• Journal of Veterinary Clinics
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• v.31 no.1
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• pp.36-39
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• 2014

Many bacteria colonized in the horse semen affect quality of the sperm and some may cause infection in the mare reproductive tract and infertility of susceptible mare. This study was initiated to determine the prevalence of bacteria in testes of Jeju horses by determining rRNA sequence. The samples were swabed from the testes of nine Jeju horses (aged from 8 to 12 months after birth). Bacteria isolated from testes were identified by 16S rDNA sequencing. 1.6-kbp PCR products for 16S rRNA coding region were obtained using the universal primers. The PCR products were further purified and sequenced. Maximum similar species were found by BLAST search in the GenBank DNA database. BLAST results showed that the sequences were similar to those of Acinetobacter sp (A. schindleri, A. ursingii)., Bacillus cereus, Corynebacterium glutamicum, Escherichia coli, Gamma proteobacterium, Micrococcus luteus, Pseudomonas mendocina, Shigella sonnei, Sphingomonas sp., Staphylococcus sp (S. cohnii, S. saprophyticus, S. xylosus)., and Stenotrophomonas maltophilia. DNA sequences for 16S rRNA is provided useful informations for species identification of pathogenic microorganisms for the reproductive organs in horses.

• Asian-Australasian Journal of Animal Sciences
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• v.31 no.1
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• pp.13-18
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• 2018

Objective: Meat quality including muscle color in chickens is an important trait and continuous selective pressures for fast growth and high yield have negatively impacted this trait. This study was conducted to investigate genetic variations responsible for regulating muscle color. Methods: Whole genome re-sequencing analysis using Illumina HiSeq paired end read method was performed with pooled DNA samples isolated from two broiler chicken lines divergently selected for muscle color (high muscle color [HMC] and low muscle color [LMC]) along with their random bred control line (RAN). Sequencing read data was aligned to the chicken reference genome sequence for Red Jungle Fowl (Galgal4) using reference based genome alignment with NGen program of the Lasergene software package. The potential causal single nucleotide polymorphisms (SNPs) showing non-synonymous changes in coding DNA sequence regions were chosen in each line. Bioinformatic analyses to interpret functions of genes retaining SNPs were performed using the ingenuity pathways analysis (IPA). Results: Millions of SNPs were identified and totally 2,884 SNPs (1,307 for HMC and 1,577 for LMC) showing >75% SNP rates could induce non-synonymous mutations in amino acid sequences. Of those, SNPs showing over 10 read depths yielded 15 more reliable SNPs including 1 for HMC and 14 for LMC. The IPA analyses suggested that meat color in chickens appeared to be associated with chromosomal DNA stability, the functions of ubiquitylation (UBC) and quality and quantity of various subtypes of collagens. Conclusion: In this study, various potential genetic markers showing amino acid changes were identified in differential meat color lines, that can be used for further animal selection strategy.

• Microbiology and Biotechnology Letters
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• v.18 no.3
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• pp.309-316
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• 1990

The sequence of a 1795 bp restriction fragment containing the B. circulans F-2 gene for NaC1- dependent $\alpha$-amylase (CI-amylase) is reported. The probable coding region of the gene is 1005 base pairs (335 amino acida) long. The NaC1-dependent $\alpha$-amylase (el-amy) sequence shows an open reading frame (ORF) with the translated molecular weight of about 38, 006, which correspond to a molecular weight of about 35, 000 (Mi). The gene is preceded by the sequence resembling promoter for the vegetative B, subtitis RNA polymerases. These are followed by the sequences resembling a B. subtilis ribosome binding site 5 nucleotides before the first codon of the gene. Homologous regions with other amylases were found. The N-terminal sequences of the mature proteins expressed in E. eoli were identical to the N-terminal sequences which are anaIysed.

• The Plant Pathology Journal
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• v.19 no.2
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• pp.123-127
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• 2003

A severe disease of muskmelon (Cucumis melo cv. Alsnight) grown on rockwool in a plastic house was characterized by leaf and stem necrosis followed by death of the plants. In 2001, an isolate of Melon necrotic spot virus-MN (MNSV-MN) of the genus Camovirus was identified as the causal agent of the disease on the basis of biological reactions and nucleotide sequence analyses of coat protein (CP) gene. MNSV-MN induced necrotic local lesions on mechanically inoculated leaves and systemic necrotic spots on the upper leaves of melon cvs. Alsnight, Rui III, Party, Imperial, and Seolhang. However, the inoculated leaves of watermelon and cucumber showed only necrotic lesions. DsRNAs extracted from the melon infected with MNSV-MN were separated into three components. Molecular sizes of the dsRNAs were estimated at approximately 4.5, 1.8, and 1.6 kbp. The amplified cDNA products of CP gene for MNSV-MN by RT-PCR showed approximately 1.2 kbp. The amplified DNA was digested to three fragments by MspI treatment. The cDNA of the genomic RNA of MNSV-MN was cloned and the region deduced to encode the CP was sequenced. The CP coding region, located near 3' end of the genome, consisted of 1,170 nucleotides and had the potential to encode a 390 amino acid protein. The nucleotide and amino acid sequences of MNSV-MN CP gene were 84.0-94.6% and 90.8-94.9% identical with other MNSV isolates found in the GeneBank database, respectively. This is the first report on the occurrence of MNSV in Korea.

• The Plant Pathology Journal
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• v.27 no.2
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• pp.170-182
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• 2011

Plants possess multiple resistance mechanisms that protect themselves against pathogen attack. To identify unknown components of the defense machinery in Arabidopsis, gene-expression changes were monitored in Arabidopsis thaliana under 18 different biotic or abiotic conditions using a DNA microarray representing approximately 25% of all Arabidopsis thaliana genes (www.genevestigator.com). Seventeen genes which are early responsive to salicylic acid (SA) treatment as well as pathogen infection were selected and their T-DNA insertion mutants were obtained from SALK institute. To elucidate the role of each gene in defense response, bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 was inoculated onto individual T-DNA insertion mutants. Four mutants exhibited decreased resistance and five mutants displayed significantly enhanced resistance against Pst DC3000-infection as measured by change in symptom development as compared to wild-type plants. Among them, member of uridin diphosphate (UDP)-glycosyltransferase (UGT) was of particular interest, since a UGT mutant (At1g05680) showed enhanced resistance to Pst-infection in Arabidopsis. In systemic acquired resistance (SAR) assay, this mutant showed enhanced activation of SAR. Also, the enhanced SAR correlated with increased expression of defense-related gene, AtPR1. These results emphasize that the glycosylation of UGT74E2 is a part of the SA-mediated disease-resistance mechanism.

• Korean Journal of Plant Resources
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• v.28 no.3
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• pp.341-349
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• 2015

Magnoliae Flos (Sini in Korean) is one of the most important oriental medicinal plants. In the Korean Herbal Pharmacopeia, the bud of the all species in Manolia denudate and Manolia genus were regarded as the botanical sources for ‘Sini’. Most the dried bud of Manolia denudata, Manolia biondii and Manolia sprengeri were used as ‘Xin-yi’ in China. Therefore, the purpose of this study was to determine and compare the ‘Magnolia’ species, four species including Manolia denudata, M. biondii, M. liliiflora and M. Kobus were analysis of sequencing data revealed DNA polymorphisms. The based on tRNA coding leucine/phenylalanine (trnL-F) and NADH-plastoquinone oxidoreductase subunit 5 (ndhF) sequences in chloroplast DNA. For the identification of ‘Magnolia’ species, polymerase chain reaction (PCR) analysis of chloroplast DNA regions such as ndhF have proven an appropriate method. A single nucleotide polymorphism (SNP) has been identified between genuine “Sini” and their fraudulent and misuse. Specific PCR primers were designed from this polymorphic site within the sequence data, and were used to detect true plants via multiplex PCR.

• The Journal of Natural Sciences
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• v.5 no.1
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• pp.37-45
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• 1992

The gene coding for $\beta$-galactosidase of Neisseria lactamica 2118 was cloned into Escherichia coli MC 1061. The isolated 6.5 Kb EcoR I fragement and 7.2 Kb BamH I fragment of chromosomal DNA in Southern hybridization were ligated to a vector plasmid pBR322 and then transformed into Escherichia coli MC 1061 cells. Finally, I obtained three clones as $\beta$-galactosidase positive clone by colony hybridization and Southern hybridization($\beta$-galactosidase probe: lac Z gene of pMC1871). Three recombinant plasmids(pNL.13. 17 and 24) were found to contain the 7.2Kb BamH I fragment originated from Neisseria lactamica 2118 chromosomal DNA by Southern hybridization and pNL 24 was showed high homology to probe especially and also its physical map was constructed.

• Molecules and Cells
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• v.23 no.3
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• pp.280-286
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• 2007

L-asparaginase (EC 3.5.1.1) catalyzes the hydrolysis of the amide group of L-asparagine, releasing aspartate and $NH_4{^+}$. We isolated a low temperature-inducible cDNA sequence encoding L-asparaginase from soybean leaves. The full-length L-asparaginase cDNA, designated GmASP1, contains an open reading frame of 1,258 bp coding for a protein of 326 amino acids. Genomic DNA blotting and fluorescence in situ hybridization showed that the soybean genome has two copies of GmASP1. GmASP1 mRNA was induced by low temperature, ABA and NaCl, but not by heat shock or drought stress. E. coli cells expressing recombinant GmASP1 had 3-fold increased L-asparaginase activity. A possible function of L-asparaginase in the early response to low temperature stress is discussed.

• Horticultural Science & Technology
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• v.35 no.3
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• pp.344-360
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• 2017

Zoysiagrasses are important turf plants used for school playgrounds, parks, golf courses, and sports fields. The two most popular zoysiagrass species are Zoysia japonica and Zoysia sinica. These are widely distributed across different growing zones and are morphologically distinguishable from each other; however, it is phenotypically difficult to differentiate those that grow along the coastal line from those in beach area habitats. A combination of morphological and molecular approaches is desirable to efficiently identify these two plant cultivars. In this study, we used a rapid identification system based on DNA barcoding of the nrDNA-internal transcribed spacer (ITS) regions. The nrDNA-ITS regions of ITS1, 5.8S nrDNA, and ITS2 from Z. japonica, Z. sinica, Agrostis stolonifera, and Poa pratensis were DNA barcoded to classify these grasses according to their molecular identities. The nrDNA-ITS sequences of these species were found at 686 bp, 687 bp, 683 bp, and 681 bp, respectively. The size of ITS1 ranged from 248 to 249 bp, while ITS2 ranged from 270 to 274 bp. The 5.8S coding region ranged from 163 - 164bp. Between Z. japonica and Z. sinica, nineteen (2.8%) nucleotide sites were variable, and the G+C content of the ITS region ranged from 55.4 to 63.3%. Substitutions and insert/deletion (indel) sites in the nrDNA-ITS sequence of Z. japonica and Z. sinica were converted to cleaved amplified polymorphic sequence (CAPS) markers, and applied to the Zoysia grasses sampled to verify the presence of these markers. Among the 62 control and collected grass samples, we classified three groups: 36 Z. japonica, 22 Z. sinica, and 4 Z. japonica/Z. sinica hybrids. Morphological classification revealed only two groups; Z. japonica and Z. sinica. Our results suggest that used of the nrDNA-ITS barcode region and CAPS markers can be used to distinguish between Z. japonica and Z. sinica at the species level.

• Childhood Kidney Diseases
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• v.16 no.2
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• pp.73-79
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• 2012

Purpose: The association of mitochondrial DNA (mtDNA) mutations, deletions and copy number with progressive changes in patients with some glomerular disease and end-stage renal disease have been reported. In this study, we performed mtDNA mutation analysis in children with IgA nephropathy to investigate its role in progressive clinical course. Methods: Seven children with IgA nephropathy were involved in this study. MtDNA isolated from platelet was amplified by PCR and sequenced entirely. Results: The mean age at renal biopsy was $11.5{\pm}2.2$ year and the mean age at latest evaluation was $17.9{\pm}3.2$ year. The mean follow-up period were $7.8{\pm}3.1$ years. Patients was divided into 2 groups according to the amount of proteinuria at presenting manifestation. Group 2 patients were nephrotic syndrome. Renal function reveals within normal range in all patients. In group 2 patients, the mean serum albumin level was significantly lower than those of group 1 ($3.7{\pm}0.6g/dL$ vs. $4.7{\pm}0.2g/dL$, P=0.0241) and the mean total cholesterol level was significantly higher than those of group 1 ($222.7{\pm}35.7mg/dL$ vs. $148.3{\pm}29.1mg/dL$, P=0.0283). In Group 2 patients, total amount of protein of 24 hour collected urine also significantly higher than those of group 1 ($1,466.0{\pm}742.5mg$ vs. $122.5{\pm}48.1mg$, P=0.0135). Pr/Cr ratio in random urine sample was also higher in group 2 than those of group 1 but the statistical significance was not noted ($1.8{\pm}1.6$ vs. $0.2{\pm}0.2$, P=0.0961). Deletion of mtDNA nt 8272-8281 were observed in two patients, one patient in each groups, respectively. This is noncoding lesion. No patients demonstrated the mtDNA mutations. Conclusions: We have identified a deletion of mtDNA nt 8272-8281 in two children with IgA nephropathy. Further studies are needed to clarify the role of mitochondrial function in the progressive change of IgA nephropathy.