• Horticultural Science & Technology
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• v.28 no.6
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• pp.1025-1038
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• 2010

Carrot ($Daucus$ $carota$ L. var. $sativa$) is one of the most widely used crops in the world. Moreover it is an important crop because of its high content of ${\beta}$-carotene, well-known as the precursor of vitamin A carotenoid. However, seed-hair which is generated in epidermal cell of seeds inhibits absorption and germination. For that reason, carrot seeds are commercialized after mechanical hair removal process. To overcome such cumbersome weaknesses, new breeding program for developing hairless-seed carrot cultivar has been needed. Therefore, in this study, cDNA libraries from seeds of short-hair seed phenotype CT-ATR615 OP 666-13line and hairy seed CT-ATR615 OP-CK1-9 line were constructed and expression patterns related to generation of seed-hair were analyzed by comparison of EST sequences. Differential EST sequence results between two lines were classified into FunCat functional categories based on the results of BlastX search. Higher expression quantities belonging to metabolic category were shown on short-hair seed line than hairy-seed one. Differential expression quantities between those two lines in the protein folding and stabilization, subcellular localization categories were supposed to contribute variously on the generation of seed-hair. We confirmed 50 and 59 SSR sites, and 2 SNP sites by analyzing EST sequences in two lines; thereafter, we designed SNP and SSR primer sets from these EST sequence information as a molecular marker. These markers are thought to be used in research of molecular markers for classification of carrot family and related to various traits, as well as seed-hair characteristic.

• Development and Reproduction
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• v.10 no.4
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• pp.227-238
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• 2006

Genomic DNAs(gDNAs) were isolated from the venus clam(Gomphina aequilatera) from Samcheok(venus clam from Samcheok; VCS) and Wonsan(venus clam from Wonsan; VCW) located in the East Sea of the Korean Peninsula. The amplified products were generated by agarose gel electrophoresis(AGE) with oligonucleotides primer, detected by staining with ethidium bromide and viewed by ultraviolet ray. The seven arbitrarily selected primers BION-21, BION-23, BION-25, BION-27, BION-29, BION-31 and BION-33 generated the shared loci, polymorphic, and specific loci, with the molecular sizes ranging from 150 bp to 2,400 bp. In this study, 147 polymorphic loci(147/954 loci, 15.41%) in VCS population and 274(274/996 loci, 27.51%) in VCW population were generated with seven primers. These results suggest the genetic variation in VCW population is higher than in VCS population. Especially, the 700 bp bands generated by the primer BION-21 were identified commonly in two Gomphina populations, which identified populations and/or species. This specific primer was found to be useful in the identification of individuals and/or population, resulting from the different DNA polymorphism among individuals/species/population. Two Gomphina populations between the individual SAMCHEOK no. 03 and WONSAN no. 22 showed the longest genetic distance(0.696) in comparison with other individuals used. The complete linkage cluster analysis indicating three genetic groupings and dendrogram revealed close relationships among individual identities within two geographical populations of venus clam(G. aequilatera) from the Samcheok and Wonsan. The intra-species classification and clustering analyses inferred from molecular markers supported the traditional taxonomy of the species based on morphological characters such as shell size, shape and color. Accordingly, as mentioned above, RAPD analysis showed that VCS population was more or less separated from VCW population.

• Journal of Life Science
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• v.30 no.3
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• pp.230-238
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• 2020

Carcass traits are the most economically important traits in Hanwoo (Korean cattle). Recently, the development of the field of genomics has made it possible to identify DNA markers for the genetic evaluation of carcass and meat quality traits in beef cattle. The objective of this study was to assess the genetic effects of single nucleotide polymorphism (SNP) markers related to carcass traits by field evaluations in a commercial Hanwoo population. We evaluated 15 SNP markers (TG g.371T>C, APM1 g.1454G>A, FABP4 g.2834C>G, FABP4 g.3533T>A, FABP4 g.3691G>A, SCD g.10153A>G, SCD g.10329T >C, CPE g.601T>C, EDG1 g.166A>G, NPY g.4271T>C, GPD1 g.2766C>T, PDE1B g.17122A>G, PDE1B g.17507A>C, TNNT1 g.6650C>T, and RORC g.20152A>G) related to carcass traits in Hanwoo. Genotyping of these SNP markers was performed using PCR-RFLP analysis in Hanwoo steers (n = 1,536) to evaluate their association with carcass traits. Seven SNPs, APM1 g.1454G>, FABP4 g.3691G>A, SCD g.10153A>G, CPE g.601T>C, PDE1B g.17122A>G, TNNT1 g.6650C>T, and RORC g.20152A>G, were significantly associated with carcass traits such as marbling score (MS), backfat thickness (BF), musculus longissimus dorsi area (LDA), carcass weight (CW), meat grade (MG), meat color (MC), and maturity score (MA). The results suggest that these SNPs may be used as DNA markers for the selection of Hanwoo with higher meat quality.

• Development and Reproduction
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• v.10 no.1
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• pp.19-32
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• 2006

Genomic DNA isolated from two species of Korean freshwater crab(Eriocheir sinensis) and swimming crab(Portunus trituberculatus) was amplified several times by PCR reactions. The seven arbitrarily selected primers OPA-05, OPA-13, OPA-16, OPB-06, OPB-15, OPB-17 and OPD-10 were used to generate the identical, polymorphic, and specific fragments. 505 fragments were identified in the freshwater crab species, and 513 in the swimming crab from Buan: 81 specific fragments(16.0%) in the freshwater crab species and 100(19.5%) in the swimming crab. 165 identical fragments, with an average of 23.6 per primer, were observed in the freshwater crab species. 66 fragments, with an average of 9.4 per primer, were identified in the swimming crab species. The numbers of polymorphic fragments in the freshwater crab and swimming crab were 50 and 14, respectively. The oligonucleotides decamer primer OPB-17 generated identical DNA fragments, approximately 300 bp, in both the freshwater crab and swimming crab species. Compared separately, the average genetic difference was higher in the swimming crab than in the freshwater crab species. The average genetic difference was $0.726{\pm}0.004$ between the freshwater crab and swimming crab species. The dendrogram obtained by the seven primers indicates four genetic clusters: cluster 1(FRESHWATER 01), cluster 2(FRESHWATER 02, 03, 04, 05 and 06), cluster 3(FRESHWATER 07, 08, 09, 10 and 11), and cluster 4(SWIMMING 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 and 22). The shortest genetic distance displaying significant molecular difference was between individuals SWIMMING no. 18 and SWIMMING no. 17 from swimming crab(0.096). Ultimately, individual no. 02 of the freshwater crab was most distantly related to freshwater crab no. 03(genetic distance = 0.770). As stated above, the potential of RAPD-PCR to identify diagnostic markers for the identification of two crab species has been demonstrated.

• Journal of Plant Biotechnology
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• v.33 no.1
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• pp.11-18
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• 2006

Salt stress is one of major environmental factors influencing plant growth and development. To identify salt tolerance determinants in higher plants, a large-scale screen was conducted with a bialaphos marker-based T-DNA insertional collection of Arabidopsis ecotype C24 mutants. One line for salt stress-sensitive mutant (referred to as ssm1) exhibited increased sensitivity to both ionic (NaCl) and nonionic (mannitol) osmotic stress in a root growth assay. This result suggests that ssm1 mutant is involved in ion homeostasis and osmotic compensation in plant. Molecular cloning of the genomic DNA flanking T-DNA insert of ssm1 mutant was achieved by mutant genomic DNA library screening. T-DNA insertion appeared in the first exon of an open reading frame on F3M18.7, which is the same as AtSYP61. SSM1 is SYP61/OSM1 that is a member of the SNARE superfamily of proteins required for vesicular/target membrane fusions and factor related to abiotic stress.

• Journal of Mushroom
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• v.14 no.4
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• pp.220-224
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• 2016

Chronic inflammation, which results from continuous exposure to antigens, is one of major reasons for tissue damage and diseases such as rheumatoid arthritis and type 2 diabetes. In this study, we investigated the anti-inflammatory effects of extracts (hexane, $CHCl_3$, MeOH, $MeOH/H_2O$, and $H_2O$) from GW10-45, which is our new cultivar of an edible mushroom Pleurotus ferulae (ASI 2803 and ASI 2778), in RAW264.7 murine macrophages. None of the extracts showed cytotoxicity in RAW264.7 cells and the hexane, CHCl and H extracts reduced nitric oxide (NO) production, an important inflammatory marker, in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. Particularly, the extract (CG45) inhibited NO production more than the other extracts did. To elucidate the effects of CG45 on molecular targets involved in pro-inflammatory responses, we performed western blot analysis. Expression of inducible nitric oxide (iNOS) significantly decreased in LPS and CG45 co-incubated cells compared to that in LPS only-treated cells. Additionally, another protein thatplays a critical role in inflammation, was down-regulated in cells treated with both LPS and CG45. In the nuclear factor $(NF)-{\kappa}B$ pathway, phosphorylation of $I{\kappa}B{\alpha}$ decreased in RAW264.7 cells treated with both LPS and CG45. Furthermore, CG45 inhibited the phosphorylation of $NF-{\kappa}B$ in LPS-stimulated RAW264.7 cells. Conclusively, CG45 could suppress pro-inflammatory responses in LPS-stimulated RAW264.7 cells by down-regulating not only the phosphorylation of $NF-{\kappa}B$ and $I{\kappa}B{\alpha}$ but also the expression of iNOS and COX-2 without any cytotoxicity.

• Pediatric Infection and Vaccine
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• v.7 no.1
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• pp.143-151
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• 2000

Purpose : The accuracy of bacteriologic diagnosis of beta-hemolytic streptococcal pharyngotonsillitis depends on the degree of carrier rate in that area where the throat swabs are obtained and the evaluation of serological T typing as an epidemiologic marker is important to understand epidemiology of streptococcal infection. The purpose of this study is to know the carrier rates of group A streptococcus in normal children form four different areas and to find out the epidemiologic characteristic in distribution of the serotypes for 3 years. Method : Throat swabs were obtained from the tonsillar fossa of normal school children in four different areas(Uljin, Seoul, Osan, Kunsan) from March to May 1996, in Uljin in April 1997, and in Uljin in April 1998. The samples were plated on a 5% sheep blood agar plate and incubated overnight at $37^{\circ}C$ before examination for the presence of beta-hemolytic colonies. All isolated beta-hemolytic streptococcus were grouped and serotyped by T agglutination. Results : The carrier rate of beta-hemolytic streptococci and group A streptococci in 1996 were 27.6%, 18.6% at Uljin; 16.4%, 2.7% at Seoul; 33.0%, 26.0% at Osan; 20.0%, 12.3% at Kunsan, respectively. Among 1,192 normal school children from 4 different areas, we obtained 179 strains of group A streptococci. Fifty two percent of the strains were typable by T agglutination in 1996. Common T-type in 1996 were NT, T1, T3, T2 at Uljin; T12, T25 at Seoul; NT, T6, T28 at Osan; T25, T4, NT, T5 at Kunsan, in decreasing order, respectively. At Uljin, T1, T3, T25 accounted for 69% of strains in 1996, T1, T12, T25 accounted for 70% in 1997, and T12, T4 accounted for 88% in 1998. Conclusion : Higher carrier rates were found in Uljin and Osan, where there are a lower population density with scanty of medical facilities compared with another areas. We supposed that low carrier rates is likely to be related to antibiotic abuse or some epidemiologic factor. The periodic and seasonal serotyping analysis is important in monitoring and understanding the epidemiologic patterns of group A streptococci.

• Journal of the korean academy of Pediatric Dentistry
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• v.32 no.1
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• pp.75-88
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• 2005

Ameloblastoma is the most commonly occurring odontogenic tumor in oral cavity. Although most are benign epithelial neoplasm, they are generally considered to be locally aggressive and destructive, exhibiting a high rate of recurrence. The biological behavior of this neoplasm is a slowly growing, locally invasive tumor without metastasis, therefore malignant neoplasm, changed its histological appearance to carcinoma or showed distant metastasis, is only defined clinically. In this study, we identified the differentially expressed genes(DEGs) in stages under benign or malignant ameloblastoma compared with normal patient using ordered differential display(ODD) reverse transcription(RT)-PCR and $GeneFishing^{TM}$ technology. ODD RT-PCR is rather effective when the investigation of samples containing very small amounts of total RNA must be accomplished. ODD RT-PCR used the means of amplification with anchored T-primer and adaptor specific primer. bearing definite two bases at their 3' ends and so this method could display differential 3'-expressed sequence taqs(ESTs) patterns without using full-length cDNAs. Compared with standard differential display, ODD RT-PCR is more simple and have enough sensitivity to search for molecular markers by comparing gene expression profiles, However, this method required much effort and skill to perform. $GeneFishing^{TM}$ modified from DD-PCR is an improved method for detecting differentially expressed genes in two or more related samples. This two step RT-PCR method uses a constant reverse primer(anchor ACP-T) to prime the RT reaction and arbitrary primer pairs(annealing control primers, ACPs) during PCR. Because of high annealing specificity of ACPs than ODD RT-PCR, the application of $GeneFishing^{TM}$ to DEG discovery generates reproducible, authentic, and long(100bp to 2kb) PCR products that are detectable on agarose gels. Consequently, various DEGs observed differential expression levels on agarose gels were isolated from normal, benign, and malignant tissues using these methods. The expression patterns of the some isolated DEGs through ODD RT-PCR and $GeneFishing^{TM}$ were confirmed by Northern blot analysis and RT-PCR. The results showed that these identified DEGs were implicated in ameloblastoma neoplasm processes. Therefore, the identified DEGs will be further studied in order to be applied in candidate selection for marker as an early diagnosis during ameloblastoma neoplasm processes.

• Tuberculosis and Respiratory Diseases
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• v.47 no.2
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• pp.150-160
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• 1999

Background: The CREST syndrome is an indolent form of progressive systemic sclerosis. Although its clinical progress is indolent, pulmonary hypertension(PH) associated with CREST syndrome have grave prognosis with over 40 percent mortality rate at 2 year follow-up. But the pathogenesis of pulmonary hypertension in this disease is not known, and classified as either primary or secondary PH. Clonality of endothelial cell proliferation in plexiform lesion is a molecular marker which allows distinction between primary and secondary PH. We performed this study to know whether the PH associated with CREST syndrome is a variant of primary PH or is a secondary PH. Methods: We assessed the X-chromosome inactivation based on the methylation pattern of the human androgen-receptor gene by PCR(HUMARA). Endothelial cells in plexiform lesions from female patients(n=3) with PH associated with CREST syndrome were microdissected from paraffin blocks. Vascular smooth muscle cells and lung parenchyma were also microdissected for clonality studies. Results: The proliferating endothelial cells in 14 plexiform lesions were all polyclonal. Similarly proliferated smooth muscle cells from 5 vessels with medial hypertrophy were also polyclonal. Conclusion: These results suggest that the pulmonary hypertension associated with CREST syndrome has different pathogenesis from primary PH and to be classified as secondary PH.

• Nuclear Medicine and Molecular Imaging
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• v.43 no.2
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• pp.120-128
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• 2009

Purpose: Early detection of recurrence is an important factor for long term survival of patients with colorectal cancer. Measurement of serum levels of CEA, CA 19-9, CT and PET/CT has been commonly used in the postoperative surveillance of colorectal cancer. The purpose of this study was to compare the diagnostic ability of PET/CT, tumor marker and CT for recurrence in colorectal cancer patients after treatment. Materials and Methods: F-18 FDG PET/CT imaging was performed in 189 colorectal cancer patients who underwent curative surgical resection and/or chemotherapy. Measurement of serum levels of CEA, CA 19-9 and CT imaging were performed within 2 months of PET/CT examination. Final diagnosis of recurrence was made by biopsy, radiologic studies or clinical follow-up for 6 months after each study. Results: Overall sensitivity, specificity of PET/CT was 94.7%, 91.1%, while those of serum CEA were 44.7% and 97.3%, respectively. Sensitivity and specificity were 94.2%, 90.4% for PET/CT and better than those of combined CEA and CA 19-9 measurement(52.1%, 88.5%) in 174 patients measured available both CEA and CA 19-9 data. In 115 patients with both tumor markers and CT images available, PET/CT showed similar sensitivity but higher specificity(92.9%, 91.3%) compared to combination of tumor markers and CT images(92.9%, 74.1%). Conclusion: PET/CT was superior for detection of recurred colorectal cancer patients compared with both CEA, CA 19-9, and even with combination of both tumor markers and CT. Therefore PET/CT could be used as a routine surveillance examination to detect recurrence or metastasis of colorectal cancer.