• Title, Summary, Keyword: ESTs

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Identification of Expressed Sequence Tags of Genes Expressed Highly in the Activated Hepatic Stellate Cell

  • Lee Sung Hee;Chaen Keon-Sang;Sohn Dong Hwan
    • Archives of Pharmacal Research
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    • v.27 no.4
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    • pp.422-428
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    • 2004
  • Expressed sequence tags (ESTs) were generated from two 3'-directed CDNA libraries constructed from quiescent and activated rat hepatic stellate cell (HSC) to analyze the expression profiles of active genes in both cells. From quiescent and activated HSC, 694 ESTs and 779 ESTs, respectively, were obtained after excluding those having shorter than 30 bp. Amonq ESTs obtained from quiescent and activated HSC, 68 and 73 kinds of ESTs (186 clones and 236 clones), respectively, appeared more than once, implying that their genes are expressed highly in each cell type. 52 among 73 ESTs appeared only in the activated HSC 47 amonq 68 ESTs only in the normal HSC, and 21 in both cells. The genes of these 52 ESTs were assumed to be expressed more highly in the activated HSC. To confirm the high expression of genes of which the ESTs appeared more than twice in the activated HSC, northern hybridization was carried out with RNAs derived from rat normal and fibrotic liver using each of 18 EST DNAs as probe. 13 ESTs showed more intense bands with RNA isolated from the fibrotic liver than normal liver. From these results, we confirm the positive correlation between abundance of transcript in activated HSCs and the expression level in fibrotic liver, The expression profile of the transcripts serves as an important tool in understanding the biological properties of HSC.

Transcriptome Analysis in the Midgut of the Earthworm (Eisenia andrei) using Expressed Sequence Tags

  • Lee, Myung-Sik;Cho, Sung-Jin;Lee, Jong-Ae;Moon, Joo-Sik;Cho, Hyun-Ju;Park, Bum-Joon;Kim, Seong-Ki;Choo, Jong-Kil;Park, Soon-Cheol
    • Proceedings of the Korean Society of Sericultural Science Conference
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    • pp.144-144
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    • 2003
  • In order to understand the expression profile of earthworm midgut, we analyzed 1255 expressed sequence tags (ESTs) derived from earthworm midgut cDNA library. Among 1255 ESTs analyzed, 537 (42.8%) ESTs represented 231 unique genes of which 168 ESTs were singletons and 63 ESTs represented by two or more ESTs. A total of 571 unknown ESTs showed no significant homology. The remaining 147 (11.7%) ESTs whose lengths were less than 150 bp were removed. Among 231 identified unique genes, 168 genes (72.7%) were sequenced only once. (omitted)

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Characterization of EST Gene in the Bovine Corpus Luteum during the Estrous Cycle

  • Lee, Eunyoung;Kim, Sang Hwan;Kim, Byung-Gak;Yoon, Jong Taek
    • Development and Reproduction
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    • v.19 no.4
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    • pp.227-234
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    • 2015
  • The objective of this study was to investigate the expression of bovine luteum expressed sequence tags (ESTs), vascular endothelial growth factor (VEGF), and tumor necrosis factor receptor 1 (TNFR1) and the presence of functional ESTs in the bovine corpus luteum (CL) during different stages of the estrus cycle. Reverse transcription-polymerase chain reaction (RT-PCR) analysis showed a difference in the expression of ESTs during the CL stage. Concentration of ESTs in the CL tissue increased significantly from the mid-luteal stage and decreased thereafter. RT-PCR analysis showed higher levels of the EST genes in the CL of the mid-luteal stage than in other stages, and the same level of expression of VEGF. Immunohistochemistry analysis of the tissue from CL formation to regression showed low cytosol and aggregation of the nucleus. And activity caspase 3 (apoptosis detector) was most strongly detected in the CL1 stage of bovine. During the estrous cycle, the cytosol was magnified and differentiation of the nucleus was clearly manifested. The ESTs affected the CL, and the relationship between VEGF and TNFR1 played a pivotal role for CL development and activation, dependent on the stage of CL. These results suggest local production of ESTs, the presence of functional ESTs in the bovine CL, and that ESTs play a role in regulating the function of cell death in bovine CL.

Candidate Genes with Ovulation by Differential Display PCR in Small Tail Han Sheep

  • Liu, Shufang;Li, Hongbin;Song, Xuemei;Wang, Aihua;Wei, Caihong;Du, Lixin
    • Asian-Australasian Journal of Animal Sciences
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    • v.19 no.9
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    • pp.1229-1233
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    • 2006
  • To find the candidate genes concerned with ovulation rate of sheep, Differential Display Reverse Transcription Polymerase Chain Reaction was employed to find the differently expressed cDNA controlling ovulation in the Small Tail Han sheep of polyembryony and in Tan sheep of single birth. Twenty-four primer pairs of three anchored primers and eight arbitrary primers were assembled to amplify the specialized bands from these sheep. Positive cross tests were applied to optimize the ascertainable PCR conditions in which different special bands can be identified by silver strain in one PCR tube. After eliminating the false positive PCR products by Northern hybridization, 24 differential display bands were acquired from the ovary in the Small Tail Han sheep. These EST bands were sequenced and 18 different ESTs were found in which five ESTs had several copies and 13 ESTs had only one copy. Comparing these ESTs with homologous sequences by BLAST in the GenBank, there were six ESTs with known open reading frame (ORF) and function, three ESTs with known ORF and no function, and 9 ESTs without homologous sequence. These ESTs partly represent several genes such as NOS2, tensin, TCRA, CDKN1A, ESR1 and ACTB which express especially in Small Tail Han sheep.

KBUD: The Korea Brain UniGene Database

  • Jeon, Yeo-Jin;Oh, Jung-Hwa;Yang, Jin-Ok;Kim, Nam-Soon
    • Genomics & Informatics
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    • v.3 no.3
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    • pp.86-93
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    • 2005
  • Human brain EST data provide important clues for our understanding of the molecular biology associated with the function of the normal brain and the molecular pathophysiology with brain disorders. To systematically and efficiently study the function and disorders of the human brain, 45,773 human brain ESTs were collected from 27 human brain cDNA libraries, which were constructed from normal brains and brain disorders such as brain tumors, Parkinson's disease (PO) and epilepsy. An analysis of 45,773 human brain ESTs using our EST analysis pipeline resulted in 38,396 high-quality ESTs and 35,906 ESTs, which were coalesced into 8,246 unique gene clusters, showing a significant similarity to known genes in the human RefSeq, human mRNAs and UniGene database. In addition, among 8,246 gene clusters, 4,287 genes ($52\%$) were found to contain full-length cONA clones. To facilitate the extraction of useful information in collected these human brain ESTs, we developed a user-friendly interface system, the Korea Brain Unigene Database (KBUD). The KBUD web interface allows access to our human brain data through three major search modes, the BioCarta pathway, keywords and BLAST searches. Each result when viewed in KBUD offers comprehensive information concerning the analyzed human brain ESTs provided by our data as well as data linked to various other publiC databases. The user-friendly developed KBUD, the first world-wide web interface for human brain EST data with ESTs of human brain disorders as well as normal brains, will be a helpful system for developing a better understanding of the underlying mechanisms of the normal brain well as brain disorders. The KBUD system is freely accessible at http://kugi.kribb.re.kr/KU/cgi -bin/brain. pI.

Functional Analysis of ESTs from the Flower Bud of Korean Ginseng

  • Yang, Deok-Chun;In, Jun-Gyo;Kim, Moo-Sung;Jeon, Jong-Seong
    • Proceedings of the Plant Resources Society of Korea Conference
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    • pp.124-124
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    • 2003
  • In order to study gene expression in a reproductive organ, we constructed a cDNA library of immature flower buds in Korean ginseng and generated expressed sequence tags (ESTs) of 3,360 clones randomly selected. The ESTs could be clustered into 1,844 non-redundant groups. Similarity search of the non-redundant ESTs against public non-redundant databases of both protein and DNA indicated that 1,254 groups show similarity to genes of known function. These ESTs clones were divided into sixteen categories depending upon gene function. The most abundant transcripts were unknown protein (72), chlorophyll a/b-binding protein (48), and stylar glycoprotein. There are no useful informations of gene expression during the development of flower bud in Korean ginseng. These results could help to understand the development of flower bud in Korean ginseng.

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Generation of Expressed Sequence Tags for Immune Gene Discovery and Marker Development in the Sea Squirt, Halocynthia roretzi

  • Kim, Young-Ok;Cho, Hyun-Kook;Park, Eun-Mi;Nam, Bo-Hye;Hur, Young-Baek;Lee, Sang-Jun;Cheong, Jae-Hun
    • Journal of Microbiology and Biotechnology
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    • v.18 no.9
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    • pp.1510-1517
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    • 2008
  • Expresssed sequence tag (EST) analysis was developed from three cDNA libraries constructed from cells of the digestive tract, gonad, and liver of sea squirt. Randomly selected cDNA clones were partially sequenced to generate a total of 922 ESTs, in which 687 unique ESTs were identified respectively. Results of BLASTX search showed that 612 ESTs (89%) have homology to genes of known function whereas 75 ESTs (11%) were unidentified or novel. Based on the major function of their encoded proteins, the identified clones were classified into ten broad categories. We also identified several kinds of immune-related genes as identifying novel genes. Sequence analysis of ESTs revealed the presence of microsatellite-containing genes that may be valuable for further gene mapping studies. The accumulation of a large number of identified cDNA clones is invaluable for the study of sea squirt genetics and developmental biology. Further studies using cDNA microarrays are needed to identify the differentially expressed transcripts after disease infection.

Platform of Hot Pepper Defense Genomics: Isolation of Pathogen Responsive Genes in Hot Pepper (Capsicum annuum L.) Non-Host Resistance Against Soybean Pustule Pathogen (Xanthomonas axonopodis pv. glycines)

  • Lee, Sang-Hyeob;Park, Do-Il
    • The Plant Pathology Journal
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    • v.20 no.1
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    • pp.46-51
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    • 2004
  • Host resistance is usually parasite-specific and is restricted to a particular pathogen races, and commonly is expressed against specific pathogen genotypes. In contrast, resistance shown by an entire plant species to a species of pathogen is known as non-host resistance. Therefore, non-host resistance is the more common and broad form of disease resistance exhibited by plants. As a first step to understand the mechanism of non-host plant defense, expressed sequence tags (EST) were generated from a hot pepper leaf cDNA library constructed from combined leaves collected at different time points after inoculation with non-host soybean pustule pathogen (Xanthomonas axonopodis pv. Glycines; Xag). To increase gene diversity, ESTs were also generated from cDNA libraries constructed from anthers and flower buds. Among a total of 10,061 ESTs, 8,525 were of sufficient quality to analyze further. Clustering analysis revealed that 55 % of all ESTs (4685) occurred only once. BLASTX analysis revealed that 74% of the ESTs had significant sequence similarity to known proteins present in the NCBI nr database. In addition, 1,265 ESTs were tentatively identified as being full-length cDNAs. Functional classification of the ESTs derived from pathogen-infected pepper leaves revealed that about 25% were disease- or defense-related genes. Furthermore, 323 (7%) ESTs were tentatively identified as being unique to hot pepper. This study represents the first analysis of sequence data from the hot pepper plant species. Although we focused on genes related to the plant defense response, our data will be useful for future comparative studies.

One-Snapshot Algorithm for Secure Transaction Management in Electronic Stock Trading Systems (전자 주식 매매 시스템에서의 보안 트랜잭션 관리를 위한 단일 스냅샷 알고리즘)

  • 김남규;문송천;손용락
    • Journal of KIISE:Databases
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    • v.30 no.2
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    • pp.209-224
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    • 2003
  • Recent development of electronic commerce enables the use of Electronic Stock Trading Systems(ESTS) to be expanded. In ESTS, information with various sensitivity levels is shared by multiple users with mutually different clearance levels. Therefore, it is necessary to use Multilevel Secure Database Management Systems(MLS/DBMSs) in controlling concurrent execution among multiple transactions. In ESTS, not only analytical OLAP transactions, but also mission critical OLTP transactions are executed concurrently, which causes it difficult to adapt traditional secure transaction management schemes to ESTS environments. In this paper, we propose Secure One Snapshot(SOS) protocol that is devised for Secure Transaction Management in ESTS. By maintaining additional one snapshot as well as working database SOS blocks covert-channel efficiently, enables various real-time transaction management schemes to be adapted with ease, and reduces the length of waiting queue being managed to maintain freshness of data by utilizing the characteristics of less strict correctness criteria. In this paper, we introduce the process of SOS protocol with some examples, and then analyze correctness of devised protocol.

Analysis and Identification of Expressed Sequence Tags in Hairy Root Induced from Korean Ginseng (Panax ginseng C. A. Meyer)

  • Yang, Deok-Chun;In, Jun-Gyo
    • Korean Journal of Medicinal Crop Science
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    • v.12 no.2
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    • pp.154-162
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    • 2004
  • Hairy roots were induced from Korean ginseng (Panax ginseng C. A. Meyer) root explants and studied for their gene expression. A total of 3,000 ESTs (expressed sequence tags) from ginseng hairy root were determined and about 2,700 ESTs have a length of readable sequence, which result in 1,352 unique ESTs sequences. The 879 ESTs showed significant similarities to known nucleotide or amino acid sequences in other plant species, which were divided into eleven categories depending upon gene function. The remaining 473 sequences showed no significant matches, which are likely to be transcripts or to be matched to other organisms. The results indicated that the analysis of the ginseng hairy root ESTs by partial sequencing of random cDNA clones may be an efficient approach to isolate genes that are functional in ginseng root in a large scale. Our extensive EST analysis of genes expressed in ginseng hairy root not only contributes to the understanding of the dynamics of genome expression patterns in root organ but also adds data to the repertoire of all genomic genes.