• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.140-140
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• 2017

Nutritious and functional foods from crop have received great attention in recent years. Colored-grain wheat contains high phenolic compound and a large number of flavonoid. The anthocyanin and polyphenolic synthesis and accumulation is generally stimulated in response to biotic or abiotic stresses. Here, we analyzed genome wide transcripts in seedling of colored-grain wheat response to ABA and PEG treatment. About 900 and 1500 transcripts (p-value < 0.05) from ABA and PEG treatment were aligned to IWGSC1+popseq DB which is composed of over 110,000 transcripts including 100,934 coding genes. NR protein sequences of Poaceae from NCBI and protein sequence of transcription factors originated from 83 species in plant transcription factor database v3.0 were used for annotation of putative transcripts. Gene ontology analysis were conducted and KEGG mapping was performed to show expression pattern of biosynthesis genes related in flavonoid, isoflavonoid, flavons and anthocyanin biopathway. DroughtDB (http://pgsb.helmholtz-muenchen.de/droughtdb/) was used for detection of DEGs to explain that physiological and molecular drought avoidance by drought tolerance mechanisms. Drought response pathway, such as ABA signaling, water and ion channels, detoxification signaling, enzymes of osmolyte biosynthesis, phospholipid metabolism, signal transduction, and transcription factors related DEGs were selected to explain response mechanism under water deficit condition. Anthocyanin, phenol compound, and DPPH radical scavenging activity were measured and antioxidant activity enzyme assays were conducted to show biochemical adaptation under water deficit condition. Several MYB and bHLH transcription factors were up-regulated in both ABA and PEG treated condition, which means highly expressed MYB and bHLH transcription factors enhanced the expression of genes related in the biosynthesis pathways of flavonoids, such as anthocyanin and dihydroflavonols in colored wheat seedlings. Subsequently, the accumulation of total anthocyanin and phenol contents were observed in colored wheat seedlings, and antioxidant capacity was promoted by upregulation of genes involved in maintaining redox state and activation of antioxidant scavengers, such as CAT, APX, POD, and SOD in colored wheat seedlings under water deficit condition. This work may provide valuable and basic information for further investigation of the molecular responses of colored-grain wheat to water deficit stress and for further gene-based studies.

• The Journal of Korean Society of Virology
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• v.28 no.3
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• pp.267-274
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• 1998

Human cytomegalovirus (HCMV) has the ability to activate the expression of many viral and cellular genes. Among various viral proteins, the immediate early proteins (IE1-72kDa, IE2-86kDa) have been known to be potent transactivators. The product of c-jun proto-oncogene is important in cell activation and differentiation. Here, we tried to find out if the IE could activate the c-jun promoter and also tried to identify the responsible sequence elements in the c-jun activation by IE1-72kDa. We found HCMV IE expression transactivated the c-jun promoter in human embryonal lung fibroblasts (HEL). The activation fold by IE1-72kDa, IE2-86kDa and IE2-55kDa was 23, 35, and 5, respectively. When the expression of each IE was combined, it showed synergism. Expression of (IE1-72kDa + IE2-86kDa) and (IE1-72kDa + IE2-86kDa + IE2-55kDa) resulted in 131 and 162 fold increase, respectively. The c-jun promoter region between -117 and -59 contains binding sites for the transcription factors Spl, CAAT, AP-l like (ATF/CREB), and MEF2. Transient expression assays were performed using various reporter plasmids containing the c-jun promoter-regulatory region linked to the luciferase gene and a plasmid expressing HCMV IE1 gene. Deletional and point mutational analysis showed that the sequence between -225 to -160 and the CTF binding site were involved in the up-regulation of c-jun promoter.

• Korean Journal of Poultry Science
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• v.42 no.4
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• pp.315-325
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• 2015

Recently, livestock breeding is more focused on the meat quality rather than meat quantity, mainly due to the improvement of consumers' income. Among the meat quality traits, meat color is one of very important traits because meat color is the first selection criterion from the consumers in the market. Most of the economically important traits have continuous variations and these are called quantitative traits. the genomic locations affecting these traits are called quantitative trait locus (QTL), which is mostly controlled by many genes having small effects. In this study, the recent QTL and candidate gene studies were reviewed in order to meet the consumers' demand for the future market. In the chicken QTL database, three traits are related with meat colors, namely breast color (Bco), meat color (Mco), drip loss (DL) and pH. The identified number of QTLs is 33 from 13 chromosomal regions. In these QTL regions, 14 candidate genes were identified; Eight for meat color (APP, BCMO1, COL1A2, FTO, KPNA2, PSMD12, G0S2, FTSJ3), two for drip loss (AGRP, FTO) and four for pH (GALNT1, PCDH19, DIAPH1, SPP2). These QTLs and candidate genes need to be confirmed and fine mapping is ultimately needed for identification of causative variations. The recently developed chicken resource population using Korean native chicken can be used for the improvement of meat quality traits, which increase the value that needed in the chicken industry.

• Clinical and Experimental Reproductive Medicine
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• v.23 no.3
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• pp.367-377
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• 1996

Genes on the long arm of Y chromosome, particularly interval 6, are believed to playa critical role in human spermatogenesis. The objective of this study was to validate a sequenced-tagged site(STS)-mapping strategy for the detection of Yq microdeletion and to use this method to determine the proportion of men with Yq microdeletions in idiopathic, obstructive, nonobstructive azoospermia, severe OATS and in normal males. We analyzed three STS markers mapped to interval 6 within long arm of the Y chromosome from 106 nonobstructive, 30 obstructive azoospermia, 15 severe OATS patients, and normal 42 males in Korean men. By PCR, we tested leukocyte DNA, for the presences of STS markers(DAZ, sY129 and sY134) and SRY gene as internal control. And PCR results were confirmed by Southern hybridization, and were investigated by SSCP analysis for DAZ gene mutation. None of 42 normal males and 30 obstructive azoospermia had microdeletions, Of the 15 severe OATS typed with DAZ, sY129 and sY134, 3(20.0%) patients failed to amplify 1 or more STS markers, and of the 106 nonobstructive azoospermia typed with DAZ, sY129 and sY134, 12(11.3%) patients failed to amplify 1 or more STS markers. From these results, high prevalence(12.4%) of Yq deletion(DAZ, sY129, sY134) in men with nonobstructive idopathic azoospermia and severe OATS were observed in Korean infertility patients. To avoid the infertile offspring by assisted reproductive technique using ICSI or ROSI, genetic diagnosis will be needed in IVF-ET program.

• Animal Bioscience
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• v.36 no.4
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• pp.570-583
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• 2023

Objective: Fibroblast growth factors (FGFs) play critical roles in embryo development, and immune responses to infectious diseases. In this study, to investigate the roles of FGFs, we performed genome-wide identification, expression, and functional analyses of FGF family members in chickens. Methods: Chicken FGFs genes were identified and analyzed by using bioinformatics approach. Expression profiles and Hierarchical cluster analysis of the FGFs genes in different chicken tissues were obtained from the genome-wide RNA-seq. Results: A total of 20 FGF genes were identified in the chicken genome, which were classified into seven distinct groups (A-F) in the phylogenetic tree. Gene structure analysis revealed that members of the same clade had the same or similar exon-intron structure. Chromosome mapping suggested that FGF genes were widely dispersed across the chicken genome and were located on chromosomes 1, 4-6, 9-10, 13, 15, 28, and Z. In addition, the interactions among FGF proteins and between FGFs and mitogen-activated protein kinase (MAPK) proteins are limited, indicating that the remaining functions of FGF proteins should be further investigated in chickens. Kyoto encyclopedia of genes and genomes pathway analysis showed that FGF gene interacts with MAPK genes and are involved in stimulating signaling pathway and regulating immune responses. Furthermore, this study identified 15 differentially expressed genes (DEG) in 21 different growth stages during early chicken embryo development. RNA-sequencing data identified the DEG of FGFs on 1- and 3-days post infection in two indigenous Ri chicken lines infected with the highly pathogenic avian influenza virus H5N1 (HPAIV). Finally, all the genes examined through quantitative real-time polymerase chain reaction and RNA-Seq analyses showed similar responses to HPAIV infection in indigenous Ri chicken lines (R² = 0.92-0.95, p<0.01). Conclusion: This study provides significant insights into the potential functions of FGFs in chickens, including the regulation of MAPK signaling pathways and the immune response of chickens to HPAIV infections.

• Journal of Plant Biotechnology
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• v.35 no.4
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• pp.265-274
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• 2008

Glutathione S-transferases (GSTs) are multifunctional proteins encoded by a large gene family divided into Phi, Tau, Theta, Zeta, Lambda and DHAR classes on the basis of sequence identity. The Phi(F) and Tau(U) classes are plant-specific and ubiquitous. Their roles have been defined as herbicide detoxification and responses to biotic and abiotic stresses. Fifty-two members of the GST super-family were identified in the Arabidopsis thaliana genome, 13 members of which belong to the Phi class of GSTs (AtGSTFs). Based on the sequence similarities of AtGSTFs, 11 BAC clones were identified from Brassica rapa. Seven unique sequences of ORFs designated the Phi class candidates of GST derived from B. rapa (BrGSTFs) were detected from these 11 BAC clones by blast search and sequence alignment. Some of BrGSTFs were present in the same BAC clones indicating that BrGSTFs could also be clustered as usual in plant. They were mapped on B. rapa linkage group 2, 3, 9 and 10 and their nucleotide and amino acid sequences were highly similar to those of AtGSTFs. In addition, in silico analysis of BrGSTFs using Korea Brassica Genome Project 24K oligochip and microarray database for cold, salt and drought stresses revealed 15 unigenes to be highly similar to AtGSTFs and six of these were identical to one of BrGSTFs identified in the BAC clones indicating their expression. The sequences of BrGSTFs and unigenes identified in this study will facilitate further studies to apply GST genes to medical and agriculture purposes.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.42 no.4
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• pp.392-402
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• 1997

The morphological traits of different types of primary trisomics(2n=28＋1) in durum wheat, Triticum durum var. hordeiforme(2n=28 AABB) were compared with disomics (2n=28) through the examination of reciprocal gene action on the extra chromosomes. However it was not easy to distinguish morphologically the trisomies containing A genome from those containing B genome. These results suggested that the chromosomal location of the major genes for some morphological traits exists on homoeologous chromosome. It is important that these results revealed the homoeology and linkage groups of both A and B genomes in durum wheat. These primary trisomies will be valuable materials for the trisomic analysis and genetic mapping on the chromosome of both A and B genomes in durum wheat. Furthermore, it must be useful for the evolutionary study of Triticum durum(AABB) and Triticum squarrosa(DD) by way of the ancester species of Triticum aesitivum(AABBDD).

• Journal of Sericultural and Entomological Science
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• v.42 no.1
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• pp.14-23
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• 2000

The mitochondrial genome of domesticated silkworm (Bombyx mori) was mapped with five restriction endonucleases (BamHI, EcoRI, HindIII, PstI and XbaI), the entire genome was cloned with HindIII and EcoRI. From the end sequencing results of 5$^1$and 3$^1$region for full genome set of eleven mitochondrial clones, the seven mitochondrial genes (NADH dehydrogenase 6, ATPase 6, ATPase 8, tRN $A^{Lys}$, tRN $A^{Asp}$, tRN $A^{Thr}$ and tRN $A^{Phe}$ of mori were identified on the basis of their nucleotide sequence homology. The nucleotide composition of NADH dehydrogenase 6 was heavily biased towards adenine and thymine, which accounted for 87.76%. On basis of the sequence similarity with published tRNA genes from six insect species, the tRN $A^{Lys}$, tRN $A^{Asp}$ and tRN $A^{Thr}$ were showed stable canonical clover-leaf tRNA structures with acceptible anticodons. However, both the DHU and T$\psi$C arms of tRN $A^{Phe}$ could not form any stable stem-loop structure. The two overlapping gene pairs (tRN $A^{Lys}$ -tRN $A^{ASP}$ and ATPase8-ATPase6) were found from our sequencing results. The genes are encoded on the same strad. ATPase8 and ATPase6 overlaps (ATGATAA) which are a single example of overlapping events between abutted protein-coding genes are common, and there is evidence that the two proteins are transcribed from a single bicistronic message by initiation at 5$^1$terminal start site for ATPase8 and at an internal start site for ATPase6. Ultimately, this result will provide assistance in designing oligo-nucleotides for PCR amplification, and sequencing the specific mitochondrial genes for phylogenetics of geographic races, genetically improved silkworm strains and wild silkworm (mandarina) which is estimated as ancestal of domesticated silkworm.sticated silkworm.

• Journal of the Korean Society of Surveying, Geodesy, Photogrammetry and Cartography
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• v.29 no.2
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• pp.141-147
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• 2011

This study analyzed the issues and its usefulness of drawing small-scale digital map by using the large-scale digital map which was producted with high-resolution digital aerial photograph which are commonly photographed in recent years. To this end, correlation analysis of the feature categories on the digital map was conducted, and this map was processed by inputting data, organizing, deleting, editing, and supervising feature categories according to the generalization process. As a result, 18 unnecessary feature codes were deleted, and the accuracy of 1/5,000 for the digital map was met. Although the size of the data and the number of feature categories increased, this was proven to be shown due to the excellent description of the digital aerial photograph. Accordingly, it was shown that drawing a small-scale digital map with the large-scale digital map by digital aerial photograph provided excellent description and high-quality information for digital map.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2001.10a
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• pp.165-196
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• 2001

DNA chip 또는 microarray는 다수의 유전자 또는 유전자 조각을 (보통 수천내지 수만 개)칩상에 고정시켜 놓고 DNA hybridization 반응을 이용하여 유전자들의 발현 양상을 분석할 수 있는 기술이다. 이러한 high-throughput기술은 예전에는 생각하지 못했던 여러가지 분자생물학의 문제에 대한 해답을 제시해 줄 수 있을 뿐 만 아니라, 분자수준에서의 질병 진단, 신약 개발, 환경 오염 문제의 해결 등 그 응용 가능성이 무한하다. 이 기술의 실용적인 적용을 위해서는 DNA chip을 제작하기 위한 하드웨어/웻웨어 기술 외에도 이러한 데이터로부터 최대한 유용하고 새로운 지식을 창출하기 위한 bioinformatics 기술이 핵심이라고 할 수 있다. 유전자 발현 패턴을 데이터마이닝하는 문제는 크게 clustering, classification, dependency analysis로 구분할 수 있으며 이러한 기술은 통계학과인공지능 기계학습에 기반을 두고 있다. 주로 사용된 기법으로는 principal component analysis, hierarchical clustering, k-means, self-organizing maps, decision trees, multilayer perceptron neural networks, association rules 등이다. 본 세미나에서는 이러한 기본적인 기계학습 기술 외에 최근에 연구되고 있는 새로운 학습 기술로서 probabilistic graphical model (PGM)을 소개하고 이를 DNA chip 데이터 분석에 응용하는 연구를 살펴본다. PGM은 인공신경망, 그래프 이론, 확률 이론이 결합되어 형성된 기계학습 모델로서 인간 두뇌의 기억과 학습 기작에 기반을 두고 있으며 다른 기계학습 모델과의 큰 차이점 중의 하나는 generative model이라는 것이다. 즉 일단 모델이 만들어지면 이것으로부터 새로운 데이터를 생성할 수 있는 능력이 있어서, 만들어진 모델을 검증하고 이로부터 새로운 사실을 추론해 낼 수 있어 biological data mining 문제에서와 같이 새로운 지식을 발견하는 exploratory analysis에 적합하다. 또한probabilistic graphical model은 기존의 신경망 모델과는 달리 deterministic한의사결정이 아니라 확률에 기반한 soft inference를 하고 학습된 모델로부터 관련된 요인들간의 인과관계(causal relationship) 또는 상호의존관계(dependency)를 분석하기에 적합한 장점이 있다. 군체적인 PGM 모델의 예로서, Bayesian network, nonnegative matrix factorization (NMF), generative topographic mapping (GTM)의 구조와 학습 및 추론알고리즘을소개하고 이를 DNA칩 데이터 분석 평가 대회인 CAMDA-2000과 CAMDA-2001에서 사용된cancer diagnosis 문제와 gene-drug dependency analysis 문제에 적용한 결과를 살펴본다.