• Journal of Genetic Medicine
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• v.6 no.1
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• pp.81-86
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• 2009

Multiple epiphyseal dysplasia (MED) is a clinically and genetically heterogeneous chondroplasia, characterized by delayed development of the ossification centers and, deformities of the extremities that involve only the epiphysis and result in mild short stature. Mutations in the cartilage oligomeric matrix protein (COMP) gene are most commonly found, and most of the mutations are located in the calmodulin-like repeats and the C-terminal domain. We report a Korean kindred of 12 family members with MED in four generations who were found to have a novel mutation in the COMP gene. A pedigree showed early onset osteoarthritis requiring arthroplasty that was an autosomal dominant inherited trait. Radiological examinations demonstrated the presence of osteochondral defects in the medial femoral condyles, and the knee and hip joints showed variable degrees of precocious degenerative changes. Mutation analysis of the COMP gene in the proband and five other affected family members identified a novel missense mutation, c.1280G>C (p.Gly427Ala) in exon 12, which was not found in three unaffected family members. Direct sequencing of the COMP gene may yield pathogenic mutations in dominantly inherited MED cases, and may provide opportunities of carrier detection among high-risk family members, leading to genetic counseling for early diagnosis and intervention before the onset of complications.

• Korean Journal of Ecology and Environment
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• v.47 no.4
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• pp.342-349
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• 2014

This study was conducted to identify the bloom-forming Anabaena strains with two phenotypes (straight-type and coil-type) isolated from North Han River (Sambong-ri Joam-myun) using 16S rDNA sequence. The odor material producing potential was also examined using the geosmin-synthesizing gene cluster. Despite of striking morphological difference of the two stains, resembling A. circinalis and A. crassa species, the phylogenetic analysis using 16S rDNA identified the both strains as a single species of A. circinalis with high genetic similarity (98%~100%). Also, two Anabaena strains showed to possess the geosmin-synthesizing gene cluster, indicating that they are capable of producing the odor substance. This study is the first report that provides the direct evidence of geosmin production in the gene level by A. circinalis in Korea, and provides important basic information to identify the source alga of geosmin increase and its management in North Han River.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.14 no.2
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• pp.186-190
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• 2014

Citrullinemia type 2 (citrin deficiency) is an autosomal recessive inborn error metabolism, caused by the SLC25A13 gene mutation. Citrin deficiency is associated with two clinical phenotype; neonatal-onset type II citrullinemia (CTLN2), also known as neonatal intraphepatic cholestasis caused by citrin deficiency (NICCD) and adult-onset CTLN2. Clinical manifestations of NICCD include poor growth, intrahepatic cholestasis, liver dysfunction and increased plasma citrulline, methionine, threonine, arginine. The molecular diagnosis could be confirmed by SLC25A13 gene mutation analysis. A 3-month-old male infant with persistent jaundice was referred for evaluation. Newborn screening was normal at birth. Mild elevation of serum ammonia and AST/ALT were observed. Plasma amino acid analysis showed significantly elevated citrulline, methionine, threonine. DNA sequence analysis of the SLC25A13 gene revealed two compound heterozygous mutations, c.[852_855del]($p.Met285Profs^*2$) and [1180+1G>A]. We suggest that NICCD should be considered as one of the cause of in infants with cholestatic jaundice, although the newborn screening was normal.

• Journal of Mushroom
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• v.2 no.4
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• pp.169-174
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• 2004

A hot water extract(HWE-P4) was separated from the fruit bodies of PMO-P4, and its antitumor and immunomodulatory activities against sarcoma-180 in ICR mice were investigated. The internal transcribed spacer(ITS) regions from PMO-P4 were amplified using polymerase chain reaction(PCR) and sequenced. The results revealed that PMO-P4 was belong to the Phellinus baumii. When oral administration at the dose of 160mg/kg/day in the mice until the end of the experiment with 2 week's pre-feeding of the HWE-P4, the survival rate of the mice was 152% for 50days after the inoculation of sarcoma-180 and the suppression rate of the tumor growth was 35.3%(p<0.05) for 28 days after inoculation of sarcoma-180. The HWE-P4 increased 71.4% of the CD4/CD8 ratio and 5-fold of the expression of CD25(IL-2 receptor chain) compared with the control. From these results, the antitumor activity of HWE-P4 is exerted through its immunomodulating activity on the host's immune system.

• Journal of Animal Science and Technology
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• v.50 no.5
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• pp.633-640
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• 2008

With a double mismatch primer set designed for amplifying the modified DNA sequence fragments, bovine melanocortin-1 receptor(MC1R) gene encoded in Extension locus which plays a critical role in coat color development was analyzed using polymerase chain reaction mediated restriction fragment length polymorphism(PCR-RFLP). Amplified PCR fragments were successfully discriminated with combining the MspI- and AluI-RFLP into three major alleles(ED, E+, and e), directly related to bovine coat color phenotypes. The genotyping results showed that Jeju black cattle contained three MC1R alleles, but yellowish-red colored Hanwoo and bridle colored Korean Brindle cattle did not contained the dominant black allele ED. However, two dominant black-colored cattle breeds, Holstein and Angus, contained the ED allele over 96% in frequency. Hanwoo×Holstein F1 and Hanwoo×Angus F1 crossbred calves showed ED/e MC1R genotypes, and uniformly black coat color. the results suggested that this MC1R genotyping method be useful in allele discrimination for bovine MC1R gene which used for breed classification and characterization, as one of the important genetic markers, using combination of MspI- and AluI-RFLP for modified PCR product amplified with a newly designed double mismatch primer set.

• Korean Journal of Soil Science and Fertilizer
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• v.45 no.6
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• pp.1100-1107
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• 2012

Bacterial endophytes may be important factors in plant growth and ecologically relevant functions in rice. Using pyrosequencing technology, we analyzed the composition of endophytic bacterial communities that colonized the roots of rice cultivated in long-term fertilized (APK) and non-fertilized (NF) paddy soils. A total of 1,900 reads were obtained from 2 samples. All sequences were classified into 177 OTUs (APK sample) or 72 OTUs (NF sample) at a 97% similarity cut-off. Twenty-two OTUs were shared between the 2 samples, and these were also the most dominant OTUs in both samples. Proteobacteria was the most dominant phylum with 90.2%, followed by Actinobacteria (7.1%) and Bacteroidetes (1.1%). Furthermore, Pseudomonas was the most abundant genus in both samples. We observed clear differences in the structure of the endophytic bacterial community structure between the 2 samples. Notably, the distributions of Alphaproteobacteria and Gammaproteobacteria were markedly different. The diversity index of the APK sample was higher than that of the NF sample. These findings showed that the endophytic bacterial community of rice roots was affected by the presence of fertilizers in the rice field soil.

• Clinical and Experimental Pediatrics
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• v.48 no.8
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• pp.877-880
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• 2005

Purpose : Glycogen storage disease type Ia(GSD Ia) is an autosomal recessive disorder caused by the deficiency of glucose-6-phosphatase(G6Pase). The aim of the study was to investigate the spectrum of G6Pase gene mutations and relationship between genotype and clinical findings in Korean patients with GSD Ia. Methods : Genomic DNA was extracted from peripheral leukocytes of 20 patients with GSD Ia. The five exons of G6Pase gene were amplified and PCR products were directly sequenced. The frequency of short stature, hypoglycemia, hypercholesterolemia, hyperuricemia, hypercalciuria, nephrocalcinosis and hepatic adenoma was compared between 727G>T homozygotes and 727G>T compound heterozygotes. Results : A total of 5 different mutations were identified. The most common mutation was the 727G>T with an allele frequency of 80%. All patients were either homozygous(12/20) or heterozygous(8/20) for the 727G>T mutation. G122D was found in 3 patients, P178A in 1, G222R in 2, and S339R in 2. There was no difference in the frequency of short stature, hypoglycemia, hypercholesterolemia, hyperuricemia, nephrocalcinosis, and hepatic adenoma between 727G>T homozygotes and heterozygotes. Conclusion : Diagnosis of GSD Ia can be based on clinical and biochemical abnormalities combined with mutation analysis instead of enzymatic diagnosis that requires liver biopsy. Homozygosity for the 727G>T does not seem to alter the disease phenotype as compared with the heterozygous state.

• Korean Journal of Ecology and Environment
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• v.38 no.2 s.112
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• pp.137-145
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• 2005

Traditional screening techniques have missed up to 99% of microbial resources existing in the nature. Strategies of direct cloning of environmental DNAs comprising tine genetic blueprints of entire microbial metagenomes provide vastly more genetic information than is contained in the culturable. Therefore, one way to screening the useful gene in a variety of environments is the construction of metagenomic DNA library. In this study, the water samples were collected from Daecheong Reservoir in the mid Korea, and analyzed by T-RFLP to examine the diversity of the microbial communities. The crude DNAs were extracted by SDS-based freezing-thawing method and then further purified using an $UltraClean^{TM}kit$ (MoBio, USA). The metagenomic libraries were constructed with the DNAs partially digested with EcoRI, BamHI, and SacII in Escherichia coli DH10B using the pBACe3.6 vector. About 14.0 Mb of metagenomic libraries were obtained with average inserts 13 ${\sim}$ 15 kb in size. The genes responsible for degradation of 1, 2-dichloroethane (1, 2-DCE) via hydrolytic dehalogenation were identified from the metagenomic libraries by colony hybridization. The 1, 2-dichloroethane dehalogenase gene (dhlA) was cloned and its nucleotide sequence was analyzed. The activity of the 1, 2-DCE dehalogenase was highly expressed to the substrate. These results indicated that the dhlA gene identified from the metagenomes derived from Deacheong Reservoir might be useful to develop a potent strain for degradation of 1, 2-DCE.

• Tuberculosis and Respiratory Diseases
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• v.70 no.1
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• pp.21-27
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• 2011

Background: Although the gold standard method for research trials on epidermal growth factor receptor (EGFR) mutations has been direct sequencing, this approach has the limitations of low sensitivity and of being time-consuming. Peptide nucleic acid (PNA)-mediated polymerase chain reaction (PCR) clamping is known to be a more sensitive detection tool. The aim of this study was to compare the detection rate of $EGFR$ mutation and EGFR-tyrosine kinase inhibitor (TKI) responsiveness according to $EGFR$ mutation status using both methodologies. Methods: Clinical specimens from 112 NSCLC patients were analyzed for $EGFR$ mutations in exons 18, 19, 20, and 21. All clinical data and tumor specimens were obtained from 3 university hospitals in Korea. After genomic DNA was extracted from paraffin-embedded tissue specimens, both PNA-mediated PCR clamping and direct-sequencing were performed. The results and clinical response to $EGFR$-TKIs were compared. Results: Sequencing revealed a total of 35 (22.9%) mutations: 8 missense mutations in exon 21 and 26 deletion mutations in exon 19. PNA-mediated PCR clamping showed the presence of genomic alterations in 45 (28.3%) samples, including the 32 identified by sequencing plus 13 additional samples (6 in exon 19 and 7 in exon 21). Conclusion: PNA-mediated PCR clamping is simple and rapid, as well as a more sensitive method for screening of genomic alterations in $EGFR$ gene compared to direct sequencing. This data suggests that PNA-mediated PCR clamping should be implemented as a useful screening tool for detection of $EGFR$ mutations in clinical setting.

• Korean Journal of Microbiology
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• v.48 no.2
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• pp.79-86
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• 2012

ErmSF is one of the Erm family proteins which catalyze S-adenosyl-$_L$-methionine dependent modification of a specific adenine residue (A2058, E. coli numbering) in bacterial 23S rRNA, thereby conferring resistance to clinically important macrolide, lincosamide and streptogramin B ($MLS_B$) antibiotics. $^{222}FXPXPXVXS^{230}$ (ErmSF numbering) sequence appears to be a consensus sequence among the Erm family. This sequence was supposed to be involved in direct interaction with the target adenine from the structural studies of Erm protein ErmC'. But in DNA methyltarnsferase M. Taq I, this interaction have been identified biochemically and from the complex structure with substrate. Arginine 223 and 227 in this sequence are not conserved among Erm proteins, but because of the basic nature of residues, it was expected to interact with RNA substrates. Two amino acid residues were replaced with Ala by site-directed mutagenesis. Two mutant proteins still maintained its activity in vivo and resistant to the antibiotic erythromycin. Compared to the wild-type ErmSF, R223A and R227A proteins retained about 50% and 88% of activity in vitro, respectively. Even though those arginine residues are not essential in the catalytic step, with their positive charge they may play an important role for RNA binding.