• The Korean Journal of Applied Statistics
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• v.25 no.2
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• pp.269-277
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• 2012

In microarray data analysis, recent efforts have focused on the discovery of gene sets from a pathway or functional categories such as Gene Ontology terms(GO terms) rather than on individual gene function for its direct interpretation of genome-wide expression data. We introduce a meta-analysis method that combines $p$-values for changes of each gene in the group. The method measures the significance of overall treatment-induced change in a gene group. An application of the method to a real data demonstrates that it has benefits over other statistical methods such as Fisher's exact test and permutation methods. The method is implemented in a SAS program and it is available on the author's homepage(http://cafe.daum.net/go.analysis).

• Journal of Microbiology and Biotechnology
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• v.4 no.4
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• pp.285-289
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• 1994

An insecticidal crystal protein gene, cryIA(c), from Bacillus thuringiensis HD-73 was integrated into the chromosome of a xanthan-producing bacterium, Xanthomonas campestris XP92. The cryIA(c) gene expression cassette was constructed that placed the gene between the trc promoter and rrnB transcriptional terminator. The $lacl^q$ gene was also included to prevent the expression of cryIA(c) gene in X campestris cells. Southem blot analysis confirmed the integration of the cryIA(c) gene expression cassette in chromosome of X campestris XP92 transconjugant. Expression of the insecticidal crystal protein was confirmed by Western blot analysis and bioassay against the larvae of Hyphantria cunea (Lepidoptera： Arctiidae) and Plutella xylostella (Lepidoptera：Plutellidae).

• Molecular & Cellular Toxicology
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• v.1 no.4
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• pp.281-283
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• 2005

Extraction of biologically meaningful data and their validation are very important for toxicogenomics study because it deals with huge amount of heterogeneous data. BINGO is an annotation mining tool for biological interpretation of gene groups. Several statistical modeling approaches using Gene Ontology (GO) have been employed in many programs for that purpose. The statistical methodologies are useful in investigating the most significant GO attributes in a gene group, but the coherence of the resultant GO attributes over the entire group is rarely assessed. BINGO complements the statistical methods with graph-theoretic measures using the GO directed acyclic graph (DAG) structure. In addition, BINGO visualizes the consistency of a gene group more intuitively with a group-based GO subgraph. The input group can be any interesting list of genes or gene products regardless of its generation process if the group is built under a functional congruency hypothesis such as gene clusters from DNA microarray analysis.

• Korean Journal of Environmental Biology
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• v.23 no.3 s.59
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• pp.269-274
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• 2005

The 2D/E gel analysis for polypeptide expression reflecting I-18 C gene (early-ecdysterone inducible gene) has conducted the emerged C. riparius adults from larval phase exposure to tebufenozide acting as an ecdysteroidal molting hormone. Control group, the amount of ORE II of the I-18 C gene was larger than that of ORE I of this gene. After treatments, ORE I of the I-18 C gene was overexpressed as the polypeptide, whereas ORF II of this gene was expressed as the polypeptide and was clearly reduced expression. Accordingly, we consider that tebufenozide exhibited endocrine disruptions related processing of ecdysteroid receptor protein reflecting ORF II of I-18 C gene. Also, earlier emergence day was related overexpressed polypeptide reflecting ORE I of I-18 C gene. In this study result, tebufenozide induced changing of physiological condition, and then polypeptide expression reflecting early-ecdysterone inducible I-18 C gene was different between control group and exposure group.

• Journal of the Korean Society of Environmental Restoration Technology
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• v.17 no.1
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• pp.81-90
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• 2014

A Fairy Pitta is a bird known to breed only in mainland China, Taiwan, Japan and Korea and is listed as Vulnerable in the IUCN Red List. We carried out a DNA analysis to contribute to conserve the genetic diversity of Fairy Pitta. 32 samples were collected at Jeju Island, the Korean Peninsula and Taiwan from 2004 to 2013 and DNA was extracted from them and several sequences were amplified-it through PCR. And then we performed the population genetic analysis. We found there was a transversion between nucleotide sequences at CO1 gene, while there was no changes at Cyt-b gene. And we confirmed the polymorphism from two genes was caused from genetic drift not from selection. Through this analysis, the group within the Peninsula was found bigger than other two groups based on the analysis of CO1 gene, and the group from Taiwan was found bigger than other two groups through the analysis of Cyt-b gene. The population genetic structure of mitochondria gene of three group was showing CO1 gene had 5 haplotypes and Cyt-b gene had 6 haplotypes. Haplotype 2 in CO1 gene was found in three group and many individuals of samples had this haplotype. Like CO1 gene, haplotype 2 in Cyt-b gene was found in three group and was included in plenty of individuals. Other haplotypes were not overlaped and broke off among the three groups. To prevent from the extinction of Fairy Pitta and to obtain the genetic diversity, we need to compare with other regional group such as Japan, China and perform additional research in the non-breeding area.

• Korean Journal of Veterinary Research
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• v.36 no.3
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• pp.627-633
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• 1996

To analyze the genomic diversity of transmissible gastroenteritis virus (TGEV), the N-terminal half of the spike (S) glycoprotein gene and nonstructural protein gene (open reading frames 3 and 3-1) were amplified by reverse transcriptase reaction and polymerase chain reaction (RT-PCR), and analyzed using restriction fragment length polymorphism (RFLP) patterns of the amplified DNA. In this study, TGEV Miller (M6) and Purdue (P115) strains were used as reference strains, and two vaccine strains (MSV and STC3) and four Korea isolates (P44, VRI-WP, VRI-41, and VRI-48) were analyzed. All TGEV strains were amplified with three TGEV primer pairs. Although there was some exception in RFLP analysis, this method differentiated TGEV strains into following groups : Miller group (M6 and MSV), Purdue group (PUS, STC3, P44, VRI-WP, VRI-41, and VRI-48). Using Sau3AI and SspI, VRI-48 was differentiated from the Miller and Purdue type viruses. The RT/PCR in conjuction with RFLP analysis was a rapid and valuable tool for differentiating several strains of TGEV. This study revealed the occurences of distinct difference in genome of TGEV strains.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.6
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• pp.2857-2861
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• 2014

More and more evidence indicates that the G801A polymorphism in the CXCL12 gene might be associated with susceptibility to breast carcinoma in humans being. However, individually published results have been inconsistent. The purpose of this meta-analysis was to investigate the association between the G801A polymorphism in the CXCL12 gene and breast carcinoma risk. A complete search strategy was done by the electronic databases including PubMed and Chinese Biomedical Literature Database. A meta-analysis including seven individual studies was carried out in order to explore the association between the G801A polymorphism in the CXCL12 gene polymorphisms and breast carcinoma. The pooled odds ratios (ORs) and their corresponding 95% confidence intervals (95%CIs) between the G801A polymorphism in the CXCL12 gene and breast carcinoma risk were assessed by the random-effects model. A significant relationship between the G801A polymorphism in the CXCL12 gene and breast carcinoma was discovered in an allelic genetic model (OR: 1.214, 95%CI: 1.085-1.358, p=0.001), a homozygote model (OR: 1.663, 95%CI: 1.240-2.232, p=0.001), a heterozygote model (OR: 1.392, 95%CI: 1.190-1.629, p=0.000), a recessive genetic model (OR: 1.407, 95%CI: 1.060-1.868, p=0.018) and a dominant genetic model (OR: 1.427, 95%CI: 1.228-1.659, p=0.000). On sub-group analysis based on ethnicity, significance was observed between the European group and the mixed group. A significant relationship was found between the G801A polymorphism in the CXCL12 gene and breast carcinoma risk. Individuals with the A allele of the G801A polymorphism in the CXCL12 gene are under a higher risk for breast carcinoma.

• The Korea Journal of Herbology
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• v.28 no.6
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• pp.53-58
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• 2013

Objectives : Pinelliae Tuber has been used as a typical unauthentic herbal medicines. Due to the morphological similarity between Pinelliae Tuber and adulterants, the correct authentication is very difficult. Therefore, we introduced DNA barcode to establish a powerful tool for the authentication of Pinelliae Tuner from adulterants. Methods : To obtain DNA barcode regions, genomic DNA was extracted from nineteen specimens of Pinellia ternata, Pinellia pedatisecta, Pinellia tripartita, and Typhonium flagelliforme, and matK and rbcL genes were amplified. For identification of species specific sequences and analysis phylogenetic relationship, a comparative analysis were performed by the ClastalW and UPGMA based on entire sequences of matK and rbcL genes, respectively. Results : In comparison of two DNA barcode sequences, we elucidated the phylogenetic relationship showing distinct four groups depending on species and identified 40 and 20 species specific nucleotides enough to distinguish each species from matK and rbcL gene, respectively. The sequence differences at the corresponding positions were avaliable genetic marker nulceotides to discriminate the correct species among analyzed four species. These results indicated that phylogentic and comparative analysis of matK and rbcL genes are useful genetic markers to authenticate Pinelliae Tubers. Conclusions : The marker nucleotides enough to distinguish P. ternata, P. tripatrita, P. peditisecta, and T. flagelliform, were observed at 40 positions in matK gene and 20 positions in rbcL gene sequence, respectively. These differences can be used to authenticate Pinelliae Tuber from adulterants as well as discriminate each four species.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.7
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• pp.885-891
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• 2004

To evaluate the feasibility of using sperm-mediated gene transfer (SMGT) for carrying foreign gene into chicken oocyte, a reporter gene, CX-EGFP, was used in this study. The reporter gene was first mixed with liposome or liposome-like compound and the mixtures were further combined with ejaculated cock spermatozoa. The spermatozoa treated with liposome and CX-EGFP mixture was subsequently coincubated with DNaseI to remove the extra DNA which insured the authenticity of positive signals. The treated sperms were then subjected to transgene (reporter gene) existence analysis and artificial insemination of laying hens. Obtained results indicated that the spermatozoa were able to take-in the foreign DNA; which was confirmed by polymerase chain reaction and Southern blot analysis. In the following experiment, fresh ejaculated sperms were mixed with CX-EGFP-liposome or CX-EGFP-liposome-like complex then used for artificial insemination of each of six laying hens. Eggs laid between day-3 and day-7 post insemination were collected. Newly hatched chicks, two out of 53 from CX-EGFP/liposome treated group and two out of 21 from CXEGFP/liposome-like treated group, were proven to be transgenic. This study suggests that SMGT is a powerful method for generating transgenic chickens.

• Journal of Ginseng Research
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• v.47 no.6
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• pp.766-772
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• 2023

Background: Korean Red Ginseng (KRG) is an effective anti-stress treatment. In this study, we investigated the therapeutic potential effects of KRG on relieving stress in a general population using transcriptome analysis. Methods: We conducted an 8-week clinical pilot study on 90 healthy men who reported stress. The study was completed by 43 participants in the KRG group and 44 participants in the placebo group. Participants were randomized 1:1 to the KRG and placebo groups. We evaluated the stress by stress response inventory (SRI) at baseline and 8 weeks. The main outcomes were changes in the levels of neurotransmitters (NTs) and NT-related gene expression. NTs were analyzed using automated (GC) content, and levels of gene expression were measured by reads per kilobase of transcript per million mapped reads (RPKM). Results: The KRG group showed significantly preserved epinephrine decrease compared with placebo group at 8 weeks (changes in epinephrine, KRG vs. placebo; -1623.2 ± 46101.5 vs. -35116.3 ± 86288.2, p = 0012). Among subjects who higher SRI score, meaning stress increased compared to baseline, the KRG group showed a smaller decrease in serotonin than the placebo group (changes in serotonin, KRG vs. placebo; -2627.5 ± 5859.1 vs, -8087.4 ± 7162.4, p = 0.005) and a smaller increase in cortisol than the placebo group (changes in cortisol, KRG vs. placebo; 1912.7 ± 10097.75 vs. 8046.2 ± 8050.6 , p = 0.019) in subgroup analysis. Transcriptome findings indicated that KRG intake affects gene expression related with metabolism of choline, adrenalin, and monoamine. Conclusion: These findings suggest that KRG has beneficial effects on the amelioration of stress response in NTs, and this effect is more prominent in stressful situations. Further clinical studies are required to confirm the anti-stress effect of KRG.