• Restorative Dentistry and Endodontics
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• v.34 no.5
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• pp.430-441
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• 2009

The purpose of this study was to characterize functional distinction between human dental pulp cells(PC) and periodontal ligament cells(PDLC) using cDNA micro array assay and to confirm the results of the microarray assay using RT-PCR. 3 genes out of 51 genes which were found to be more expressed(>2 fold) in PC were selected, and 3 genes out of 19 genes which were found to be more expressed(>2 fold) in PDLC were selected for RT-PCR as well. According to this study, the results were as follows: 1. From the micro array assay, 51 genes were more expressed (2 fold) from PC than PDLC. 2. RT-PCR confirmed that ITGA4 and TGF ${\beta}2$ were more expressed in PC than in PDLC 3. From the micro array assay, 19 genes were more expressed (2 fold) from PDLC than PC. 4. RT-PCR confirmed that LUM, WISP1. and MMP1 were more expressed in PDLC than in PC. From the present study, different expression of the genes between the PC and PDLC were characterized to show the genes which play an important role in dentinogenesis were more expressed from PC than PDLC, while the genes which were related with collagen synthesis were more expressed from PDLC than PC.

• Reproductive and Developmental Biology
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• v.31 no.3
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• pp.207-213
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• 2007

This study was carried out to examine gene expression altered in endometrium of Korean cattle (Hanwoo) with endometritis using microarray. In this study, 4,560 diferentially expressed genes (DEGs) were identified in the endometrium of Hanwoo. Of 4,560 DEGs, 2,026 genes were up-regulated, while 2,536 genes were down-regulated in endometritis. Of them, top 10 regulated genes were listed. Filamin A, pancreatic anionic trypsinogen, Rho GDP dissociation inhibitor alpha, collagen type VI alpha 1, butyrate response factor 2, aggrecanses-2, annexin 14, aminopeptidease A, orphan transporter v7-3, and epithelial stromal interaction 1 were up-regulated, while MHC class II antigen, integrin-binding sialoprotein, uterine milk protein precursor, down-regulated in colon cancer 1, glycoprotein 330, dickkopf-1, cfh protein, $Ca^{2+}-dependent$ secretion activator, UL16 binding protein 3, and proenkephalin were down-regulated in the endometritis. Our results suggest that these genes could be useful biomarkers for diagnosis Hanwoo's endometritis.

• KSBB Journal
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• v.18 no.1
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• pp.39-44
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• 2003

A Gene content phylogenetic tree and a 16s rRNA based phylogenetic tree were compared for 33 whole-genome sequenced procaryotes, neighbor joining and bootstrap methods (n=1,000). Ratio of conserved COG (clusters of orthologous groups of proteins) to orthologs revealed that they were within the range of 4.60% (Mezorhizobium loti) or 56.57% (Mycopiasma genitalium). This meant that the ratio was diverse among analyzed procaryotes and indicated the possibility of searching for useful genes. Over 20% of orthologs were independent among the same species. The gene content tree and the 16s rDNA tree showed coincidence and discordance in Archaeabacteria, Proteobacteria and Firmicutes. This might have resulted from non-conservative genes in the gene content phylogenetic tree and horizontal gene transfer. The COG based gene content tree could be regarded as a midway phylogeny based on biochemical tests and nucleotide sequences.

• Proceedings of the Korea Water Resources Association Conference
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• 2011.05a
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• pp.226-226
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• 2011

최적 저수지운영을 위한 운영률 도출이나 강우-유출 및 수질 모형의 매개변수 추정 문제처럼 비선형적이고 추정해야할 변수의 수가 많은 경우, 수학적으로 모형화하기에 너무 복잡해서 선형계획법, 비선형계획법, 동적계획법 등을 사용하여 최적해를 구할 수 없는 경우도 있다. 이러한 문제에 대해서는 구조적 진화를 통해 최적해를 구하는 방법들이 사용된다. 일반적으로 미지수의 개수가 많아지면 전역최적해를 찾기가 어려워진다. 전역최적해를 찾는 여러 가지 방법들이 수자원 분야에서는 강우-유출모형의 매개변수를 추정하는데 많이 사용되고 있으며, 특히 유전자 알고리즘, SCE-UA 알고리즘 등 전역최적해를 찾는 메타휴리스틱 방법이 많이 사용되고 있다. 전역최적화 방법을 개발하는 연구자들은 최적화방법의 성능을 평가하기 위해 다양한 검사함수(test function)를 만들어 성능을 평가하고 있다. 본 연구에 사용한 검사함수는 Mishra의 연구(2006a, 2006b)에서 사용한 중요하고 복잡한 검사함수이다. 유전자 알고리즘, SCE-UA 알고리즘, DDS 알고리즘을 검사함수 중 전역해를 찾기 어려운 2 차원 함수 2 가지, 다차원 함수 4 가지 함수에 적용하여 각각의 탐색 성능을 평가하였다. 2차원 함수인 Bukin 함수에 대해서는 모든 최적화 방법이 전역최적해를 찾을 수 없었지만, 유전자 알고리즘이 가장 전역최적해에 가까웠고 다음으로 DDS 알고리즘 순서였다. 지역수렴 영역이 많을 것으로 판단되는 10, 30, 50 차원 Michalewicz 함수에 대해서는 DDS 알고리즘으로 구한 최적해가 전역최적해와 매우 근접하였고 다음으로 SCE-UA 알고리즘, 유전자 알고리즘 순이었다. 지역수렴 영역이 상대적으로 다른 함수보다 넓은 10 차원 Schwefel 함수에 대해서는 DDS 알고리즘으로 구한 최적해가 전역최적해와 거의 근접하였고 유전자 알고리즘과 SCE-UA 알고리즘은 매우 큰 편차를 보였다. 40, 80 차원 Schwefel 함수에 대해서는 3 가지 알고리즘 모두 전역최적해와 편차를 보였지만 DDS 알고리즘에 의한 최적해와 다른 두 알고리즘에 의한 최적해는 1 오더(order) 정도의 차이가 났다. 지역수렴 영역이 큰 Michalewicz 함수와 Schwefel 함수에 대한 결과는 매우 흡사한 결과이다. 이상과 같은 결과로, 유전자 알고리즘은 매개변수의 수가 적을 경우 우수한 탐색성능을 가졌으며, SCE-UA 알고리즘은 Griewank, Rastrigin 함수와 같은 형태인 경우 우수한 성능을 보였다. DDS 알고리즘은 전체적으로 우수한 탐색 능력을 가진 것으로 판단된다. 그러므로 수위구간 영역별 저수지운영률 도출을 위한 적절한 최적화방법으로 DDS 알고리즘을 선정하였다.

• Journal of Veterinary Clinics
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• v.24 no.3
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• pp.295-299
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• 2007

The detrimental effects of gene transfection on embryo development and the molecular mechanism behind the differential expression of genes related to early embryo development were assessed in the production of transgenic cow embryos through somatic cell nuclear transfer (NT). Parthenogenetic, IVF, and transgenic NT embryos derived from ${\alpha}_1$-antitrypsin transfected ear fibroblast cells was produced. To investigate the molecular mechanism behind lower developmental competence of transgenic NT embryos, the differential mRNA expression of three genes ($IFN-{\tau}$, Oct4, Fgf4) in the 3 types of embryo (Parthenogenetic, IVF, transgenic NT) was examined. RNA was extracted from ten blastocysts derived from 3 types of embryos and reverse-transcripted for synthesis of the first cDNA. The quantification of 3 gene transcripts ($IFN-{\tau}$, Oct4, and Fgf4) was carried out in three replicate by quantitative real-time reverse transcriptase PCR. Expression level of $IFN-{\tau}$ mRNA was significantly higher in transgenic NT embryos than parthenogenetic and IVF embryos (P<0.05). However, expression level of Oct4 and Fgf4 of transgenic NT embryos was significantly lower than IVF embryos (P<0.05). Altered levels of these three mRNA transcripts may explain some of the embryonic/fetal/neonatal abnormalities observed in offspring from transgenic NT embryos.

• Proceedings of the IEEK Conference
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• 2003.07d
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• pp.1275-1278
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• 2003

본 논문에서는 오차 역전파 알고리즘의 전역 최소값을 찾지 못하는 문제점에 대해서 설명하였고, 이 문제를 해결하기 위한 방법으로 유전자 알고리즘에 대해서 설명하였다. 오차 역전파 알고리즘은 기본적으로 경도 하강법을 따른다. 따라서 신경망의 각 가중값 행렬이 만드는 고차의 오차 평면이 대부분의 문제에서 다수의 국부 최소값들을 가지는게 일반적인데, 가중값의 변화가 한방으로 진행하기 시작하여, 오차가 증가되어지는 언덕이 학습 계수보다 크다면 더 이상 학습은 진행되지 않고 거기에서 빠져나가지 못한다. 따라서 초기의 위치가 중요한 역할을 하는데, 이 문제를 해결하기 위해서 유전자 알고리즘을 이용한 신경망 초기화 방법을 제안하였다. 끝으로, 간단한 실험으로 제안된 방법을 구현하고 결과에 대해서 논하였다

• The Journal of the Korean bone and joint tumor society
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• v.6 no.4
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• pp.143-151
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• 2000

Purpose : The p53 tumor suppressor gene is one of the most frequently altered genes in human malignancies. We try to explore the implication of p53 alteration in Ewing's sarcoma. Materials and Methods : We analyzed 35 paraffin blocks to explore the deletion and sequence alterations of p53. Results : Quantitative PCR analysis showed that 2 tumors showed a homozygous deletion of the gene. Mutational analysis of exons 4 to 9 of p53 by PCR-SSCP revealed that 3 tumors carry sequence alterations in exons 5 or 8, and DNA sequencing analysis identified missense point mutations. Conclusion : Taken together, our data demonstrate that p53 is genetically altered in a small fraction of Ewing's sarcoma.

• Journal of Genetic Medicine
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• v.6 no.2
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• pp.146-154
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• 2009

Multiplex ligation dependent probe amplification (MLPA) is a PCR-based method to detect gene dosage. Since its introduction, MLPA has been used to test a large number of genes for major deletions or duplications. Genetic testing, as a diagnostic tool for genetic disease, has been used primarily to identify point mutations, including base substitutions and small insertions/deletions, using PCR and sequence analysis. However, it is difficult to identify large deletions or duplications using routine PCR- gel based assays, especially in heterozygotes. The MLPA is a more feasible method for identification of gene dosage than another routine PCR-based methods, and better able to detect deleterious deletions or duplications. In addition to detection of gene dosage, MLPA can be applied to identify methylation patterns of target genes, aneuploidy during prenatal diagnoses, and large deletions or duplications that may be associated with various cancers. The MLPA method offers numerous advantages, as it requires only a small amount of template DNA, is applicable to a wide variety of applications, and is high-throughput. On the other hand, this method suffers from disadvantages including the possibility of false positive results affected by template DNA quality, difficulties identifying SNPs located in probe sequences, and analytical complications in quantitative aspects.

• Tuberculosis and Respiratory Diseases
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• v.49 no.4
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• pp.453-465
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• 2000

Background : Lung carcinogenesis is a multistage process involving alterations in multiple genes and diverse pathway. Mutational activation of oncogenes and inactivation of tumor suppressor genes, and subsequent increased genetic instability are the major genetic events. The p53 gene and FHIT gene as tumor suppressor genes contribute to the pathogenesis of lung cancer, evidenced by mutation, microsatellite instability(MI) and loss of heterozygosity(LOH). Methods : We analysed genetic mutations of p53 and FHIT gene in 29 surgical specimens of nonsmall cell lung cancer using PCR-single strand conformation polymorphism, DNA sequencing and RT-PCR. MI and LOH were analyzed in loci of D3S1285, D9S171, and TP53. Results : In 2 cases, point mutation of p53 gene was observed on exon 5. MI of 3 times and LOH of 14 times were observed in at least one locus. In terms of the location of microsatellite, D3S1285 as a marker of FH1T was observed in 5 cases out of 26 specimens; D9S171 as a marker of p16 in 5 out of 17; and TP53 as a marker of p53 in 7 out of 27. In view of histologic type, squamous cell carcinoma presented higher frequency of microsatellite alteration, compared to others. Mutation of FHIT gene was observed in 11 cases and 6 cases of those were point mutation as a silent substitution on exon 8. FHIT mRNA expression exhibited deletion on exon 6 to 9 in 4 cases among 15 specimens, presenting beta-actin normally. Conclusion : Our results show comparable frequency of genetic alteration in nonsmall cell lung cancer to previous studies of Western countries. Microsatellite analysis might have a role as a tumor marker especially in squamous cell carcinoma. Understanding molecular abnormalities involved in the pathogenesis could potentially lead to prevention, earlier diagnosis and the development of novel investigational approaches to the treatment of lung cancer.

• Proceedings of the Korean Aquaculture Society Conference
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• 2005.05a
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• pp.84-84
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• 2005