• Journal of Life Science
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• v.33 no.11
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• pp.897-904
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• 2023

This study was done to develope genetic markers with the unique characteristics of genes according to the genomic information of Bacillus velezensis K10. B. velezensis K10 maintained a total of 4,159,835 bps, which was found to encode 5,136 open reading frames (orfs). B. velezensis K10 was found to have much more gene migration due to external factors overall compared to standard strain B. velezensis JS25R. In order to discover genetic selection markers, orfs on the genome to be easily induced to gene mutation were surveyed such as recombinase, integrase, transposase, and phage-related genes. As a result of the investigation, 9 candidate markers were isolated with high possibility as genetic selection markers. Although a part in the various origin's areas showed specificities in comparison with homology, the selected markers were all existed in phage-related areas because they were relatively lower homologies in phage-related genes. PCR analysis was done on B. licheniformis K12, B. velezensis K10, B. subtilis, and B. cereus to establish them as inter-species candidate selection markers. As a result, it was confirmed that B. velezensis K10-specific PCR products were formed in a total of 6 primer sets such as BV3 and BV5 to 9. On the other hand, analysis at the subspecies level observed the formation of B. velezensis K10-specific PCR products in 4 primer sets such as BV3, 5, 8, and 9. Among them, since BV5 and BV8 were detected by very specific results, we suggest that BV5 and 8 can be used as B. velezensis K10 gene selection markers at the species and sub-species level.

• Korean Journal of Biological Psychiatry
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• v.14 no.2
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• pp.115-121
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• 2007

Objetives : Identification of target genes for ethanol in neurons is important for understanding its molecular and cellular mechanism of action and the neuropathological changes seen in alcoholics. The purpose of this study is to identify of altered gene expression after acute treatmet of ethanol in rat gliom cells. Methods : We used high density cDNA microarray chip to measure the expression patterns of multiple genes in cultured rat glioma cells. DNA microarrays allow for the simultaneous measurement of the expression of several hundreds of genes. Results : After comparing hybridized signals between control and ethanol treated groups, we found that treatment with ethanol increased the expression of 15 genes and decreased the expression of 12 genes. Upregulated genes included Orthodenticle(Drosophila) homolog 1, procollagen type II, adenosine A2a receptor, GATA bindning protein 2. Downregulated genes included diacylglycerol kinase beta, PRKC, Protein phosphatase 1, clathrin-associated protein 17, nucleoporin p58, proteasome. Conclusion : The gene changes noted were those related to the regulation of transcription, signal transduction, second messenger systems. modulation of ischemic brain injury, and neurodengeneration. Although some of the genes were previously known to be ethanol responsive, we have for the most part identified novel genes involved in the brain response to ethanol.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.15 no.3
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• pp.1724-1733
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• 2014

This paper presents a pattern recognition analysis of two spirals problem and optimization of Cascade Correlation learning algorithm using in combination with a non-monotone function as CosExp(cosine-modulated symmetric exponential function) and a monotone function as sigmoid function. In addition, the algorithm's optimization is attempted. By using genetic algorithms the optimization of the algorithm will attempt. In the first experiment, by using CosExp activation function for candidate neurons of the learning algorithm is analyzed the recognized pattern in input space of the two spirals problem. In the second experiment, CosExp function for output neurons is used. In the third experiment, the sigmoid activation functions with various parameters for candidate neurons in 8 pools and CosExp function for output neurons are used. In the fourth experiment, the parameters are composed of 8 pools and displacement of the sigmoid function to determine the value of the three parameters is obtained using genetic algorithms. The parameter values applied to the sigmoid activation functions for candidate neurons are used. To evaluate the performance of these algorithms, each step of the training input pattern classification shows the shape of the two spirals. In the optimizing process, the number of hidden neurons was reduced from 28 to15, and finally the learning algorithm with 12 hidden neurons was optimized.

• Proceedings of the Korean Information Science Society Conference
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• 2005.11a
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• pp.970-972
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• 2005

유전자 데이터베이스의 서열의 길이가 수백만에서 수백억 정도의 대용량 텍스트이기 때문에 기존의 Smith-waterman 알고리즘으로 정확한 서열의 유사성을 검색하는 것은 매우 비효율적이다. 따라서 빠른 유사성 검색을 위해 데이터베이스에 저장된 문자열에 대해 특정 길이의 모든 부분문자열에 나타나는 문자의 출현 빈도를 이용한 휴리스틱 방법들이 제안되었다. 이러한 방법들은 질의 서열과 일치될 가능성이 높은 후보들만을 추출한 후 이들 각각에 대하여 질의 서열과의 일치 여부를 조사하므로 빠르게 유사성 검색을 할 수 있다. 그러나 이 방법은 문자의 출현 빈도만을 사용하므로 서로 다른 서열을 같은 서열로 취급하는 단점이 있어 정확도가 Smith-Waterman 알고리즘에 비해 떨어진다. 본 논문에서는 문자가 부분문자열에 나타나는 위치 정보를 포함하여 문자의 출현빈도를 인덱싱함으로써 질의 처리를 효율적으로 수행하는 알고리즘을 제안한다. 실험결과 제안된 알고리즘은 문자 빈도만을 사용하는 알고리즘에 비해 $5\~15\%$정도 정확성이 향상되었다.

• Journal of Animal Science and Technology
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• v.46 no.3
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• pp.295-300
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• 2004

The identification of the leptin gene in 1994 and it's adipocytes specific protein leptin hal provided the first physiological links to the regulatory system controlling body weight and fat deposits. The meat tastes is mainly determined by quantifY and quality of triglyceride stored in adipose tissue. This study was conducted to analyze genetic cbaracteristics of Hanwoo leptin gene and also to investigate the association of DNA marlcer with some economic meat traits for Hanwoo. The leptin hormone gene polymorphisms were identified by digestion with Kpn2 I and Msp I. Slaughter weight(SWI), slaughter peroentage(SP), longissimus muscle area(LMA), beef marbling score(MS) and back fat thickness(BF) were compared among three genotypes by P(R..RFlJ> and showed significant differences among genotypes. PCR-RFLP(Kpn2 I) were detected significant for SP, MS and BF. The allele was essociated with fatter carcasses and C allele with leaner carcasses.

• The Korean Journal of Applied Statistics
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• v.22 no.6
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• pp.1239-1247
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• 2009

Study the gene about economical characteristic of human disease or domestic animal is a matter of grave interest, preserve and elevation of gene of Korea cattle is key subject. Studies have been done on the gene of Korea cattle using EST based SNP map, but it is based on statistical model, therefore there are difference between real position and statistical position. These problems are solved using both EST_based SNP map and Gene on sequence by Lee et al. (2009b). We have used multifactor dimensionality reduction(MDR) method to study interaction effect of statistical model in general. But MDR method cannot be applied in all cases. It can be applied to the only case-control data. So, method is suggested E-MDR method using CART algorithm. Also we identified interaction effects of single nucleotide polymorphisms(SNPs) responsible for average daily gain(ADG) and marbling score(MS) using E-MDR method.

• Journal of Life Science
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• v.14 no.5
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• pp.847-854
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• 2004

Allergy is a multi-factorial disease influenced by genetic and environmental factors. As the number of allergy-affected people is increasing in developed countries, there is an increasing interest in genetic predisposition to the allergy. A number of genes and chromosomal region have been identified to be linked to allergy including rhinitis, asthma and atopy. In order to understand the genetic background for the allergy-affected people, we investigated genetic predisposition among students enrolled in Busan Science Academy. Among 138 students, about 30% students had some allergy-related disorder including rhinitis, asthma and atopy. We analyzed several single nucleotide polymorphisms (SNPs) within two genes, Inter-leukin-4(IL-4) and Interleukin-4 receptor(IL-4R), which are involved in the induction of allergy reaction with the Th2 immunity. For 96 samples obtained from students, we analyzed 9 SNPs including -590 C/T and -34 C/T in IL-4, and I75V, Q576R, E375A, e406R, 5411L, S761P and S727A in IL-4R. From the analysis, these SNPs showed slight differences among normal and allergy-affected students, but these differences was not enough to predict the predisposition to the allergy. In contrast to previous reports, we could not find SNP(s) related with allergy. These results suggest that genetic tests recently performed in Korea widely have to be reassessed for its validity of genetic predisposition. [Supported by grants from MOST]

• Tuberculosis and Respiratory Diseases
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• v.62 no.6
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• pp.492-498
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• 2007

Background: Several lines of evidence suggest that a host's genetic factors influence the outcome of exposure to Mycobacterium tuberculosis. The aim of this study was to determine whether polymorphism in NRAMP1 (natural resistance associated macrophage protein 1) gene is associated with the susceptibility or resistance to tuberculosis infection for patients with drug-sensitive pulmonary tuberculosis (DS-TB) and multi-drug resistant pulmonary tuberculosis (MDR-TB). Methods: Eight genetic polymorphisms of the NRAMP1 gene were investigated in patients suffering with DS-TB (n=100) or MDR-TB (n=102), and in healthy normal controls (NC, n=96). The genetic polymorphisms of NRAMP1 were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Results: The frequency of D543N A/G heterogygotes was significantly higher in the DS-TB subjects than the NCs (OR=2.10, 95% CI: 1.00 to 4.41, p=0.049). The frequency of 823C/T T/C heterozygotes was significantly higher in the DS-TB subjects (OR=2.79, 95% CI: 1.11 to 7.04, p=0.029) and the MDR-TB subject (OR=3.30, 95% CI 1.33 to 8.18, p=0.010) than in the NCs. However, the frequency of these genotypes was not different between the DS-TB and MDR-TB subjects. Conclusion: A significant association was found between NRAMP1 823 C/T polymorphism and pulmonary tuberculosis. This result suggests that NRAMP1 polymorphism may be involved in the development of pulmonary tuberculosis in Koreans.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.67 no.1
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• pp.41-52
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• 2022

As a cultivar of Korean wheat, 'Keumgang' wheat variety has a fast growth period and can be grown stably. Hexaploid wheat (Triticum aestivum) has moderately high salt tolerance compared to tetraploid wheat (Triticum turgidum L.). However, the molecular mechanisms related to salt tolerance of hexaploid wheat have not been elucidated yet. In this study, the candidate genes related to salt tolerance were identified by investigating the genes that are differently expressed in Keumgang variety and examining salt tolerant mutation '2020-s1340.'. A total of 85,771,537 reads were obtained after quality filtering using NextSeq 500 Illumina sequencing technology. A total of 23,634,438 reads were aligned with the NCBI Campala Lr22a pseudomolecule v5 reference genome (Triticum aestivum). A total of 282 differentially expressed genes (DEGs) were identified in the two Triticum aestivum materials. These DEGs have functions, including salt tolerance related traits such as 'wall-associated receptor kinase-like 8', 'cytochrome P450', '6-phosphofructokinase 2'. In addition, the identified DEGs were classified into three categories, including biological process, molecular function, cellular component using gene ontology analysis. These DEGs were enriched significantly for terms such as the 'copper ion transport', 'oxidation-reduction process', 'alternative oxidase activity'. These results, which were obtained using RNA-seq analysis, will improve our understanding of salt tolerance of wheat. Moreover, this study will be a useful resource for breeding wheat varieties with improved salt tolerance using molecular breeding technology.

• Journal of Life Science
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• v.23 no.1
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• pp.116-124
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• 2013

The aim was to examine resistance exercise-related genes after 8 weeks of resistance training. Thirty-two male Sprague-Dawley rats were divided into four groups: 4 weeks sedentary (4 wks CON, n=8), 8 weeks sedentary (8 wks CON, n=8), 4 weeks exercise training (4 wks REG, n=8), and 8 weeks exercise training (8 wks REG, n=8). The rats were trained to climb a 1-m vertical incline (85-degree), with weights secured to their tails. They climbed 10 times, 3 days per week, for 8 consecutive weeks. Skeletal muscle was taken from the flexor halucis longus after the exercise training. After separating the total RNA, large-scale gene expression was investigated by beadarray (Illumina RatRef-12 Expression BeadChip) analysis, and qPCR was used to inspect the beadarray data and to analyze the RNA quantitatively. The detection p-value for the genes was p<0.01, the M-value {M=$log_2$(condition)-$log_2$(reference)} was >1.0, and the DiffScore was >20. In total, the expression of 30 genes significantly increased 4 weeks after the exercise training, and the expression of six genes decreased. At 8 weeks, the expression of five genes significantly increased and that of 12 decreased. Several genes are potentially involved in resistance exercise and muscle hypertrophy, including 1) regulation of cell growth (IGFBP1, PLA2G2A, OKL38); 2) myogenesis (CSRP3); 3) tissue regeneration and muscle development (MUSTN1, MYBPH); 4) hypertrophy (CYR61, ATF3, NR4A3); and 5) glucose metabolism (G6PC, PCK1). These results may help to explain previously reported physiological changes of the skeletal muscle and suggest new avenues for further investigation.