• Korean Journal of Clinical Laboratory Science
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• v.39 no.2
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• pp.113-121
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• 2007

Hearing loss is a common congenital disorder that is frequently associated with mutations in the Cx26 gene (GJB2). Recently, the mutation analysis of GJB2 has been used in a newborn screening test for the detection of hearing impairment. Population-based studies should be performed before the application of genetic testing for the identification of deaf newborns. In this study, 8 positions of GJB2 mutations-including 35delG, 167delT, 235delC, V27I, V37I, M34T, E114G, and I203T-were analyzed using PCR-direct sequencing in a total of 437 healthy Korean neonates. DNAs from dried blood spots were extracted using a commercial DNA extraction kit. The PCR-amplified products (783 bps) of the GJB2 gene were detected using 2% agarose gel electrophoresis and subjected to direct sequencing. The sequences were compared with those in the GenBank database by using the BLAST program. In this study, 5 GJB2 mutations -including V27I (79G>A), V37I (109G>A), E114G (341A>G), I203T (608T>C), and 235delC- were found. Of the 437 neonate samples, 301 subjects showed GJB2 mutations (68.9%, 301/437). The V27I mutation was found in 271 subjects and was the most frequent (62.0%, 271/437). The E114G, I203T and V37I mutations were shown in 146, 17 and 14 subjects, respectively. The 235delC mutation was found in 1 subject. The E114G mutation was frequently accompanied by the V27I mutation. V27I/E114G (97.2%, 143/147) was the most common double mutation and 3 subjects had the double mutation V27I/I203T. A triple mutation, V27I/E114G/I203T, was found in 1 subject. In conclusion, PCR-direct sequencing is a convenient tool for the rapid detection of GJB2 mutations and this data might provide information for the genetic counseling of the GJB2 gene.

• Korean Journal of Environmental Biology
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• v.34 no.4
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• pp.304-313
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• 2016

One of the issues currently facing nuclear power plants is how to store spent nuclear waste materials which are contaminated with radionuclides such as $^{134}Cs$, $^{135}Cs$, and $^{137}Cs$. Bioremediation processes may offer a potent method of cleaning up radioactive cesium. However, there have only been limited reports on $Cs^+$ tolerant bacteria. In this study, we report the isolation and identification of $Cs^+$ tolerant bacteria in environmental soil and sediment. The resistant $Cs^+$ isolates were screened from enrichment cultures in R2A medium supplemented with 100 mM CsCl for 72 h, followed by microbial community analysis based on sequencing analysis from 16S rRNA gene clone libraries(NCBI's BlastN). The dominant Bacillus anthracis Roh-1 and B. cereus Roh-2 were successfully isolated from the cesium enrichment culture. Importantly, B. cereus Roh-2 is resistant to 30% more $Cs^+$ than is B. anthracis Roh-1 when treated with 50 mM CsCl. Growth experiments clearly demonstrated that the isolate had a higher tolerance to $Cs^+$. In addition, we investigated the adsorption of $0.2mg\;L^{-1}$ $Cs^+$ using B. anthracis Roh-1. The maximum $Cs^+$ biosorption capacity of B. anthracis Roh-1 was $2.01mg\;g^{-1}$ at pH 10. Thus, we show that $Cs^+$ tolerant bacterial isolates could be used for bioremediation of contaminated environments.

• Korean journal of applied entomology
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• v.53 no.3
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• pp.247-260
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• 2014

To identify the species of Trichogramma occurring in the corn fields of Korea as egg parasitoids of Ostrinia furnacalis, we sequenced the full-length of ITS2 nuclear rDNA from 112 parasitoids collected during this study. As a reference to distinguish species, we also retrieved full-length ITS2 sequences of 60 Trichogramma species from the NCBI GenBank database. On the basis of the size and 3'terminal sequence pattern of the ITS2 sequences, the Trichogramma samples collected in this study were divided into three groups (K-1, -2, and -3). Evolutionary distances (d) within and between groups based on ITS2 sequences were estimated to be ${\leq}0.005$ and ${\geq}0.080$, respectively. In the net average distance between groups or species, the d value between K-1 and T. ostriniae, K-2 and T. dendrolimi, and K-3 and T. confusum was the lowest, with values of 0.016, 0.001, and 0.002, respectively. In the phylogenetic tree, K-1 and K-2 were clustered with T. ostriniae and T. dendrolimi, respectively. However, K-3 was clustered with three different species, namely, T. confusum, T. chilonis, and T. bilingensis. NCBI BLAST results revealed that parasitoids belonging to K-1 and K-2 showed 99% identity with T. ostriniae and T. dendrolimi, respectively. Parasitoids in K-3 collected from Hongcheon showed 99-100% identity with T. confusum and T. chilonis, and one parasitoid in K-3 collected from Gochang had 98% identity with T. bilingensis, T. confusum, and T. chilonis. On the basis of these results, we infer that the species of Trichogramma collected in this study are closely related to T. ostriniae (K-1) and T. dendrolimi (K-2). However, it was not possible to distinguish species of K-3 using the ITS2 sequence alone.

• BMB Reports
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• v.40 no.5
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• pp.757-764
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• 2007

Marbling of cattle meat is dependent on the coordinated expression of multiple genes. Cattle dramatically increase their intramuscular fat content in the longissimus dorsi muscle between 12 and 27 months of age. We used the annealing control primer (ACP)-differential display RT-PCR method to identify differentially expressed genes (DEGs) that may participate in the development of intramuscular fat between early (12 months old) and late fattening stages (27 months old). Using 20 arbitrary ACP primers, we identified and sequenced 14 DEGs. BLAST searches revealed that expression of the MDH, PI4-K, ferritin, ICER, NID-2, WDNMI, telethonin, filamin, and desmin (DES) genes increased while that of GAPD, COP VII, ACTA1, CamK II, and nebulin decreased during the late fattening stage. The results of functional categorization using the Gene Ontology database for 14 known genes indicated that MDH, GAPD, and COP VII are involved in metabolic pathways such as glycolysis and the TCA cycle, whereas telethonin, filamin, nebulin, desmin, and ACTA1 contribute to the muscle contractile apparatus, and PI4-K, CamK II, and ICER have roles in signal transduction pathways regulated by growth factor or hormones. The final three genes, NID-2, WDNMI, and ferritin, are involved in iron transport and extracellular protein inhibition. The expression patterns were confirmed for seven genes (MDH, PI4-K, ferritin, ICER, nebulin, WDNMI, and telethonin) using real-time PCR. We found that the novel transcription repressor ICER gene was highly expressed in the late fattening stage and during bovine preadipocyte differentiation. This information may be helpful in selecting candidate genes that participate in intramuscular fat development in cattle.

• Journal of Mushroom
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• v.6 no.1
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• pp.20-26
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• 2008

The stromatal forms of T. fuciformis and the mycelia of Hypoxylon sp. were collected. The DNA sequence in the ITS region of the 5.8S ribosomal genes of isolated strain KG103 was very similar to that of T. fuciformis AF042409 with a homology of over 98% in the EMBL/GenBank database through BLAST searching. A second isolate, No KG201, one of the symbiotic strains for cultivating T. fuciformis also exhibited high homology with Annulohhypoxylon stygium AJ390406. Potato Dextrose Medium exhibited the best mycelial growth of 14 mm/14 days and 85 mm/14 days for T. fuciformis and its symbiotic fungi, respectively. Optimum culture conditions for the micelial growth were pH 5 at $25^{\circ}C$. For the optimization of artificial cultivation of T. fuciformis in bottle with sawdust medium, several conditions such as type of sawdust, supplements, pH, moisture content, and incubation temperature were investigated. T. fuciformis and symbiotic fungi showed fast mycelial growth on corn cob media (77 and 52%) followed by oak tree sawdust and cotton seed meal. The optimal temperature for mycelial growth of T. fuciformis and symbiotic fungi on corn cob media was $25^{\circ}C$ at 55% of moisture content.

• Research in Plant Disease
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• v.21 no.4
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• pp.337-340
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• 2015

During July to November 2014, severe rust infection was consistently found on Peucedanum japonicum growing farm in Yeosu, Korea. The rust was observed mainly on lower leaf surfaces. Symptoms of typical plants included yellow-orange rust pustules were observed on the petiole and leaf surface with small yellowish to chlorotic lesions on the upper surface. No symptom was observed on flowers. Uredinia were occurred amphigenous on leaf surface, and occasionally caulicolous, scattered or loosely aggregate, rounded to oblong, 0.4 to 4 mm in diameter, covered by epidermis, then naked, surrounded by ruptured epidermis, pulverulent, and brown. Urediniospores were ovate-ellipsoid, ellipsoid or subglobose, light brown, 20 to $45{\times}15$ to $35{\mu}m$, walls 2 to $4{\mu}m$ thick. The resulting sequences were deposited in GenBank with accession No. KT778808, KT778809, and KT778810, respectively. Since this was the first accession of 28S sequence Puccinia jogashimensis, there was no exact match in GenBank nucleotide database. On the basis of the morphological characteristics and phylogenetic analyses of 28S rDNA, the fungus was identified as P. jogashimensis. To our knowledge, this is the first confirmed report on the occurrence of P. jogashimensis on P. japonicum in Korea.

• Microbiology and Biotechnology Letters
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• v.41 no.4
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• pp.383-390
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• 2013

Several yeasts were isolated from flowers found in Gyonggi-do Province and Jeju island in Korea. They were then identified by a comparison of their PCR-amplified D1/D2 regions of 26S rDNA, internal transcribed spacer 1 and 2 inclusive of 5.8S rDNA, using the BLAST database. A total of fifty four yeast strains were isolated from wild flowers in Gyonggi-do and the genus Pseudozyma was noted as being dominant. A total of thirty two strains were isolated from Songaksan and Seongsan-ilchulbong in Jeju island and Sporobolomyces ruberrimus was seen to be dominant. The anti-gout xanthine oxidase inhibitory activities of the culture broths and cell-free extracts from eighty six yeast strains were then determined. The cell-free extracts of Pseudozyma hubeiensis 228-S-1 exhibited the highest xanthine oxidase inhibitory activity of 19.6%. The XOD inhibitor was also maximally produced when Pseudozyma hubeiensis 228-S-1 was cultured at $30^{\circ}C$ for 36h in YEPD medium.

• Korean journal of applied entomology
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• v.55 no.3
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• pp.245-256
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• 2016

Elytra of Harmonia axyridis exhibit varied color patterns. In the present study, we deciphered the genetic basis for intraspecific diversity of elytra color patterns in H. axyridis, using amplified fragment length polymorphism (AFLP). Twenty-eight AFLP reactions were performed to generate a total of 2,741 bands. Of these, 20 bands were polymorphic for each color pattern. The polymorphic bands showed differences of genetic character among different color patterns of H. axyridis. Among them, ten candidate AFLP markers were color-linked. S1, S2, and S20 markers were detected in Succinea 1 and 2 variants of H. axyridis, whereas S3 and S5 were specifically detected in the Conspicua variant. S15, S18, and S19 were specific to the Succinea 2 variant. Polymerase chain reaction (PCR) products of these ten AFLP markers were sequenced. BLAST analysis of these sequences against the GenBank database revealed their homology to DNA fragments of unknown function. Based on the color-linked AFLP markers, sequence characterized amplified region (SCAR) markers were designed for PCR amplification of genomic DNA. Of the ten AFLP markers, five were successfully converted into SCAR markers, which could discriminate elytra color polymorphism in H. axyridis.

• Journal of Life Science
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• v.20 no.9
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• pp.1306-1313
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• 2010

The gene encoding esterase enzyme was cloned from a metagenomic library of cow rumen bacteria. The esterase gene (est1R) was 2,465 bp in length, encoding a protein of 366 amino acid residues, and the molecular weight of the enzyme was 61,166 Da. Est1R of rumen cosmid library shared 5.9% amino acid identity with Est1R (P37967) of PNB carboxylesterase, 6.1% with Est1R (1EEAA) of acetylcholinesterase and 6.1% with Est1R (1H23A) of chain A. BlastP in NCBI database analysis of Est1R revealed that it was not homologous to previous known lipases and esterases. Est1R showed optimum activity at pH 7.0 and $40^{\circ}C$. On the other hand, the enzyme was found to be most active without organic solvent, followed by 95% activity with methanol, and the enzyme activity was highly affected by hexane (lost 51% activity). Therefore, the novel esterase gene est1R is likely obtainable from cow rumen metagenome and may be utilized for industrial purposes.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.141-141
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• 2017

The ubiquitin-proteasome pathway is the major regulatory mechanism in a number of cellular processes for selective degradation of proteins and involves three steps: (1) ATP dependent activation of ubiquitin by E1 enzyme, (2) transfer of activated ubiquitin to E2 and (3) transfer of ubiquitin to the protein to be degraded by E3 complex. F-box proteins are subunit of SCF complex and involved in specificity for a target substrate to be degraded. F-box proteins regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence. However, little is known about the F-box genes in wheat. The draft genome sequence of wheat (IWGSC Reference Sequence v1.0 assembly) used to analysis a genome-wide survey of the F-box gene family in wheat. The Hidden Markov Model (HMM) profiles of F-box (PF00646), F-box-like (PF12937), F-box-like 2 (PF13013), FBA (PF04300), FBA_1 (PF07734), FBA_2 (PF07735), FBA_3 (PF08268) and FBD (PF08387) domains were downloaded from Pfam database were searched against IWGSC Reference Sequence v1.0 assembly. RNA-seq paired-end libraries from different stages of wheat, such as stages of seedling, tillering, booting, day after flowering (DAF) 1, DAF 10, DAF 20, and DAF 30 were conducted and sequenced by Illumina HiSeq2000 for expression analysis of F-box protein genes. Basic analysis including Hisat, HTseq, DEseq, gene ontology analysis and KEGG mapping were conducted for differentially expressed gene analysis and their annotation mappings of DEGs from various stages. About 950 F-box domain proteins identified by Pfam were mapped to wheat reference genome sequence by blastX (e-value < 0.05). Among them, more than 140 putative F-box protein genes were selected by fold changes cut-offs of > 2, significance p-value < 0.01, and FDR<0.01. Expression profiling of selected F-box protein genes were shown by heatmap analysis, and average linkage and squared Euclidean distance of putative 144 F-box protein genes by expression patterns were calculated for clustering analysis. This work may provide valuable and basic information for further investigation of protein degradation mechanism by ubiquitin proteasome system using F-box proteins during wheat development stages.