본 연구에서는 감마선으로 유도된 돌연변이체들에서 공통으로 발현되는 방사선 관련 유전자들의 발현을 연구하기 위하여, B. lentimorbus WJ5 의 방사선 유도 돌연변이체에서 발현되는 유전자를 DNA microarray로 동시에 탐색하였다. DNA microarray는 B. lentimorbus WJ5 genome을 무작위로 절단하여 2,000 단편으로 구성하였으며, 감마선 (60/Co)으로 유도된 7 돌연변이체의 발현을 정량적으로 관찰하였

To identify genes implicated in the control of pluripotency as well as characteristics of stem cells, we analyzed expression profiles of genes derived from mouse morulas, blastocysts, embryonic stem cells, mesenchymal stem cells, and uterus tissue using cDNA microarray. Comparative analyses of their expression profiles identified putative clones that expressed specifically in specific samples or not in a specific sample. The expression pattern of these condidate clones was analyzed using RT-PCR and non-radioactive in situ hybridization. Functional annotation of these clones on pluripotency and stem cell plasticity is in ongoing. These studies may further our understanding on the nature of the stem cells and molecular mechanisms underlying many facets of mammalian development and differentiation.

Expression profiling was conducted with the Oryza sativa alternative splicing detecting microarray v.4 (OsASDM). Probe features are designed based on rice genome IRGSP_1.0 (http://rapdb.dna.affrc.go.jp/ ). The genome contains 37,868 genes. Among these 5,254 genes have alternative spliced sites, 11,938 transcripts. In the microarray, a total of 41,953 transcripts are covered from all the loci and 9112 alternative spliced transcripts. Four 60-nt long probes were designed from each transcript starting 60 bp ahead the end of stop codon and with shifting 30 bp so 4 probes cover 150 bp in the 3’ region of the gene. Genes from chloroplast (123) and mitochondria (74) and selection markers such as gfp, gus, hyg, bar, and kan are included. In total, he 125,956 probes were designed. To find organ specific transcripts RNA was prepared from leaf, root, panicle at 1 cm (P1cm). The signal intensity files were analyzed with limma package. Background correction and normalization were performed with libraries in the package. 13,486 genes are organ specific and 1,856 transcripts are alternatively spliced. Transcripts that specifically alternatively spliced in leaf are Os02t0197600-02_UE; Chlorophyll a-b binding protein 8, Os11t0707000-01_UE; Ribulose bisphosphate carboxylase/oxygenase, Os12t0291100-01_UE; ribulose 1,5-bisphosphate carboxylase small subunit. Transcripts that specifically alternatively spliced in root are Os03t0669100-02_UE; Deoxyuridine 5’-triphosphate nucleotidohydrolase, Transcripts that specifically alternatively spliced in tissues at P1cm are Os11t0210300-02_UE; Alcohol dehydrogenase 1, Os04t0631200-02_UE; Xyloglucan endotransglycosylase. Os03t0669100-02_UE ; Deoxyuridine 5’-triphosphate nucleotidohydrolase, Os11t0210300-02_UE ; Alcohol dehydrogenase 1, Os04t0631200-02_UE; Xyloglucan endotransglycosylase. These results show that OsASDM could be used to find alternatively spliced gene at ease.

Salt and drought stresses affect virtually every aspect of plant physiology and metabolism and thus limiting the productivity of crop plants worldwide. Salt and drought tolerance and adaptation in rice has been improved by engineering various genes related to transcription, signaling, accumulation of antioxidants and compatible solutes etc. Previously, we have produced 2,000 non-GM mutants induced by Tos17 in rice. We analyzed >2,000 flanking sequences of newly transposed Tos17 copies by the adaptor-ligation PCR method. We also identified significantly up- or down-regulated genes under drought, salt, or ABA stress in rice based on expression microarray data, which previously were performed from leaf at different developmental stages and conditions. For screening and characterizing the salt or drought tolerance mutations by extensive phenotypic analysis as well as the functional analysis of genes, we selected 133 mutant lines. To evaluate rice phenotypic traits under abiotic stress condition, we plan to investigate phenomics, which integrates technologies such as photonics, biology, computers, and robotics.

Microarray technology provides a unique tool for the determination of gene expression at the level of messenger RNA (mRNA). This study, the mRNA expression profiles provide insight into the mechanism of action of cadmium in Fleshy shrimp (Fenneropenaeus chinensis). The ability of genomic technologies was contributed decisively to development of new molecular biomarkers and to the determination of new possible gene targets. Also, it can be approach for monitoring of trace metal using oligo-chip microarray-based in potential model marine user level organisms. 15K oligo-chip for F. chinensis that include mostly unique sets of genes from cDNA sequences was developed. A total of 13,971 spots (1,181 mRNAs up- regulated and 996 down regulated) were identified to be significantly expressed on microarray by hierarchical clustering of genes after exposure to cadmium for different conditions (Cd24-5000 and Cd48-1000). Most of the changes of mRNA expression were observed at the long time and low concentration exposure of Cd48-1000. But, gene ontology analysis (GO annotation) were no significant different between experiments groups. It was observed that mRNA expression of main genes involved in metabolism, cell component, molecular binding and catalytic function. It was suggested that cadmium inhibited metabolism and growth of F. chinensis .

Chinese cabbage is one of most important vegetable crop in Eastern Asian countries including Korea. Because Chinese cabbage is a leafy vegetable, genetic research with respect to the leaf morphology is important. In this research, we have used two inbred lines of Chinese cabbages (Kenshin and RCBr) and generated recombinant lines having various leaf morphology. In F2 population of Kenshin X RCBr, leaf shape showed very dramatic variations with normal distribution in terms of leaf size, petiole length, leaf margin and etc. Microarray with a 135K DNA chip (version 3) integrated 2 sets of total Chinese cabbage genes. Biological process of candidate genes was classified into transcription factor, genes encoding kinase activity protein, protein folding related genes, oxidation-reduction process genes. Putative leaf-morphology-related genes were 142 that are involed in phytohormone pathway genes, cell proliferation & cell elongation related genes and genes controlling leaf morphogenesis etc. These genes are further classified to phytohormone signaling-associated genes (SAUR44, PIN2, CPK6, RDUF2), leaf development regulating genes (DWF4, CUC2, TCP15, BLH4, NGA4), and cell division and cell growth related genes (ILP1, TCTP, EMB1027).

Early growth response 1 (Egr1) is a zinc-finger transcription factor to direct second-wave gene expression leading to cell growth, differentiation and/or apoptosis. While it is well-known that Egr1 controls transcription of an array of targets in various cell types, downstream target gene(s) whose transcription is regulated by Egr1 in the uterus has not been identified yet. Thus, we have tried to identify a list of potential target genes of Egr1 in the uterus by performing multi-step in silico promoter analyses. Analyses of mRNA microarray data provided a cohort of genes (102 genes) which were differentially expressed (DEGs) in the uterus between Egr1(+/+) and Egr1(–/–) mice. In mice, the frequency of putative EGR1 binding sites (EBS) in the promoter of DEGs is significantly higher than that of randomly selected non-DEGs, although it is not correlated with expression levels of DEGs. Furthermore, EBS are considerably enriched within –500 bp of DEG’s promoters. Comparative analyses for EBS of DEGs with the promoters of other species provided power to distinguish DEGs with higher probability as EGR1 direct target genes. Eleven EBS in the promoters of 9 genes among analyzed DEGs are conserved between various species including human. In conclusion, this study provides evidence that analyses of mRNA expression profiles followed by two-step in silico analyses could provide a list of putative Egr1 direct target genes in the uterus where any known direct target genes are yet reported for further functional studies.

본 연구는 벼에서 양성자 펌프의 활성을 증가시키는 것으로 알려진 오옥실 결합단백질 ABP57 유전자의 과발현에 따른 분자생물학적 특성을 분석해 작물 분자육종을 위한 기초자료로 활용하고자 수행하였다.ABP57 유전자 과발현 형질전환체와 대비 품종 낙동벼의 뿌리조직에서 유전자 발현 변화를 비교 분석한 결과는 다음과 같다. 두 식물체간에 발현량이 2배 이상 차이를 보인 유전자 수는 29,389개 중 총 148개였으며, 그 가운데 65개는 발현량 증가를 보였다. ABP57 유전자 과발현 형질전환체에서 발현량 변화를 보인 유전자들의 생물적 기능을 분석하기 위해 유전자 온톨로지 분석을 수행한 결과 각 부문별로 생물적 작용 부문에 67개 세부항, 세포 구성요소 부문에 59개 세부항, 분자기능 부문에 29개 세부항에 각각 영향을 미치는 것으로 나타났다. ABP57 유전자 과발현에 따라 세 개 부문 모두에서 공통적으로 나타난 영향은 H+-ATPases의 활성 증가, 여기에 필요한 에너지원 관련 화합물(ATPs, purines) 생합성 및 대사관련 활동 증가, 이온의 막투과 및 운반체 활동 증가 등이 확인되어 Kim et al.(2001)의 선행 연구결과와 일치하는 경향이었다. 그러나, 엽록체의 일부 구성요소나 G-protein 결합 단백질 신호전달경로, cytokine 신호전달 경로 등과 관련된 단백질 활성 감소는 식물 생육에 부정적 영향을 미칠 것으로 추정된다.따라서, 향후 작물의 효율적 분자육종을 위해서는 개별 유전자의 명확한 기능 분석과 더불어 유전자 상호작용에 대한 네트워크 분석 등에 대한 연구개발 노력과 함께 형질전환 식물체에 대한 생리적 특성, 표현형, 농업형질 특성 등에 대한 효과적 분석을 위해 전통육종과의 지속적 교류와 협력이 반드시 필요할 것이다.

This study was carried out to identify Korean ginseng cultivars using peptide nucleic acid (PNA) microarray. Sixty-seven probes were designed based on nucleotide variation to distinguish Korean ginseng cultivars of Panax ginseng. Among those PNA probes, three (PGB74, PGB110 and PGB130) have been developed to distinguish five Korean ginseng cultivars. Five Korean ginseng cultivars were denoted as barcode numbers depending on their fluorescent signal patterns of each cultivar using three probe sets in the PNA microarray. Five Korean ginseng cultivars, Chunpoong, Yunpoong, Gopoong, Gumpoong and Sunpoong, were simply denoted as '111', '222', '211', '221' and '122', respectively. This is the first report of PNA microarray which provided an objective and reliable method for the authentication of Korean ginseng cultivars. Also, the PNA microarray will be useful for management system and pure guarantee in ginseng seed.

Citrus is one of the major fruits produced in Korea. There are about 20 species mainly grown in Jeju Island, Korea. Four representative species, which are quite different in the shape of leaf and the taste of fruit, were selected and were used to profile the transcriptomes. These species are ‘Miyagawa Wase’ (C. unshiu Marcov.) satsuma mandarin, ‘Kiyomi’ (C. unshiu Marcov. × C. sinensis) mandarin hybrid, ‘Dangyuja’ (C. grandis) and ‘Natsudaidai’ (C. natsudaidai). Classification of the up-regulated and down-regulated genes using the Cluster of Orthologous Groups of proteins (COG) database reveals that the number of genes included in each group differed significantly among the four species. Several genes that showed significant differences in expression on the microarray were selected and their expression patterns were examined by reverse transcription- ploymerase chain reaction. Metabolic genes such as tyrosine decarboxylase and β-glucosidase ligase were found to be highly expressed in Miyagawa Wase, relative to other species. On the other hand, the expression level of mannose phosphate isomerase was lower in Miyagawa Wase. An efflux pump gene was found to be up-regulated in Kiyomi, whereas cinnamyl-alcohol dehydrogenase was down-regulated. β-carotene 15,15’-dioxygenase, which is involved in the vitamin metabolism, was up-regulated in Natsudaidai. Interspecific differentiations of gene expression are analyzed in terms of the metabolic pathways and their possible roles in citrus species.

For sensitive and accurate gene expression analysis, normalization of gene expression data against housekeeping genes is required. There are conventional housekeeping gene (e.g. ACT) that primarily function as an internal control of transcription. In this study, we performed an in silico analysis of 278 rice gene expression samples (GSM) in order to identify the gene that is most consistently expressed. Based on this analysis, we identified novel candidate housekeeping genes that displayed improved stability among the cross experimental conditions. Furthermore four of the most conventional housekeeping genes were included in our 30 other housekeeping genes among the most stable genes. Therefore, these 30 genes can he used to normalize transcription results in gene expression studies on rice at a broad range of experimental conditions.

콩에서 발생하는 세균성 병해 중 가장 문제시 되고 있는 콩불마름병의 저항성 유전자를 Microarray 분석을 통해 유전자를 탐색 하고자 본 연구를 수행중이다. 콩불마름병 병원균접종 후 3시간, 12시간, 1일, 3일, 그리고 10일 후의 저항성에 대한 유의성을 ANOVA로 한 결과 총 42,564개의 Probe 중에서 268개의 probe들에서 유의 성이 있는 것으로 나타났다. 위에서 선발된 불마름병 저항에 유의성을 나타내는 probe들의 각 시간대별 양상 을 보면 3시간 후에 control과 비교하여 3배이상 발현을 나타내는 probe수는 5개이며 12시간은 43개이며 1일차 는 10개, 3일차는 29개이며 10일차는 probe수 가 3개였다. 이 결과를 보면 12시간에 저항성 유전자 발현이 가장 활발하게 나타나 나는 것을 볼 수 있다. 또한 선발된 유전자들 중 2개 이상의 probe 들에서 공통적으로 콩 불마름병 저항성 유전자들로 선발되는 것도 있다. 본 연구결과는 콩 불마름병 저항성 품종 분자육종 및 기능연구에 활용할 수 있는 것으로 기대된다.