• Journal of Wetlands Research
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• v.22 no.2
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• pp.100-105
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• 2020

Northern pipevine (Aristolochia contorta) commonly inhabits marginal areas between waterside and terrestrial vegetation. In particular, A. contorta is ecologically important in the marginal areas as a food plant of dragon swallowtail butterfly (Sericinus montela), which is designated as vulnerable species in the Republic of Korea. For long-term sustainability of the plant population, assessment of the genetic diversity of exist populations should be conducted. Genomic DNA of A. contorta leaf samples were extracted from four populations where the vigorous growth were observed in the South Korea. Intra-population genetic diversity and inter-population genetic distance were assessed using randomly amplified polymorphic DNA (RAPD) with five polymorphic random primers. Overall genetic diversity was lower, compared to other wetland species (h: 0.0607 ~ 0.1401; I: 0.0819 ~ 0.1759), while GP showed the highest intra-population genetic diversity. Despite of the geographical distance, GP showed the larger genetic distance from other populations. This result seemed to be caused by the fragmented habitat and lower sexual reproduction of A. controta. Mixture of the different source populations and construction of the proper environmental condition such as shade and physical support for sexual reproduction should be considered for conservation of A. contorta population.

• The Korean Journal of Mycology
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• v.26 no.4 s.87
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• pp.574-582
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• 1998

Five basidiocarps of Pholiota species have been collected from the areas of BubJu Temple for last two years, and identified to those of P. adiposa or Pholiota species. The taxonomy of these basidiocarps with the morphological aspects was compared with the analysis obtained from the polymorphisms of PCR-RAPD bands made after reacted with the random primers. The polymorphic variations were observed within the species of the basidiocarps, but not between genomic DNA's of the mycelia obtained and the basidiocarps. Several different bands made from the primers (28 and 36) in PCR-RAPD reactions were identified within the genus of Pholiota and speculated to be specific for the individual basidiocarp of P. adiposa collected. The primers employed here were considered to be very useful for distinguishing the individual isolates or basidiocarps collected from the fields. Also, the basidiospores were obtained from the sporeprints of the above basidiocarps as a simple agar and confirmed with observations of clamp connection under microscopes. The matings of them indicated the 'tetrapolar' type, being different from the 'bipolar' type reported by Japanese basidiocarps of P. adiposa or P. nameko. Based on our work, the edible fungi collected were speculated to be a new breeding resource for those of Pholiota commercialized in Japan.

• Journal of Microbiology and Biotechnology
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• v.14 no.1
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• pp.110-115
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• 2004

This study was undertaken to develop PCR primers for the simultaneous detection of Fusobacterium nucleatum and Actinobacillus actinomycetemcomitans, using two species-specific reverse primers in combination with a single conserved forward primer. These primers target the variable and conserved regions of the 16S rDNA. The primer specificity was tested against (i) four F. nucleatum and three A. actinomycetemcomitans strains and (ii) seven representatives of the different species of oral bacteria. The primer sensitivity was determined by testing serial dilutions of the purified genomic DNA of F. nucleatum and A. actinomycetemcomitans. The data indicate that species-specific amplicons could be obtained for all the F. nucleatum and A. actinomycetemcomitans strains tested, which were not found in the seven other species. The multiplex PCR could detect as little as 4 fg of chromosomal DNA of F. nucleatum and A. actinomycetemcomitans simultaneously. These findings suggest that these PCR primers are highly sensitive and are suitable for applications in epidemiological studies, diagnosis, and monitoring F. nucleatum and A. actinomycetemcomitans after the treatment of periodontitis.

• Journal of Microbiology
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• v.45 no.6
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• pp.541-546
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• 2007

Red algae are distributed globally, and the group contains several commercially important species. Griffithsia okiensis is one of the most extensively studied red algal species. In this study, we conducted expressed sequence tag (ESTs) analysis and synonymous codon usage analysis using cultured G. okiensis samples. A total of 1,104 cDNA clones were sequenced using a cDNA library made from samples collected from Dolsan Island, on the southern coast of Korea. The clustering analysis of these sequences allowed for the identification of 1,048 unigene clusters consisting of 36 consensus and 1,012 singleton sequences. BLASTX searches generated 532 significant hits (E-value <$10^{-4}$) and via further Gene Ontology analysis, we constructed a functional classification of 434 unigenes. Our codon usage analysis showed that unigene clusters with more than three ESTs had higher GC contents (76.5%) at the third position of the codons than the singletons. Also, the majority of the optimal codons of G. okiensis and Chondrus crispus belonging to Bangiophycidae were G-ending, whereas those of Porphyra yezoensis belonging to Florideophycidae were G-ending. An orthologous gene search for the P. yezoensis EST database resulted in the identification of 39 unigenes commonly expressed in two rhodophytes, which have putative functions for structural proteins, protein degradation, signal transduction, stress response, and physiological processes. Although experiments have been conducted on a limited scale, this study provides a material basis for the development of microarrays useful for gene expression studies, as well as useful information for the comparative genomic analysis of red algae.

• Korean Journal of Poultry Science
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• v.36 no.1
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• pp.85-88
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• 2009

One of the mitochondrial genes, called cytochrome c oxidase I (COI), has been widely used for the species identification (called bio-barcode) in birds. In this study, the bio-barcode has been applied to chicken breeds in Korea whether it also can be used as a molecular marker for breed identification. Data indicated that Korean native chicken has the mixed SNP (single nucleotide polymorphism) patterns between White Leghorn (Layer) and Cornish (Broiler) and ultimately, it can not be used as the marker for breed identification. However, this result indicates the mixed use of the Korean native chicken, since it has been used for dual purpose for producing meat and egg for a long time. In order to use as a marker for species identification, more reliable mitochondrial and/or nuclear DNA markers need to be developed.

• 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.

• Ocean and Polar Research
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• v.38 no.3
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• pp.185-193
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• 2016

In this study, antioxidative potentials of the crude extract and its four solvent fractions from the Arctic terrestrial plant Ranunculus heperporeus were evaluated by using four different activity tests, including the inhibition of intracellular reactive oxygen species (ROS) and lipid peroxidation in Raw 264.7 cells as well as determining the extent of both the scavenging of peroxynitrite ($ONOO^-$) and the oxidative damage of genomic DNA purified from Raw 264.7 cells. Based on a comparative analysis, n-BuOH, and 85% aq.MeOH solvent fractions showed good scavenging effects on the production of intracellcular ROS and inhibited membrane lipid peroxidation and DNA oxidation. In addition, n-BuOH and 85% aq.MeOH fractions exhibited good scavenging effects on both authentic peroxynitrite and one generated from SIN-1. Among the samples tested, the n-BuOH fraction revealed the strongest antioxidant effect.

• Journal of Microbiology and Biotechnology
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• v.16 no.11
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• pp.1826-1831
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• 2006

A novel hyperthermophilic, anaerobic, heterotrophic archaeon, designated strain $NA1^T$, was isolated from a deep-sea hydrothermal vent area (depth, 1,650 m) within the Papua New Guinea-Australia-Canada-Manus (PACMANUS) field. Cells of this strain were motile by means of polar flagella, coccoid-shaped with a diameter of approximately $0.5-1.0{\mu}m$, and occurred as single cells. Optimal temperature, pH, and NaCl concentration for growth were $80^{\circ}C$, 8.5, and 3.5%, respectively. The new isolate was an obligate heterotroph that utilized yeast extract, beef extract, tryptone, peptone, casein, and starch as carbon and energy sources. Elemental sulfur was required for growth and was reduced to hydrogen sulfide. The G+C content of the genomic DNA was 52.0 mol%. Phylogenetic analysis of the 16S rRNA gene indicated that strain $NA1^T$ belongs to the genus Thermococcus, and the organism is most closely related to T. gorgonarius, T. peptonophilus, and T. celer; however, no significant homology was observed among species by DNA-DNA hybridization. Strain $NA1^T$ therefore represents a novel species for which the name Thermococcus onnurineus sp. novo is proposed. The type strain is $NA1^T$ (=KCTC 10859, =JCM 13517).

• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.15-20
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• 2010

A Gram negative, aerobic, nonspore-forming, straight or curved rod-shaped bacterium, designated Gsoil $317^T$, was isolated from soil of a ginseng field in Pocheon Province (South Korea) and was characterized using a polyphasic approach. Cells were dimorphic, with stalk (or prostheca) and nonmotile or nonstalked and motile, by means of a single polar flagellum. Comparative analysis of 16S rRNA gene sequences revealed that strain Gsoil $317^T$ was most closely related to Caulobacter mirabilis LMG $24261^T$ (97.2%), Caulobacter fusiformis ATCC $15257^T$ (97.1 %), Caulobacter segnis LMG $17158^T$ (97.0%), Caulobacter vibrioides DSM $9893^T$ (96.8%), and Caulobacter henricii ATCC $15253^T$ (96.7%). The sequence similarities to any other recognized species within Alphaproteobacteria were less than 96.0%. The detection of Q-10 as the major respiratory quinone and a fatty acid profile with summed feature 7 ($C_{18:1}\;{\omega}7c$ and/or $C_{18:1}\;{\omega}9t$ and/or $C_{18:1}\;{\omega}12t;$ 56.6%) and $C_{16:0}$ (15.9%) as the major fatty acids supported the affiliation of strain Gsoil $317^T$ to the genus Caulobacter. The G+C content of the genomic DNA was 65.5 mol%. DNA-DNA hybridization experiments showed that the DNA-DNA relatedness values between strain Gsoil $317^T$ and its closest phylogenetic neighbors were below 11%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain Gsoil $317^T$ should be classified as representing a novel species in the genus Caulobacter, for which the name Caulobacter ginsengisoli sp. novo is proposed. The type strain is Gsoil $317^T$ (=KCTC $12788^T=DSM\;18695^T$).

• Journal of Microbiology and Biotechnology
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• v.12 no.1
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• pp.176-181
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• 2002

In order to isolate and identify Bifidobacterium spp. that originated in Korea, feces were sampled from healthy Korean adults and children living in three villages, the first having a history of longevity and the other two where the diet did not include fermented milk or any pharmaceutical preparations. Through the use of Gram staining and microscopic examination for cell morphology, 23 bacterial strains presumed to be the Bifidobacterium genus were isolated from the feces of 13 out of a total of 59 Korean people. To identify the Bifidobacterium strains at the genus level, these bacteria were then analyzed by TLC and the fructose-6-phosphate phosphoketolase (F6PPK) test. The result showed that 22 of the isolated strains were confirmed to be members of the genus Bifidobacterium. All of these bifidobacteria were also identified as Bifidobacterium spp. by the fermentation test. Using a RFLP analysis, an attempt was made to identify the Bifidobacterium spp. that had been isolated from both Korean adults and children. In a genomic Southern blot analysis after digestion with two restriction enzymes (EcoRI, HindIII), all of the 14 randomly selected Korean isolates showed patterns identical to those of three different B. longum species. Another restriction enzyme, CfoI (4-bp recognition enzyme), was then used to identify the strain. Interestingly, all the Korean isolates were identified as B. longum ATCC 15708, indicating that a RFLP analysis was effective for identifying Bifidobacterium spp. at both the strain and species levels.