• Journal of fish pathology
• /
• v.23 no.3
• /
• pp.429-440
• /
• 2010

We constructed a rock bream (Oplegnathus fasciatus) gill cDNA library and a total of 1450 expressed sequence tag (EST) clones were generated. Gene annotation procedures and homology searches of the sequenced ESTs were locally done by BLASTX for amino acid similarity comparisons. Of the 1450 EST clones, 1022 EST clones showed significant homology to previously described genes while 428 ESTs were unidentified, and 259 clones were hypothetical, or unnamed proteins. Encoding 313 different sequences were identified as putative bio-defense genes or genes associated with immune response.

• Korean Journal of Fisheries and Aquatic Sciences
• /
• v.35 no.6
• /
• pp.676-681
• /
• 2002

Different types of transcripts encoding growth hormone (GH) were identified from cDNA libraries constructed with pituitaries of a marine fish species, greenling (Hexagrammos otakii). GH-homologous cDNA clones were isolated using the high-density filter hybridization and the expressed sequence tag techniques. Of 39 full-length positive cDNA clones, 31 clones ($79\%$) displayed an identical sequence, however, remaining 8 clones exhibited several polymorphisms in their sequences including (1) the length and sequence variability in the 5' upstream region, (2) insertional sequences in open reading frame, and (3) deletion and/or single nucleotide polymorphism in the untranslated 3' region. Based on RT-PCT and RNA dot blot analyses, these transcripts were proven to be expressed in a pituitary-specific manner.

• Archives of Pharmacal Research
• /
• v.27 no.4
• /
• pp.422-428
• /
• 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.

• Journal of Plant Biology
• /
• v.38 no.4
• /
• pp.381-388
• /
• 1995

Four cONA clones expressed in late root nodules of Canavalia lineata were isolated by differential screening using total RNA from uninfected roots, Clb1 and uricase II cONAs as competitors and named Cnod1, Cne2, Cne3 and Clb2, respectively. Cnod1, hybridized to 1450 nt mRNA, was highly homologous to cysteine proteinase gene from rice and showed nodule-specific expression, especially in late nodules. Cne2, hybrdized to 900 nt mRNA, was moderately homologous to Expressed Sequence Tag of rice and expressed mainly in root nodules. Its expression was increased at 13 OAI and subsequently remained at the same level. Cne3, hybridized to 1700 nt and 1400 ot mRNAs, was highly homologous to tonoplast membrane intrinsic protein TRG31 gene from pea and was expressed strongly in roots and nodules, but weakly in leaves. Temporal expression pattern of Cne3 was coincided with the life cycle of root nodules. Clb2, hybridized to 800 nt mRNA, was expressed from 8 OAI, amplified at 13 DAI and remained steady thereafter.eafter.

• Asian-Australasian Journal of Animal Sciences
• /
• v.21 no.1
• /
• pp.11-18
• /
• 2008

We created a cDNA microarray representing approximately 3,500 pig genes for functional genomic studies. The array elements were selected from 6,494 cDNA clones identified in a large-scale expressed sequence tag (EST) project. These cDNA clones came from normalized and subtracted porcine adipose tissue cDNA libraries. Sequence similarity searches of the 3,426 ESTs represented on the array using BLASTN identified 2,790 (81.4%) as putative human orthologs, with the remainder consisting of "novel" genes or highly divergent orthologs. We used the gene microarray to profile transcripts expressed by adipose tissue of fatty Chinese Xiang pig (XP) and muscley Large White (LW). Microarray analysis of RNA extracted from adipose tissue of fatty XP and muscley LW identified 81 genes that were differently expressed two fold or more. Transcriptional differences of four of these genes, adipocyte fatty acid binding protein (aP2), stearyl-CoA desaturase (SCD), sterol regulatory element binding transcription factor 1 (SREBF1) and lipoprotein lipase (LPL) were confirmed using SYBR Green quantitative RT-PCR technology. Our results showed that high expression of SCD and SREBF1 may be one of the reasons that larger fat deposits are observed in the XP. In addition, our findings also illustrate the potential power of microarrays for understanding the molecular mechanisms of porcine development, disease resistance, nutrition, fertility and production traits.

• Journal of Plant Biotechnology
• /
• v.29 no.3
• /
• pp.161-170
• /
• 2002

For the hairy root of Panax ginseng, we have got mass spectrums from MALDI/TOF/MS analysis and Tandem mass spectrums from ESI/Q-TOF/MS analysis. While mass spectrum provides the molecular weights of peptide fragments digested by protease such as trypsin, tandem mass spectrum produces amino acid sequence of digested peptides. Each amino acid sequences can be a query sequence in BLAST search to identify proteins. For the specimens of animals or plants of which genome sequences were known, we can easily identify expressed proteins from mass spectrums with high accuracy. However, for the other specimens such as ginseng, it is difficult to identify proteins with accuracy since all the protein sequences are not available yet. Here we compared the mass spectrums and the peptide amino acid sequences with ginseng expressed sequence tag (EST) DB. The matched EST sequence was used as a query in BLAST search for protein identification. They could offer the correct protein information by the sequence alignment with EST sequences. 90% of peptide sequences of ESI/Q-TOF/MS are matched with EST sequences. Comparing 68% matches of the same sequences with the nr database of NCBI, we got more matches by 22% from ginseng EST sequence search. In case of peptide mass fingerprinting from MALDI/TOF/MS, only about 19% (9 proteins of 47 spots) among peptide matches from nr DB were correlated with ginseng EST DB. From these results, we suggest that amino acid sequencing using tandem mass spectrum analysis may be necessary for protein identification in ginseng proteome analysis.

• Proceedings of the Korean Society of Developmental Biology Conference
• /
• 2005.10a
• /
• pp.76-77
• /
• 2005

• Proceedings of the Korean Society of Embryo Transfer Conference
• /
• 2005.10a
• /
• pp.76-77
• /
• 2005

• Journal of Aquaculture
• /
• v.18 no.2
• /
• pp.81-85
• /
• 2005

We isolated two parvalbumin cDNAS by expressed sequence tag analysis (1,577 ESTs in total) from the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae). Two isoforms of parvalbumin genes showed high similarity to those of carp at 88% and 91% amino acid residues identity, respectively, and showed 79.8% similarity between two parvalbumin isoforms. Of 1,577 ESTs from R. marmroatus sequenced, parvalbumin 1 gene was most abundant. This gene was strongly expressed in the order of muscle, eye, and brain, while it was expressed slightly in other tissues. In this paper, we discussed on the R. marmoratus parvalbumin genes on its sequence and basic characteristics.

• Korean Journal of Ichthyology
• /
• v.18 no.4
• /
• pp.283-292
• /
• 2006

Expressed sequence tag (EST) analysis was conducted using a complementary DNA (cDNA) library made from the kidney mRNA of olive flounder (Paralichthys olivaceus). In the survey of 390 ESTs chosen from the kidney cDNA library, 250 ESTs showed significant homology to previously described genes while 140 ESTs were unidentified or novel. Comparative analysis of the 250 identified ESTs showed that 14 (5.6%) clones were representing 11 unique genes identified as homologous to the previously reported olive flounder ESTs, 198 (79.2%) clones representing 160 unique genes were identified as orthologs of known genes from other organisms, and orthologs were established for 38 (15.2%) clones representing 37 genes of known sequences with unknown functions. We also identified several kinds of immune associated proteins, indicating EST as a powerful method for identifying immunerelated genes of fish as well as identifying novel genes. Further studies using cDNA microarrays are needed to identify the differentially expressed transcripts after disease infection.