• Journal of Applied Biological Chemistry
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• 제51권3호
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• pp.83-87
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• 2008

Tension wood, a specialized tissue developed in the upper side of the leaning stem and drooping branches of angiosperm, is an attractive experimental system attractive for exploring the development and the biochemical pathways of the secondary cell wall formation, as well as the control mechanism of the carbon flux into lignin, cellulose, and hemicellulose. However, the mechanism underlying the induction and the development of the tension wood is largely unknown. Recently, several researchers suggested the possible roles of the plant growth hormones including auxin, gibberellin, and ethylene mainly based on the expression pattern of the genes in this specialized tissue. In addition, expressed sequence tag of Poplar and Eucalyptus provide global view of the genetic control underlying the tension wood formation. However, the roles of the majority of the identified genes have not yet been clearly elucidated. The present review summarized current knowledge on the biosynthesis of tension wood to provide a brief synopsis of the molecular mechanism underlying the development of the tension wood.

• Proceedings of the Korea Information Processing Society Conference
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• 한국정보처리학회 2001년도 추계학술발표논문집 (상)
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• pp.105-108
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• 2001

cDNA(complementary DNA)를 복제(cloneing)하여 염기 서열화 한 EST(Expressed Sequence Tag) 데이터는 여러 생물체들의 염기서열 정보들과 비교를 통해 유사점을 찾거나 기능적 부위 검색을 통해 유전자 기능을 추정한 수 있어 기능 유전체 연구에 많이 사용되고 있다. EST 데이터를 식물은 특정종(Species)별로, 동물의 경우 종의 조직별로 클러스터링 함으로써 아직 알려지지 않은 종의 유전자를 밝혀낼 수 있음은 물론 유전자의 발현에 따른 단백질의 기능도 알아낼 수 있다. 따라서 이 논문에서는 NCBI에서 flatfile 형태로 제공하는 EST 데이터를 분석하여 관계형 데이터베이스로 모델링하고 구축하였다. 또한 EST 데이터의 효율적인 사용을 위하여 데이터를 특정 종의 조직별로 클러스터링하여 제공하는 시스템을 설계하고 구현하였다.

• KOREAN JOURNAL OF CROP SCIENCE
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• 제55권2호
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• pp.151-158
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• 2010

Camelina sativa L., known as popular names "gold-of-pleasure" or "false flax" is an alternative oilseed crop that can be grown under different climatic and soil conditions. Up to date, however, the genomic information of Camelina has not been studied in detail. Therefore, a cDNA library was constructed and characterized from young leaves. The constructed cDNA library incorporated of 1334 cDNA clones and the size of the insertion fragments average was 736 base pair. We generated a total of 1269 high-quality expressed sequence tags (ESTs) sequences. The result of cluster analysis of EST sequences showed that the number of unigene was 851. According to subsequent analysis, the 476 (55.9%) unigenes were highly homologous to known function genes and the other 375 (44.1%) unigenes were unknown. Remaining 63 (7.4%) unigenes had no homology with any other peptide in NCBI database, indicating that these seemed to be novel genes expressed in leaves of Camelina. The database-matched ESTs were further classified into 17 categories according to their functional annotation. The most abundant of categories were "protein with binding function or cofactor requirement (27%)", "metabolism (11%)", "subcellular localization (11%)", "cellular transport, transport facilities and transport routes (7%)", "energy (6%)", "regulation of metabolism and protein function (6%)". Our result in this study provides an overview of mRNA expression profile and a basal genetic information of Camelina as an oilseed crop.

• Journal of Life Science
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• 제27권4호
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• pp.398-407
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• 2017

BTG 1 (B-cell translocation gene 1) gene was first identified as a translocation gene in a case of B-cell chronic lympocytic leukemia. BTG1 is a member of the BTG/TOB family with sharing a conserved N-terminal region, which shows anti-proliferation properties and is able to stimulate cell differentiation. In this study, we identified and characterized the pacific oyster Crassostrea gigas BTG1 (cg-BTG1) gene from the gill cDNA library by an Expressed Sequence Tag (EST) analysis and its nucleotide sequence was determined. The cg-BTG1 gene encodes a predicted protein of 182 amino acids with 57% 56% identities to its zebrafish and human counterparts, and is an intron-less gene, which was confirmed by PCR analysis of genomic DNA. Maximal homologies were shown in conserved Box A and B. The deduced amino acid sequence shares high identity with other BTG1 genes of human, rat, mouse and zebrafish. The phylogenic analysis and sequence comparison of cg-BTG1 with other BTG1 were found to be closely related to the BTG1 gene structure. In addition, the predicted promoter region and the different transcription-factor binding site like an activator protein-1 (AP-1) response element involved in negative regulation and serum response element (SRE) were able to be identified by the genomic DNA walking experiment. The quantitative real-time PCR analysis showed that the mRNA of cg-BTG1 gene was expressed in gill, heart, digestive gland, intestine, stomach and mantle. The cg-BTG1 gene was expressed mainly in heart and mantle.

• The Journal of the Korea Contents Association
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• 제10권10호
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• pp.102-110
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• 2010

Alternative splicing is an important process in gene expression. Alternative Splicing can lead to mutations and diseases. Most studies detect alternatively spliced genes with ESTs (Expressed Sequence Tags). However, reliance on ESTs might have some weaknesses in predicting alternative splicing. ESTs have been stored in the libraries. The EST libraries are often not clearly organized and annotated. We can pick erroneous ESTs. It is also difficult to predict whether or not alternative splicing exists for those genes where ESTs are not available. To address these issues and to improve the quality of detection and prediction for alternative splicing, we propose the One-leaf One-node Tree Algorithm that uses pre-mRNAs. It is achieved by codons, three nucleotides, as attributes for each chromosome in Arabidopsis thaliana. The proposed decision tree shows that alternative and normal splicing have different splicing patterns according to triplet nucleotides in each chromosome. Based on the patterns, alternative splicing of unlabeled genes can also be predicted.

• The Plant Pathology Journal
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• 제28권4호
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• pp.409-417
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• 2012

We identified two novel expansin (EXP) genes in the expressed sequence tag database of Bursaphelenchus xylophilus, designated as Bx-EXPB2 and -EXPB3. Novel Bx-EXPBs encoded 150 amino acids and their similarities in coding sequence were 70.7-84.0% to the previously reported EXPB1 of B. xylophilus. Bx-EXPB2 and Bx-EXPB3 were clustered with Bx-EXPB1 and Bm-EXPB1, respectively, forming the independent phylogeny with other nematode EXPs. All identified Bx-EXPBs contained the signal peptide and were only expressed during the propagative stage, suggesting that they are secreted to facilitate nematode migration through hosts by loosening cell walls during infection. Quantitative real-time PCR analysis showed that the relative accumulation of Bx-EXPB3 mRNAs was the highest among the three Bx-EXPs examined and the order of mRNA accumulation was as follows: Bx-EXPB3 > Bx-EXPB2 >> Bx-EXPB1. Homology modeling of Bx-EXPBs showed that the structurally optimum template was EXLX1 protein of Bacillus subtilis, whichshared residues essential for catalytic activity with Bx-EXPB1 and Bx-EXPB2 except for Bx-EXPB3. Taken together, Bx-EXPB1 and Bx-EXPB2 may be involved migration through plant tissues and play a role in pathogenesis.

• Journal of Life Science
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• 제13권1호
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• pp.128-135
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• 2003

102 ESTs (Expressed Sequence Tags) were obtained by sequencing clones from a library of rainbow trout kidney cDNAs. Of the sequences generated, 55.8% of the ESTs were represented by 37 known genes. The 45 clones of unknown gene products potentially represent 40 novel genes. The genes involved in structural function (14.5%) and transcription/translation (11.6%) account for the major gene expression activities in the kidney Microarray experiment was conducted to compare gene expression of the unique ESTs in young and adult rainbow trout kidneys. While mitochondrion, cytochrome b, rho G, spastin protein, and three unknown genes were down-regulated in the mature fish kidney, calponin 1, calcium binding protein, histone deacetylase 1, and an unknown gene were up-regulated in the mature fish kidney. This research demonstrates the feasibility and power of functional genomics in rainbow trout.

• Parasites, Hosts and Diseases
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• 제49권4호
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• pp.341-347
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• 2011

Acanthamoeba infection is difficult to treat because of the resistance property of Acanthamoeba cyst against the host immune system, diverse antibiotics, and therapeutic agents. To identify encystation mediating factors of Acanthamoeba, we compared the transcription profile between cysts and trophozoites using microarray analysis. The DNA chip was composed of 12,544 genes based on expressed sequence tag (EST) from an Acanthamoeba ESTs database (DB) constructed in our laboratory, genetic information of Acanthamoeba from TBest DB, and all of Acanthamoeba related genes registered in the NCBI. Microarray analysis indicated that 701 genes showed higher expression than 2 folds in cysts than in trophozoites, and 859 genes were less expressed in cysts than in trophozoites. The results of real-time PCR analysis of randomly selected 9 genes of which expression was increased during cyst formation were coincided well with the microarray results. Eukaryotic orthologous groups (KOG) analysis showed an increment in T article (signal transduction mechanisms) and O article (posttranslational modification, protein turnover, and chaperones) whereas significant decrement of C article (energy production and conversion) during cyst formation. Especially, cystein proteinases showed high expression changes (282 folds) with significant increases in real-time PCR, suggesting a pivotal role of this proteinase in the cyst formation of Acanthamoeba. The present study provides important clues for the identification and characterization of encystation mediating factors of Acanthamoeba.

• Animal cells and systems
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• 제9권2호
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• pp.87-94
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• 2005

Spindle position checkpoint monitors the orientation of mitotic spindle for proper segregation of replicated chromosomes into mother cell and the daughter, and prohibits mitotic exit when mitotic spindle is misaligned. BUB2 forms one of the key upstream element of spindle position checkpoint in budding yeast, but its functional homologues have not been identified in higher eukaryotes. Here, we analyzed the functions of two putative BUB2 homologues of C. elegans in the spindle orientation checkpoint. From the C. elegans genome database, we found that two open reading frames (ORFs), F35H12_2 and C33F10_2, showed high sequence homology with BUB2. We obtained the expressed sequence tag (EST) clones for F35H12_2 (yk221d4) and C33F10_2 (yk14e10) and verified the full cDNA for each ORF by sequencing and 5' RACE with SL1 primer. The functional complementation assays of yk221d4 and yk14e10 in ${\Delta}bub2$ of S. cerevisiae revealed that these putative BUB2 homologues of C. elegans could not replace the function of BUB2 in spindle position checkpoint and mitotic exit. Our attempt to document the component of spindle position checkpoint in metazoans using sequence homology was not successful. This suggests that structural information about its components might be required to identify functional homologues of the spindle position checkpoint in higher eukaryotes.

• BMB Reports
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• 제40권6호
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• pp.952-958
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• 2007

We isolated many genes induced from pepper cDNA microarray data following their infection with the soybean pustule pathogen Xanthomonas axonopodis pv. glycines 8ra. A full-length cDNA clone of the Capsicum annuum ankyrin-repeat domain $C_3H_1$ zinc finger protein (CaKR1) was identified in a chili pepper using the expressed sequence tag (EST) database. The deduced amino acid sequence of CaKR1 showed a significant sequence similarity (46%) to the ankyrin-repeat protein in very diverse family of proteins of Arabidopsis. The gene was induced in response to various biotic and abiotic stresses in the pepper leaves, as well as by an incompatible pathogen, such as salicylic acid (SA) and ethephon. CaKR1 expression was highest in the root and flower, and its expression was induced by treatment with agents such as NaCl and methyl viologen, as well as by cold stresses. These results showed that CaKR1 fusion with soluble, modified green fluorescent protein (smGFP) was localized to the cytosol in Arabidopsis protoplasts, suggesting that CaKR1 might be involved in responses to both biotic and abiotic stresses in pepper plants.