• Korean Journal of Ichthyology
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• v.23 no.1
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• pp.1-9
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• 2011

Differentially Expressed Gene (DEG) was obtained from Differential Display Reverse Transcription (DDRT)-PCR using Annealing Control Primer (ACP) to search and clone genes related to developmental stages of Sebastes inermis. By using 120 ACPs, the nucleotide sequences obtained from 16 DEGs showing higher expression in 6-month-old skeletal muscle than 18-month-old ones and from 22 DEGs displaying stronger expression in 18-month-old than 6-month-old were analyzed and BLAST was conducted. The results identified that DEGs shared 69~95% homology with genes of parvalbumin (PVALB), nucleoside diphosphate kinase (NDK) B, tropomyosin (TPM), troponin I (TnI), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), muscle-type creatine kinase (CKM2), small EDRK-rich factor 2 (SERF2), adenosine monophosphate deaminase (AMPD), Trimeric intracellular cation channel type A (TRICA), Rho GTPase-activating protein 15 (ARHGAP15), S-formylglutathione hydrolase (Esterase D; ESD), heat shock protein 70 (hsp70), type 1 collagen alpha 2 (COL1A2), glutathione S-transferase, Mid1-interacting protein 1 (Mid1lip1), myosin light chain 1 (MYL1), sarcoplasmic/endoplasmic reticulum calcium ATPase 1B (SERCA1B), and ferritin heavy subunit (FTH1). Expression pattern by developmental stage of DEG14 and PVALB exhibiting strong expression in 6-month-old skeletal muscle was investigated using real time PCR. Expression was reduced as Sebastes inermis grew. Expression of PVALB gene was extremely low after 6 months of age. Expression of CKM2 showed higher expression in 18-month-old skeletal muscle than in 6-month-old muscles, and increased continuously until 4 years old, after which CKM2 expression became gradually reduced. By analysis of tissue-specific expression patterns of DEG, DEG14 was expressed mainly in skeletal muscle, liver, kidney and spleen tissues, whereas PVALB expression was expressed in skeletal muscle and kidney, but not in liver and spleen tissues. CKM2 was expressed in skeletal muscle, kidney, and spleen tissues, but not in liver tissues. PVALB gene was composed of 110 amino acids, which constituted 659 bp nucleotides. The results reported here demonstrate that the expression patterns of parvalbumin and CKM2 could be used as molecular markers for selecting fishes exhibiting fast growth.

• Journal of Life Science
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• v.13 no.5
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• pp.596-603
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• 2003

Cells respond to an accumulation of unfolded proteins in the endoplasmic reticulum (ER) by increasing transcription of genes encoding molecular chaperones and folding enzymes. The information is transmitted from the ER lumen to the nucleus by intracellular signaling pathway, called the unfolded protein response (UPR). To obtain genes related to UPR from B. mori, the cDNA library was constructed with mRNA isolated from Bm5 cell lines in which N-glycosylation was inhibited by tunicamycin treatment. From the cDNA library, we selected 40 clones that differentially expressed when cells were treated with tunicamycin. Among these clones, we have isolated ATFC gene showing similarity with Hac1p, encoding a bZIP transcription factor of 5. cerevisiae. Basic-leucine zipper (bZIP) domain in amino acid sequences of ATFC shared homology with yeast Hac1p. Also, ATFC is up-regulated by accumulation of unfolded proteins in the ER through the treatment of ER stress drugs. Therefore we suggest that ATFC represents a major component of the putative transcription factor responsible for the UPR leading to the induction of ER-localized stress proteins.

• Horticultural Science & Technology
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• v.30 no.2
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• pp.162-170
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• 2012

The objectives of this study were to isolate and the sequence of novel $F3'H$ gene related to an anthocyanin pathway, and to confirm the expression patterns of the gene involved in the flower color variations of chrysanthemum mutants. In this study, we isolated the full-length cDNAs and the genomic DNAs of an $F3'H$ gene from a wild type (WT) chrysanthemum (cv. Argus) and its three color mutants. The sequence analysis revealed a putative open reading frame of 1,527 bp that encodes a polypeptide of 509 amino acids. Sequence homology ranged from 97% to 99% between 'Argus' and its three color mutants. The sequence analysis from the genomic DNA revealed that the chrysanthemum $DgF3'H$ gene consisted of three exons and two introns spanning a 3,830 bp length. The sizes of the gene for three mutants ranged from a shorter size of 3,828 bp to a longer size of 3,838 bp when compared to the size of WT. The total size of the two introns was 2,157 bp for WT, but those for three color mutants ranged from 2,154 bp to 2,159 bp. A result of an RT-PCR analysis indicated that the color variations of the mutants AM1 and AM2 can be partly explained by the structural modification derived from the sequencial changes in the gene caused by gamma ray. A Southern blot analysis revealed that the $DgF3'H$ gene existing as multiple copies in the chrysanthemum genome. A systemic study will be further needed to provide a genetic mechanism responsible for the color mutation and to uncover any involvement of genetic elements for the expression of the $DgF3'H$ gene for the color variation in chrysanthemum.

• Radiation Oncology Journal
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• v.19 no.4
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• pp.389-396
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• 2001

Purpose : To detect differentially expressed genes in the patients with uterine cervical cancer during the radiation therapy. Materials and Methods : In patients with biopsy proven uterine cervical cancer, we took tumor tissue just before radiation therapy and at 40 minutes after external irradiation of 1.8 Gy. Total RNAs isolated from non-irradiated and irradiated tumor tissue samples were analyzed using the differential-display reverse transcription-polymerase chain reaction (DDRT-PCR). Complementary DNA (cDNA) fragments corresponding to differentially expressed messenger RNAs(mRNAs) were eluted, and cloned. The differential expression of the corresponding mRNAs was confirmed by reverse northern blot. Differentially expressed cDNA bands were sequenced. Nucleotide sequence data were analyzed in the Gene Bank and EMBL databases via the BLAST network sewer to identify homologies to known genes or cDNA fragments. Expression pattern of down-regulated clone was examined using RT-PCR in S patients undergoing radiotherapy. Results : We identified 18 differentially expressed bands by DDRT-PCR, which were eluted and cloned. There were 10 up-regulated clones and 1 down-regulated clone in reverse northern blot. One cDNA fragment had homology to chemokine receptor CXCR4, four were identified as Human ESTs in the EMBL database in EST clones. Down-regulated CxCa-11 was also down regulated in all patients. Conclusion : Using the DDRT-PCR, we have identified 10 up-regulated and 1 down-regulated clone(s) in the patients with uterine cervical cancer during the radiation therapy. The clinical relevance and the functions of these genes will be further investigated.

• Journal of the korean academy of Pediatric Dentistry
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• v.30 no.2
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• pp.308-319
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• 2003

Mechanical forces are known to have an effect on bone formation, maintenance and remodeling, and there is evidence that the development of the mandibular condyle in the rat or mouse is influenced by altered functional force. However, studies are lacking in molecular-biologic mechanism such as the identification of differentiation factor induced from functional force. Here a mouse model was used to investigate the functional stress-responsive gene or factors which is related to the altered force by comparing the expression genes of functional state and hypo-functional state of the mouse mandible. ICR mice were provisioned with either a soft, mushy diet (soft-diet group) or hard rat pellets (hard-diet group) beginning at weaning for the alteration of functional force and subsequently sacrificed at 89 days of age. Incisor of mice in group 1 were trimmed twice a week to reduce occlusal forces. After killing the animals, mandibular bone including condyle were collected for RNA extraction, subtractive hybridization, northern blot analysis and mRNA in-situ hybridization. The results as follows; 1. A total of 39 clones were sequenced, and 11 individual sequence types were subsequently identified by subtractive hybridization, as 28 clones were represented twice in the analyzed sets. 2. Consequently four candidate clones, FS-s (functional stress-specific)2, -5, -18, and -22 were identified and characterized by homolgy search and northern analysis. Four of these clones, FS-s2, -5, -18, and -22, were shown to be expressed differentially in the hard-diet group. 3. Histologic sections showed that osteoblastic activity along the bone trabeculae and active bone remodeling were significantly lower in soft than in hard diet animals. A soft diet seems to enable a longer period of endochondral ossification in the mandibular condyle. 4. Although the mRNAs of FS-s2, -5, -18, and -22 were expressed rarely by cells of the soft-diet group, highest expression was detected in the cells of the hard-diet group. Together with the above results, it is suggested that FS-s2, -5, -18, and -22 could act as an important factors controlling the tissue changes in response to functional stress. The exact functional significance of these findings remains to be established.

• The Korean Journal of Mycology
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• v.31 no.2
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• pp.59-66
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• 2003

Laccase produced by Pycnoporus cinnabarinus SCH-3 isolated from Korea was partially purified using ultrafiltration, anion exchange chromatography and affinity chromatography, The laccase was produced as the predominant extracellular phenoloxidase during primary metabolism. Neither lignin peroxidase nor manganese-dependent peroxidase were detected in the culture fluid. In order to examine the effect of inducers in laccase production, 2,5-xylidine was added in the culture of Pycnoporus cinnabarinus SCH-3. Addition of 2,5-xylidine enhanced 25-fold laccase production. Purified laccase was a single polypeptide having a molecular mass of approximately 66 kDa, as determined by SDS-polyacrylamide gel electrophoresis, and carbohydrate content of 9%. $K_{m}\;and\;V_{max}$ values for laccase with ABTS [2,2-azinobis (3-ethylbenzthiazoline 6-sulfonic acid)] as a substrate (Lineweaver-Burk plot) was determined to be $44.4{\mu}M\;and\;56.0{\mu}mole$, respectively. The optimal pH for laccase activity was found to be 3.0. The enzyme was very stable for 1 hour at $60{\circ}C$. Half-life ($t_{1/2}$) of the enzyme was about 10 min at $80{\circ}C$. Spectroscopic analysis of purified enzyme indicated that the enzyme was typical of copper-containing protein. Substrate specificity and inhibitor studies for laccase also indicated to be a typical fungal laccase. The N-terminal amino acid sequence of the P. cinnabarinus SCH-3 laccase showed 94% of homology to the N-terminal sequences of laccases from P. cinnabarinus PB and P. coccineus.

• Radiation Oncology Journal
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• v.17 no.2
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• pp.151-157
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• 1999

Purpose : By sequencing the Erpressed Sequence Tags of human 걸ermal papilla CDNA library, we identified a clone named K872 of which the expression decreased during differentiation of HL6O cell line. Materials and Methods : K872 plasmid DNA was isolated according to QIA plasmid extraction kit (Qiagen GmbH, Germany). The nucleotide sequencing was performed by Sanger's method with K872 plasmid DNA. The most updated GenBank EMBL necleic acid banks were searched through the internet by using BLAST (Basic Local Alignment Search Tools) program. Nothern bots were performed using RNA isolated from various human tissues and cancer cell lines. The gene expression of the fusion protein was achieved by His-Patch Thiofusicn expression system and the protein product was identified on SDS-PAGE. Results : K872 clone is 1006 nucleotides long, and has a coding region of 675 nucleotides and a 3' non-coding region of 280 nucleotides. The presumed open reading frame starting at the 5' terminus of K872 encodes 226 amino acids, including the initiation methionine residue. The amino acid sequence deduced from the open reading frame of K872 shares $70\%$, identity with that of rat glutathione 5-transferase kappa 1 (rGSTKl). The transcripts were expressed in a variety of human tissues and cancer cells. The levels of transcript were relatively high in those tissues such as heart, skeletal muscle, and peripheral blood leukocyte. It is noteworthy that K872 was found to be abundantly expressed in coloreetal cancer and melanoma cell lines. Conclusion : Homology search result suggests that K872 clone is the human homolog of the rGSTK1 which is known to be involved in the resistance of cytotoxic therapy. We propose that meticulous functional analysis should be followed to confirm that.

• Journal of Plant Biotechnology
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• v.32 no.3
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• pp.167-173
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• 2005

Three different cDNAS for cinnamate 4-hydroxylase (C4H) which are involved in the second step of the general phenylpropanoid pathway were isolated and designated as pc4h1 (1,755 bp), pc4h2 (1,655 bp), and pc4h3 (1,316 bp), respectively. The nucleotide sequence analysis revealed that both pc4h1 and pc4h2 clones encode polypeptides of 505 amino acids frame but pc4h3 clone was truncated at the 5'-end of coding region. The alignment of the deduced amino acid sequences showed that PC4H1 and PC4H2 are highly homologous (95.8% identical) with each other and contain three conserved domains which are typical in cytochrome P450 monooxygenase: proline-rich region, threonine-containing binding pocket for the oxygen molecule, and heme binding region. In addition, result of the phylogenic tree analysis revealed that both pepper C4Hs belong to Class 1. pc4h2 transcription was strongly induced in wounded fruit (400%) and root (200%) relative to its very low basal level but not in leaf or stem tissue. In case of pc4h1, the basal level of transcription was higher than pc4h2 but induction by wounding was lower in fruit and root while leaf and stem tissues did not respond to wounding. The basal level of pc4h3 transcripts was not, if any, detectable and response to wounding was not observed.

• Journal of Plant Biotechnology
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• v.42 no.1
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• pp.25-33
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• 2015

A PyrcpPR-10 gene with differentially expressed was isolated by using the suppression subtractive hybridization assay between '93-3-98' (highly resistant against scab caused by Venturia nashicola) and 'Sweat Skin'(highly susceptible) and analyzed the expression pattern according to organs and cultivars. The full length of PyrcpPR-10 was cloned as 743bp with 480bp's ORP, and was determined to encode a protein of 159 amino acid residues. On analyzing PyrcpPR-10 gene sequence compared with resistant and susceptible cultivars, 'Hwangsilri' (resistant), 'Gamcheonbae' (moderately resistant), 'Wonhwang' (moderately susceptible), 'Niitaka' (highly susceptible), and 'Sweat Skin' (highly susceptible) had identical gene sequence but 'Bartlett' (highly resistant) showed partly different sequences. The deduced amino acid sequence showed 64 ~ 98% homology and had the GXGGXG motif to known amino acid of other plants PR-10 by the BLAST X analysis. Among several organs or tissues, petal was showed highest expression level of PyrcpPR-10 gene followed by leaf, floral axis, bud, and bark. The expression level of PyrcpPR-10 gene was dramatically increased at 24 hr after inoculation in all cultivars and also up-regulated in accordance with resistant degree of cultivars. While resistant cultivars ('Bartlett', '93-3-98', and 'Hwangsilri') induced relatively high expression level of PyrcpPR-10 gene, susceptible cultivars ('Niitaka', and 'Sweat Skin') showed low expression level. PyrcpPR-10 gene is assumed that it is directly connected with defense mechanisms to pear scab.

• Journal of Plant Biotechnology
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• v.38 no.1
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• pp.15-21
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• 2011

We developed 14 transgenic lines of Chinese cabbage (Brassica rapa) harboring the T-DNA border sequences and CryIAc1 transgene of the binary vector 416 using Agrobacterium tumefaciens-mediated DNA transfer. Six lines had single copy cryIAc1 gene and four of them contained no vector backbone DNA. Of the left border (LB) flanking sequences six nucleotides were deleted in transgenic lines 416-2 and 416-3, eleven nucleotides in line 416-9, and 65 nucleotides including the whole LB sequences in line 416-17, respectively. And we defined 499 bp of genomic DNA (gDNA) of transformed Chinese cabbage, and blast results showed 96% homology with Brassica oleracea sequences. PCR with specific primer for the right border (RB) franking sequence revealed 834 bp of PCR product sequence, and it was consisted of 3' end of cryIAc1, nosterminal region and 52 bp of Chinese cabbage genomic DNA near RB. RB sequences were not found and the 58 nucleotides including 21 bp of nos-terminator 3' end were deleted. Also, there were deletion of 10 bp of the known genomic sequences and insertion of 65 bp undefined genomic sequences of Chinese cabbage in the integration site. These results demonstrate that the integration of T-DNA can be accompanied by unusual deletions and insertions both in transgenic and genomic sequences.