of cloned DNA probes was determined by chain termination method. The PCR primers were designed based on the nucleotide sequence of cloned DNA fragment. The data showed that Pig6 DNA probe were hybridized with the genomic DNA from P. intermedia strains (ATCC $25611^T$ and 49046) isolated from the Westerns, not the strains isolated from Koreans. The Pig6 DNA probe were consisted of 813 bp. Pig6-F3 and Pig6-R3 primers, designed base on the nucleotide Sequences Of Pig6 DNA Probe, were 3150 specific to the only both P. intermedia ATCC $25611^T$ and P. intermedia ATCC 49046. In the other hand, Pig6-60F and Pig6-770R primers were specific to the only P. intermedia ATCC 49046. The two PCR primer sets could detect as little as 4 pg of chromosomal DNA of P. intermedia. These results indicate that Pig6-60F and Pig6-770R primers have proven useful for the identification of P. intermedia ATCC 49046, especially with regard to the maintenance of the strain.

• Korean Journal of Agricultural Science
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• v.20 no.1
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• pp.56-67
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• 1993

To applying of genetic markers of milk proteins as dairy cow registration and selection aids for genetic improvement, genopypes controlling the 4 milk protein loci, ${\alpha}S1$-casein (${\alpha}S1$-CN), ${\beta}$-casein(${\beta}$-CN), ${\kappa}$-casein(${\kappa}$-CN), and ${\beta}$-lactoglobulin(${\beta}$-LG), from a total of 159 Holstein lactating cows reared at National Animal Breeding Station in 1992 were detected by polyacrylamide gel(PAGE) electrophoresis, and associations between genetic polymorphisms of milk proteins and milk compositions were analyzed. The observed distribution of phenotypes for ${\alpha}S1$-CN, ${\beta}$-CN, ${\kappa}$-CN and ${\beta}$-LG were agreement with those expected under the assumption of genetic equilibrium. The observed genotypic frequencies of the ${\alpha}S1$-CN BB, ${\beta}$-CN AA, ${\kappa}$-CN AA and ${\beta}$-LG AB genotypes were founded to be very high as 79.87%, 84.28%, 71.70% and 49.10%, respectively. Gene frequencies were 0.899 and 0.101 for ${\alpha}S1-CN^B$ and ${\alpha}S1-CN^C$, 0.921 and 0.079 for ${\beta}-CN^A$ and ${\beta}-CN^B$, 0.837 and 0.163 for ${\kappa}-CN^A$ and ${\kappa}-CN^B$, 0.378 and 0.622 for ${\beta}-LG^A$ and ${\beta}-CN^B$. According to the results of analysis of variance, the genotypes of the ${\alpha}S1-CN$, ${\beta}-CN$, ${\kappa}-CN$ and ${\beta}-LG$ were significantly difference for fat, protein and total solid percentage in milk compositions. On milk compositions, the ${\kappa}$-CN BB genotype was very high fat and protein percentage more than ${\kappa}$-CN AA and AB genotypes, and ${\beta}$-LG AA genotype was very high fat percentage more than ${\beta}$-LG AB and BB genotype at 5% level of significant difference, respectively. As a consequence, the fat and protein percentage may be improved to select to ${\kappa}$-CN BB and ${\beta}$-LG AA genotypes.

• The Korean Journal of Applied Statistics
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• v.22 no.4
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• pp.781-792
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• 2009

At an early stage of genomic investigations, a small sample of microarrays is used in gene expression experiments to identify small subsets of candidate genes for a further accurate investigation. Unlike the statistical analysis methods for a large sample of microarrays, an appropriate statistical method for identifying small subsets is a randomization test that provides exact P values. These exact P values from a randomization test for a small sample of microarrays are discrete. The possible existence of differentially expressed genes in the sample of a full set of genes can be tested for the null hypothesis of a uniform distribution. Subsets of smaller P values are of prime interest for a further accurate investigation and identifying these outlier cells from a multinomial distribution of P values is possible by M test of Fuchs et al. (1980). Above all, the genome-wide gene expressions in microarrays are correlated, but the majority of statistical analysis methods in the microarray analysis are based on an independence assumption of genes and ignore the possibly correlated expression levels. We investigated with simulation studies the effect that correlated gene expression levels could have on the randomization test results and M test results, and found that the effects are often not ignorable.

• Korean Journal of Plant Tissue Culture
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• v.25 no.5
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• pp.341-346
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• 1998

In this paper we describe the cloning and expression of the genes encoding the flavonoid-biosynthetic enzyme dihydroflavonol 4-reductase (DFR) in Matthiola incana R. Br. A heterologous cDNA probe from Zea mays was used to isolate full-size DFR cDNA clone from a corolla-specific cDNA library. Comparison of the coding region of this DFR cDNA sequence including the sequences of Zea mays, Anthirrinum majus, Petunia hybrida, Callistephus chinensis, Dianthus caryophyllus and Rosa hybrida reveals a identity higher than 61% at the nucleotide level. The DFR transcript is G/C rich in monocotyledonous plants show a strong codon bias preferring codons with a G or C in the third position. The function of this nucleotide sequences were verified by comparison with amino acid sequences of the amino-terminus and tryptic peptides from purified plant enzyme, by northern blotting with mRNA from wild type and mutant plants and by in vitro expression yielding an enzymatically active reductase. Genomic southern blot analysis showed the presence of one gene for DFR in Matthiola incana. Northern blot analysis of the DFR wild type and mutant lines showed that the lack of DFR activity in the stable acyanic mutant k17b is clearly by a transcriptional block of the DFR gene.

• Korean Journal of Poultry Science
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• v.46 no.3
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• pp.173-183
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• 2019

Based on their virulence, the avian influenza viruses (AIVs) are classified into two pathotypes: low pathogenic avian influenza (LPAI) virus and highly pathogenic avian influenza (HPAI) virus. Among the 16 HA subtypes of AIV, only the H5 and H7 subtypes are classified as HPAI. Some AIVs, including H5 and H7 viruses, can infect humans directly. Six H7 subtype isolates from wild birds of the H7N7 (n=4) and H7N1 (n=2) subtypes were characterized in this study. Phylogenetic analysis showed that eight viral genes (HA, NA, PB2, PB1, PA, NP, M, and NS) of the H7 isolates clustered in the Eurasian lineage, the genetic diversity of which is indicated by its division into several sublineages. The Korean H7 isolates had two motifs, PEIPKGR and PELPKGR, at the HA cleavage site, which have been associated with LPAI viruses. Six H7 isolates encoded glutamine (Q) and glycine (G) at positions 226 (H3 numbering) and 228 of HA, suggesting avian-type receptor-binding specificity. None of the Korean H7 isolates had the amino acid substitutions E627K in PB2 and I368V in PB1, which are critical for efficient replication in human cells. The Korean H7 isolates showed no deletions in the NA stalk region and in NS. These results suggest that the Korean H7 isolates from wild birds are different from the H7N9 influenza viruses isolated in China in 2013, which are capable of infecting humans.

• Journal of Life Science
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• v.32 no.9
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• pp.690-697
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• 2022

This study was conducted to analyze genome of red sea cucumber and to use it as basic data for the development of genetic markers for red sea cucumber. Microsatellite marker analysis of Ulleungdo_normal and Ulleungdo_native red sea cucumbers revealed that dinucleotide simple sequence repeats (SSRs) had the highest ratio, at 81.3~81.4%, and the number of the detected SSRs tended to decrease as the number of repeating sequence units in SSRs increased. In general, microsatellites with between 5 and 10 iterations were most common. As the size of the SSR repeating sequence units increased, the SSR iterations gradually decreased. The di-, tri-, and tetra-nucleotides in SSRs were detected in the highest numbers as (AT)₅, (AAT)₅, and (AAAT)₅, respectively. (CG) and (CCG) had very low frequencies compared to the numbers of other repeating SSR units. The numbers of di-and tri-nucleotide repeats were up to 35 and 32, respectively, and then increased discontinuously up to 44 and 43 repeats, respectively. Tetra-, penta-, and hexa-nucleotides in SSRs occurred in numbers up to 25, 21 and 14, respectively. This analysis of red sea cucumber indicated that it maintains its own repetition sequence and repetition number; therefore, we suggest that using it as basic data for molecular marker will be possible in future research.

• Korean Journal of Biological Psychiatry
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• v.15 no.1
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• pp.14-22
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• 2008

Objectives : The authors purposed to present data for explaining gene-environmental interaction causing depressive disorder by examining the effects of genetic factors related to the serotonin system and environmental factors such as stressful life events in early adulthood. Methods : The subjects were 150 young adults(mean age 25.0${\pm}$0.54), a part of 534 freshmen who had completed the previous study of genotyping of TPH1 gene. We assessed characteristics of life events, depression and anxiety scale and checked if they had a depressive disorder with DSM-IV SCID interview. Along with TPH1 A218C genotype confirmed in previous study, TPH2 -1463G/A and 5HTR2A -1438A/G genes were genotyped using the SNaPshot$^{TM}$ method. Results : In comparison with the group without C allele of TPH1 gene, the number of life events had a significant effect on the probability of depressive disorder in the group with C allele. Other alleles or genotypes did not have a significant effect on the causality of life events and depressive disorder. Conclusion : The results of this study suggest that TPH1 C allele is a significant predictor of onset of depressive disorder following environmental stress. It means that the TPH1 gene may affect the gene-environmental interaction of depressive disorder.