• Korean Journal of Veterinary Research
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• v.51 no.3
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• pp.209-216
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• 2011

Four strains of fowl adenovirus (FAdV) were isolated from 4 flocks of broiler or layer chickens affected by hydropericardium syndrome in Korea. These FAdVs were classified as serotype 4 by restriction fragment length polymorphism patterns of hexon genes and whole genomes. The virus exhibited cytopathic effects consisting of rounding, ballooning and clustering in primary chicken embryo liver cell cultures. In transmission electron microscopy, virus particles in hexagonal shape aggregated exclusively in the nuclei of hepatocytes of the chickens as the typical appearances in adenovirus infections. Buoyant density of the virus in cesium chloride (CsCl) was 1.34 g/mL. The virus was stable to chloroform, ether, 50~70% ethanol, acidic condition at pH 3, 0.25% trypsin (1 : 250), heat at $50^{\circ}C$ for 30 min, but labile to 100% ethanol, heat at $52{\sim}60^{\circ}C$ for 30 min, 1 M $MgCl_2$ at $50^{\circ}C$ for 1 h, 1 : 2,000 formalin (37%). All of the physicochemical properties pertained to the characteristics of adenoviruses. Eight viral polypeptides were determined in CsCl-purified virus by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.

• Proceedings of the Korean Aquaculture Society Conference
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• 2003.10a
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• pp.134-135
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• 2003

The geographic expansion of the toxic dinoflagellates genus Alexandrium has been shown to be world wide ranging. The members of the genus Alexandrium ocnstituted of 20-30 species did not show substantial differences in their morphology, which is mostly referred in the 'tamarensis species complex', except some species. Though rDNA sequences variations are very few and pseudogene types are so diverse that it is difficult to use them as the specific markers. In this study, we outlined Korean and Japanese A, tamarense and A. catenella regional isolates by phylogenetic analysis inferred from no cutting alignments of LSU rDNA D1-D2 and SSU rDNA sequences to group these regional isolates. The results were compared to RFLP patterns of PCR products targeted chloroplast DNA. Lastly screening of highly repeated microsatellite DNA which is frequently used for population analysis in eukaryotes was conducted. A. catenella regional strains identified by the sequencing of rDNA D1-D2 domain were divided into at least 3 groups of type E, CMC and Chinese type, divergence root may not be deep comparing with that of A. tamarense whose pseudogenes are very variable. Results of RFLP pattern and the phylogeny of the unknown gene targeting chloroplast showed that Korean and Japanese A. catenella regional isolates were divided into 3 types: Korean, Japanese and the third CMC types. Population-specific PCR amplification with Japanese A. catenella type-specific PCR primers was useful method for population analysis of A. catenella. Various types of satellite sequences such as 5 nucleotides repeats were obtained from A. tamarense and A. catenella. The 5 nucleotides repeats were primed at the both 3'and 5' ends, and these repeats were prominent as longer repeated motifs. This repeated DNA was intercalated as internal sequences containing various types subrepeats. It is expected that these satellite DNA would be a useful molecular population marker through detail comparison among Alexandrium regional isolates to trace their transferring pathway and to prevent their human-associated their regional extents.

• Korean Journal of Agricultural Science
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• v.38 no.1
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• pp.51-63
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• 2011

BoLA (bovine leukocyte antigens) have been known as gene complex related with bovine diseases and immunological traits. This study was conducted to find out the characteristics of BoLA-DRB3 gene related to mastitis and BL(bovine leukocyte) from 280 cattle [193 animals of Holstein cattle and 87 animals of Hanwoo]. As a result, five PCR-RFLP types (b, d, e, f and g) using HaeIII restriction enzyme, three BstYI restriction patterns (b, d and e) and eight RsaI restriction types(b, d, f, I, j, n, o and w) were identified. Moreover, we identified new d' type ($197{\rightarrow}175$/22), having one more cutting site by BstYI enzyme than d type allele and n' type ($180{\rightarrow}169$/11) having one more cutting site by RsaI enzyme than n allele was additionally identified. Next, we identified 53 SNPs in BoLA-DRB3 exon2 from 280 cattle. SNP frequency and heterozygosity of Holstein and Hanwoo were investigated in all the SNP genotype. These results might be based on research for identifying marker associated with bovine diseases.

• Journal of Microbiology
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• v.44 no.1
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• pp.29-34
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• 2006

The purpose of this study was to develop molecular identification method for medical mushrooms and their preparations based on the nucleotide sequences of nuclear large subunit (LSD) rDNA. Four specimens were collected of each of the three representative medicinal mushrooms used in Korea: Ganoderma Incidum, Coriolus versicolor, and Fomes fomentarius. Fungal material used in these experiments included two different mycelial cultures and two different fruiting bodies from wild or cultivated mushrooms. The genomic DNA of mushrooms were extracted and 3 nuclear LSU rDNA fragments were amplified: set 1 for the 1.1-kb DNA fragment in the upstream region, set 2 for the 1.2-kb fragment in the middle, and set 3 for the 1.3-kb fragment downstream. The amplified gene products of nuclear large subunit rDNA from 3 different mushrooms were cloned into E. coli vector and subjected to nucleotide sequence determination. The sequence thus determined revealed that the gene sequences of the same medicinal mushroom species were more than $99.48\%$ homologous, and the consensus sequences of 3 different medicinal mushrooms were more than $97.80\%$ homologous. Restriction analysis revealed no useful restriction sites for 6-bp recognition enzymes for distinguishing the 3 sequences from one another, but some distinctive restriction patterns were recognized by the 4-bp recognition enzymes AccII and HhaI. This analysis was also confirmed by PCR-RFLP experiments on medicinal mushrooms.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.244-244
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• 2017

Soil salinity due to accumulation of salts particularly sodium chloride affects agricultural lands and their vegetation. Generally, rice is a moderately sensitive plant with some cultivars with varying tolerance to salinity. Though there are physiological differences between salt-sensitive and salt-tolerant rice cultivars, both are still affected especially during high salinity and prolonged exposure. This also ultimately affects their indigenous bacterial endophytes particularly those that inhabit the rice seed endosphere. This study investigates the dynamic structure of seed bacterial endophytes of salt-sensitive and tolerant rice cultivars grown in different levels of soil salinity. Endophytic bacterial diversity was studied Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis. Results revealed a very interesting pattern of diversity and shifts in community structure of bacterial endophytes in the rice seeds. There is a general decrease in diversity for the salt-sensitive rice cultivar, IR29 as soil salinity increases. For the salt-tolerant cultivars, IC32 and IC37, diversity interestingly increased at moderate salinity then decreased at high soil salinity. The patterns of community structure is also strikingly different for the salt-sensitive and salt-tolerant rice cultivars. IR29 has a more even distribution of abundance, but under soil salinity, the community shifted where Curtobacterium, Pantoea, Flavobacterium and Microbacterium become the more dominant bacterial communities. For IC32 and IC37, the dominant bacterial groups under normal stress conditions were also the dominant bacterial groups during salt stress conditions. Their seed bacterial community is dominated by endophytes belonging to Microbacterium, Flavobacterium, Pantoea, Kosakonia and Enterobacter. Stenotrophomonas and Xanthomonas have not changed in terms of abundance under different salinity stress level in the salt-sensitive and salt-tolerant rice cultivars. This study showed that soil salinity greatly influenced the seed bacterial communities of rice seeds irrespective of their physiological tolerance to salinity.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.11
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• pp.1515-1520
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• 2012

Insulin-like growth factor binding protein-3 (IGFBP-3) gene is important for regulation of growth and development in mammals. The present investigation was carried out to study DNA polymorphism by PCR-RFLP of IGFBP-3 gene and its effect on fibre traits of Chinese Inner Mongolian cashmere goats. The fibre traits data investigated were cashmere fibre diameter, combed cashmere weight, cashmere fibre length and guard hair length. Four hundred and forty-four animals were used to detect polymorphisms in the hircine IGFBP-3 gene. A 316-bp fragment of the IGFBP-3 gene in exon 2 was amplified and digested with HaeIII restriction enzyme. Three patterns of restriction fragments were observed in the populations. The frequency of AA, AB and BB genotypes was 0.58, 0.33 and 0.09 respectively. The allelic frequency of the A and B allele was 0.75 and 0.25 respectively. Nucleotide sequencing revealed a C>G transition in the exon 2 region of the IGFBP-3 gene resulting in R158G change which caused the polymorphism. Least squares analysis revealed a significant effect of genotypes on cashmere weight (p<0.0001), cashmere fibre length (p<0.001) and hair length (p<0.05) of the animals. The effect of genotypes on cashmere fibre diameter was not statistically significant (p>0.05). The animals of AB and BB genotypes showed higher cashmere weight, cashmere fibre length and hair length than the animals possessing AA genotype. These results suggested that polymorphisms in the hircine IGFBP-3 gene might be a potential molecular marker for cashmere weight in cashmere goats.

• Parasites, Hosts and Diseases
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• v.53 no.3
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• pp.349-353
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• 2015

Anisakis simplex sensu stricto (s.s.), Anisakis pegreffii, Anisakis berlandi (=A. simplex sp. C), and Anisakis typica are the 4 major species of Anisakis type I larvae. In the Republic of Korea (Korea), A. pegreffii, A. berlandi, and A. typica larvae in fish hosts has seldom been documented. In this study, molecular analysis was performed on Anisakis larvae from the sea eels (Astroconger myriaster), the major source of human anisakiasis in Korea, collected from Tongyeong City, a southern coastal area of Korea. All 20 sea eels examined were infected with Anisakis type I larvae (160 larvae; 8 per fish). Their species were analyzed using PCR-RFLP patterns and nucleotide sequences of internal transcribed spacers (ITS1, 5.8 subunit gene, and ITS2) and mitochondrial cytochrome c oxidase 2 (cox2). Most (86.8%; 112/129) of the Anisakis type I larvae were A. pegreffii, and 7.8% (10/129) were A. typica. The remaining 5.4% (7/129) was not identified. Thus, A. pegreffii is the major species of anisakid larvae in sea eels of the southern coast of Korea.

• Parasites, Hosts and Diseases
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• v.52 no.1
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• pp.9-19
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• 2014

Anisakis spp. (Nematoda: Anisakidae) parasitize a wide range of marine animals, mammals serving as the definitive host and different fish species as intermediate or paratenic hosts. In this study, 18 fish species were investigated for Anisakis infection. Katsuwonus pelamis, Euthynnus affinis, Caranx sp., and Auxis thazard were infected with high prevalence of Anisakis type I, while Cephalopholis cyanostigma and Rastrelliger kanagurta revealed low prevalence. The mean intensity of Anisakis larvae in K. pelamis and A. thazard was 49.7 and 5.6, respectively. A total of 73 Anisakis type I larvae collected from K. pelamis and A. thazard were all identified as Anisakis typica by PCR-RFLP analysis. Five specimens of Anisakis from K. pelamis and 15 specimens from A. thazard were sequenced using ITS1-5.8S-ITS2 region and 6 specimens from A. thazard and 4 specimens from K. pelamis were sequenced in mtDNA cox2 region. Alignments of the samples in the ITS region showed 2 patterns of nucleotides. The first pattern (genotype) of Anisakis from A. thazard had 100% similarity with adult A. typica from dolphins from USA, whereas the second genotype from A. thazard and K. pelamis had 4 base pairs different in ITS1 region with adult A. typica from USA. In the mtDNA cox2 regions, Anisakis type I specimens from A. thazard and K. pelamis showed similarity range from 94% to 99% with A. typica AB517571/DQ116427. The difference of 4 bp nucleotides in ITS1 regions and divergence into 2 subgroups in mtDNA cox2 indicating the existence of A. typica sibling species in the Makassar Strait.

• Korean Journal of Microbiology
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• v.37 no.2
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• pp.137-144
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• 2001

In order to investigate the diversity of bacterial community in the mud flat of Sunchon Bay, Chunnam province, diversity of amplified 16S rDNA was examined. Total DNA was extracted from sediment soils and 16S rDNAs were amplified using PCR primers based on the universally conserved sequences in bacteria. Clonal libraries were constructed and 111 clones were examined by amplified rDNA restriction analysis (ARDRA) using HaeIII. Clones were clustered based on restriction patterns using computer program, GelCompar II. One hundred different RFLP types were detected from 111 clones. The 20 clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the bacterial diversity in the clone libraries. None of the clones were identical to any representatives in the Ribosomal Database Project small subunit RNA databases and GenBank. All sequences showed between 77 and 96.8% similarity to the known 16s rRNA sequence from cultured organisms. The 20 clones sequenced fell into seven major lineages of the domain Bacteria: alpha-, delta-, gamma-Proteobacteria, low G+C Gram positive bacteria, high G+C Gram positive bacteria, Sphingobacteria (Cytophaga) and Cyanobacteria (chloroplast). Among the clones, the Proteobacteria were dominant.

• Journal of Embryo Transfer
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• v.31 no.1
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• pp.61-64
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• 2016

We developed a polymerase chain reaction (PCR)-based molecular method for sexing and identification using sexual dimorphism between the Zinc Finger-X and -Y (ZFX-ZFY) gene and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) for mitochondrial DNA (mtDNA) cytochrome B (CYTB) gene in meat pieces and commercial sausages from animals of different origins. Sexual dimorphism based on the presence or absence of SINE-like sequence between ZFX and ZFY genes showed distinguishable band patterns between male and female DNA samples and were easily detected by PCR analyses. Male DNA had two PCR products appearing as distinct two bands (ZFX and ZFY), and female DNA had a single band (ZFX). Molecular identification was carried out using PCR-RFLP of CYTB gene, and showed clear species classification results. The results yielded identical information on the sexes and the species of the meat samples collected from providers without any records. The analyses for DNA isolated from commercial sausage showed that pig was the major source but several sausages originated from chicken and Atlantic cod. Applying this PCR-based molecular method was useful and yielded clear sex information and identified the species of various tissue samples originating from livestock.