• Asian-Australasian Journal of Animal Sciences
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• v.19 no.3
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• pp.324-328
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• 2006

Carbonic anhydrase III (CA3) is a member of a multigene family that encode carbonic anhydrase isozymes. In this study, a complete coding sequence of the pig CA3 gene which encodes a 260 amino-acid protein was determined. The amino acid comparison showed high sequence similarities with previously identified human (86.5%) CA3 gene and mouse (91.5%) Car3 gene. The partial genomic DNA sequences were also investigated. The length of intron 1 was 727 bp. Comparative sequencing of three pig breeds revealed that there was a T${\rightarrow}$C substitution at position 363 within intron 1. The substitution was situated within a NcoI recognition site and was developed as a PCR-restriction fragment length polymorphism (RFLP) marker for further use in population variation investigations and association analysis. Two alleles (A and B) were identified, and 617 bp fragments were observed for the AA genotype and 236 bp and 381 bp fragments for the BB genotype. The polymorphism of CA3 was detected in 8 pig breeds. Allele B was predominant in the Western pig breeds. In addition, association studies of the CA3 polymorphism with carcass traits in 140 $Yorkshire{\times}Meishan$ $F_2$ offspring showed that the NcoI PCR- RFLP genotype may be associated with variation in several carcass traits of interest for pig breeding. Allele B was associated with increases in lean meat percentage, loin eye height and loin eye area. Statistically significant association with backfat thickness was also found; pigs with the AB genotype had much less backfat thickness than AA or BB genotypes.

• Journal of Life Science
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• v.19 no.12
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• pp.1718-1723
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• 2009

In this study, we characterized extended-spectrum $\beta$-lactamase (ESBL)-producing Enterobacteriaceae isolated from clinical specimens in Korea and found two strains harboring plasmid-mediated $bla_{SHV-11}$, Klebsiella pneumoniae. First, the isolates were detected using the Vitek system and confirmed by the double-disk synergy test. The classification of gene coding for ESBL was also performed by polymerase chain reactions and followed by DNA sequencing. The transmission of genes was confirmed by transconjugation and transformation. Resistant expression of transformants was determined by broth microdilution minimal inhibitory concentration test. Genotypic analysis revealed that one strain harbored the $bla_{TEM-1}$, $bla_{SHV-11}$ and $bla_{CTX-M-15}$ and the other strain harbored the $bla_{SHV-11}$ and $bla_{CTX-M-15}$. They showed high resistance to oxyiminocephalosphorins (3rd-generation cephalosporins), while the transformant containing only $bla_{SHV-11}$ did not show any resistance to the antibiotics.

• Journal of Periodontal and Implant Science
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• v.31 no.4
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• pp.787-801
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• 2001

The molecular mechanisms control the function of PDL(periodonta1 ligament) cells and/or fibroblasts remain unclear. PDLsl7, PDL-specific gene, had previousely　identified the cDNA for a novel protein from cultured　PDL fibroblasts using subtraction hybridization between gingival fibroblasts and　PDL fibroblasts. The purpose　of this study was to determine the regulation by growth factors and cytokines on　PDLsl7 gene expression in　cultured human periodontal ligament cells and observe the immunohistochemical　localization of PDLsl7 protein in various tissues of mouse. Primary PDL fibroblasts isolated by scraping the root of the extracted human mandibular third molars. The cells were incubated with various concentration of human recombinant $IL-1{\beta}$, PDGF-BB and TGF\;${\beta}$ for 48h nd 2 weeks. At each time point total RNA was extracted and the levels of transcription ere assessed by reverse transcription-polymerase chain reaction (RT-PCR assay). polyclonal antiserum raised against PDLsl7 peptides, CLSVSYNRSYQINE and SEAVHETDLHDGC, were made, and stained the tooth, periodontium, developing bone, bone marrow and mid-palatal suture of the mouse. The results were as follows. 1. PDLsl7 mRNA levels were increased in response to PDGF (10ng/ml) and $TGF\;{\beta}$(20ng/ml) after treatment of the $IL-1{\beta}$, PDGF-BB and $TGF{\beta}$for 48 h. 2. PDLsl7 was up-regulated only by $TGF{\beta}$(20 ng/ml) after treatment of the $IL-1{\beta}$, PDGF-BB and $TGF\;{\beta}$ for 2 weeks and unchanged by the other stimulants. 3. PDLsl7 was a novel protein coding the 142 amino acid peptides in the ORF and the nucleotide sequences of the obtained cDNA from RT-PCR was exactly same as the nucleotides of the database. 4. Immunohistochemical analysis showed that PDLsl7 is preferentially expressed in the PDL, differentiating osteoblast-like cells and stromal cells of the bone marrow in the adult mouse. 5. The expression of PDLsl7 protein was barely detectable in gingival fibroblasts, hematopoetic cells of the bone marrow and mature osteocytes of the alveolar bone. These results suggest that PDLsl7 might upregulated by PDGF-BB or $TGF{\beta}$ and acts at the initial stage of differentiation when the undifferentiated mesenchymal cells in the bone marrow and PDL differentiate into multiple cell types. However, more research needs to be performed to gain a better understanding of the exact function of PDLsl7 during the differentiation of bone marrow mesenchymal and PDL cells.

• Journal of the Korean Chemical Society
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• v.51 no.6
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• pp.543-548
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• 2007

Maturity-onset diabetes of the young (MODY) is a genetically heterogeneous subtype of Type 2 diabetes characterized (non-insulin-dependent) by early onset, usually before 25 years of age, autosomal dominant inheritance and a primary defect in insulin secretion. Mutations in the glucokinase (GCK) and hepatocyte nuclear factor (HNF)-1α genes are the major causes of monogenic forms of Type 2 diabetes mellitus. Therefore it is need to study relation with these polymorphisms by diverse analysis methods. The promotor and coding regions inclusive intron exon boundaries of the GCK, HNF-1α genes were examined by PCR-DHPLC (Polymerase Chain Reaction - Denaturing High Performance Liquid Chromatography) and direct sequencing. We extracted DNA from 11 patients and 20 normals. Then we confirmed a single-nucleotide polymorphism using PCR-DHPLC. As results, we identified one mutation (R135G) in GCK gene and two mutations (I27L, S487N) in HNF-1a and at the same time detected mutation in intron 8.

• The Korean Journal of Malacology
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• v.25 no.3
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• pp.223-230
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• 2009

Metallothioneins (MTs) play a key role in metallic homeostasis and detoxification in most living organisms. In an attempt to study the biological functions and significance of MT in a snail, we cloned and partially characterized the MT gene from the left-handed snail, Physa acutawhich has been regarded as a potential biomonitering species for fresh water. The complete cDNA sequence of PaMT cDNA was identified from the expressed sequence tag (EST) sequencing project of Physa acuta. The coding region of 180 bp gives 60 amino acid residues including the initiation methionine and termination codon. Clustering and phylogenic analysis of PaMT with other MT amino acid sequences show that it has some identities to Helix pomatia (60%), Arianta arbustorum (58%), Perna viridis (49%), Mytilus edulis (49%), Bathymodiolus azoricus (49%), Bathymodiolus azoricus (48%) and Bathymodiolus sp. FD-2002 (48%). Time dependent induction for PaMT from P. acuta exposed with cadmium (50 ppb) indicated that PaMT was induced at 4-8 hr after exposure. It remains to further develop PaMTas a potential biomarker for water contamination in fresh water.

• Korean Journal of Ichthyology
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• v.33 no.4
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• pp.217-225
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• 2021

The family Platycephalidae is a taxonomic group of economically important demersal flathead fishes that predominantly occupy tropical or temperate estuaries and coastal environments of the Indo-Pacific oceans and the Mediterranean Sea. In this study, we for the first time analyzed the complete mitochondrial genome (mitogenome) of the flathead Platycephalus cultellatus Richardson, 1846 from Vietnam by Next Generation Sequencing method. Its mitogenome was 16,641 bp in total length, comprising 13 protein-coding genes (PCGs), two ribosomal RNA genes, and 22 transfer RNA genes. The gene composition and order of the mitogenome were identical to those of typical vertebrates. The phylogenetic trees were reconstructed based on the concatenated nucleotide sequence matrix of 13 PCGs and the partial sequence of a DNA barcoding marker, cox1 in order to determine its molecular phylogenetic position among the order Scorpaeniformes. The phylogenetic result revealed that P. cultellatus formed a monophyletic group with species belonging to the same family and consistently clustered with one nominal species, P. indicus, and two Platycephalus sp. specimens. Besides, the cox1 tree confirmed the taxonomic validity of our specimen by forming a monophyletic clade with its conspecific specimens. The mitogenome of P. cultellatus analyzed in this study will contribute valuable information for further study on taxonomy and phylogeny of flatheads.

• The Plant Pathology Journal
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• v.38 no.5
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• pp.541-549
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• 2022

Potato late blight caused by Phytophthora infestans is a destructive disease in Korea. To elucidate the genomic variation of the mitochondrial (mt) genome, we assembled its complete mt genome and compared its sequence among different haplotypes. The mt genome sequences of four Korean P. infestans isolates were revealed by Illumina HiSeq. The size of the circular mt genome of the four major genotypes, KR_1_A1, KR_2_A2, SIB-1, and US-11, was 39,872, 39,836, 39,872, and 39,840 bp, respectively. All genotypes contained the same 61 genes in the same order, comprising two RNA-encoding genes, 16 ribosomal genes, 25 transfer RNA, 17 genes encoding electron transport and ATP synthesis, 11 open reading frames of unknown function, and one protein import-related gene, tatC. The coding region comprised 91% of the genome, and GC content was 22.3%. The haplotypes were further analyzed based on sequence polymorphism at two hypervariable regions (HVRi), carrying a 2 kb insertion/deletion sequence, and HVRii, carrying 36 bp variable number tandem repeats (VNTRs). All four genotypes carried the 2 kb insertion/deletion sequence in HVRi, whereas HVRii had two VNTRs in KR_1_A1 and SIB-1 but three VNTRs in US-11 and KR_2_A2. Minimal spanning network and phylogenetic analysis based on 5,814 bp of mtDNA sequences from five loci, KR_1_A1 and SIB-1 were classified as IIa-6 haplotype, and isolates KR_1_A2 and US-11 as haplotypes IIa-5 and IIb-2, respectively. mtDNA sequences of KR_1_A1 and SIB-1 shared 100% sequence identity, and both were 99.9% similar to those of KR_2_A2 and US-11.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.11
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• pp.1519-1523
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• 2005

By screening a subtracted cDNA library constructed with mRNA obtained from the longissimus dorsi muscles of F1 hybrids Landrace${\times}$Yorkshire and their Yorkshire female parents, we isolated two partial sequences coding for the H3-K4-specific methyltransferase (KIAA1717) and skeletal muscle myosin regulatory light chain (HUMMLC2B) genes. In the present work we investigated two SNPs, one (C1354T) at the 3' untranslated region (UTR) of KIAA1717 and one (A345G) at the SINE (PRE-1) element of HUMMLC2B, in a resource population derived from crossing Chinese Meishan and Large White pig. The selected pigs were genotyped by means of a PCR-RFLP protocol. Significant associations were observed for the KIAA1717 C1354T polymorphic site with thorax-waist backfat thickness (p<0.05), buttock backfat thickness (p<0.05), average backfat thickness (p<0.05), loin eye height (p<0.05), loin eye area (p<0.05), carcass length to 1$^{st}$ spondyle (p<0.01) and carcass length to 1st rib (p<0.01). HUMMLC2B A345G were significantly associated with loin eye width (p<0.05), loin eye area (p<0.05). Further studies are needed to confirm these preliminary results.

• Journal of Embryo Transfer
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• v.23 no.3
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• pp.197-201
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• 2008

In order to provide information of genetic variants for Haptoglobin (Hp) gene, which may be related to weight traits in pig, a total of 235 animals from National Institute of Animal Science (NIAS) were screened with 3 primers. The primer sequences were selected using the porcine cDNA sequences based on NM_214000, and the exon boundaries were estimated. Genetic variants were observed using direct sequencing analysis, and there were 9 SNPs detected at nucleotide positions 503 (A/G), 509 (A/G), 709 (C/T), 734 (C/A), 742 (G/A), 769 (A/G), 840 (C/T), 876 (C/T) and 882 (C/A). All the SNPs were located in coding regions, and mutations caused amino acid changes at nucleotide positions 503, 509, 734, 742 and 769. Allele frequencies of SNPs were estimated for all segments. The SNPs at nucleotide position 509 (p<0.0001) and 734 (p<0.05) were significantly associated with average daily gain, but no significance was observed with other SNPs. From the results, the identified SNPs may be a useful candidate marker for the porcine weight gain traits.