• Korean Journal of Microbiology
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• v.45 no.2
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• pp.155-162
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• 2009

A cultivation-based approach was employed to compare the culturable bacterial diversity associated with two phylogenetically closely related marine sponges, Spirastrella abata and Spirastrella panis, which have geologically overlapping distribution patterns. The bacteria associated with sponge were cultivated using MA medium supplemented with 3% sponge extracts. Community structures of the culturable bacteria of the two sponge species were analyzed with PCR-RFLP (restriction fragment length polymorphism) based on 16S rDNA sequences. The RFLP fingerprinting of 16S rDNA digested with HaeIII and MspI, revealed 24 independent RFLP types, in which 1-5 representative strains from each type were partially sequenced. The sequence analysis showed >98.4% similarity to known bacterial species in public databases. Overall, the microbial populations of two sponges investigated were found to be the members of the classes; Alphaproteobacteria, Gammaproteobacteria, Firmicutes, and Actinobacteria. The Alphaproteobacteria were predominant in the bacterial communities of the two sponges. Gammaproteobacteria represented 38.5% of bacterial community in S. abata. Whereas only 1.6% of this class was present in S. panis. Bacillus species were dominat in S. panis. Bacillus species were found to be 44.3% of bacterial species in S. panis, while they were only 9.7% in S. abata. It is interesting to note that Planococcus maritimus (8.1%, phylum Firmicutes) and Psychrobacter nivimaris (28.9%, phylum Gammaproteobacteria) were found only in S. abata. This result revealed that profiles of bacterial communities from the sponges with a close phylogenetic relationship were highly species-specific.

• Journal of Life Science
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• v.16 no.5
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• pp.812-827
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• 2006

To investigate the population structure and geographic distance among anchovies (Engraulis japonicus) in Korea, we compared and analyzed the mitochondrial DNA control region sequences (227 bp) of anchovies from 12 localities in inshore and offshore waters. The sequence analysis of 84 individuals showed 29 haplotypes, ranging in sequence divergence by pairwise comparisons from 0.3% to 3.5% (1 bp-12 bp). E9 haplotype of anchovies were found largely in inshore waters and also in offshore waters, which was regarded as the major source in Korean waters (58.3%). However, E26, E27, E28, and E29 haplotypes were found in westsouthern (locality 10, four among 7). Phylogenetic analysis using PHYLIP was divided into two clades (clade A and B). Most of the haplotypes, excluding E26, E27, E28, and E29, were strongly supported by bootstrap analysis (>75%), whereas the relationship between clade A and B was weakly supported by bootstrap analysis (51%). High levels of genetic diversity were found; haplotype diversity (H)=0.75-1.00, and nucleotide diversity $({\pi})=0.015-0.0244$. Analysis of $F_{ST}$ between populations in inshore waters ranged in 0.01-0.05, whereas those of offshore waters ranged in 0.01-0.58. A high gene flow occurred in inshore (Nm=22.61-34.22) and offshore (Nm=11.57-45.67) populations. The distribution of mitochondrial DNA haplotypes between westsouthern and other populations was suggestive of significantly different differentiation ($F_{ST}$=0.20-0.59, p<0.05; d=0.52, p=0.00; ${\phi}=0.02-0.41$, p＜0.05). These results suggested that the overall anchovy population in the Korean peninsula caused considerable migration due to the mitochondrial gene flow between inshore and offshore populations to form a genetically homogenous and panmictic structure, although a heterogeneous population was found in this study.

• Korean Journal of Clinical Laboratory Science
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• v.49 no.4
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• pp.413-419
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• 2017

Four imipenem-resistant bacteria were isolated from the clinical specimens of a patient with pneumonia. To identify the isolates, we used the GN card of Vitek II system and performed a phylogenetic analysis based on 16S rRNA gene sequence. The isolates were identified as P. aeruginosa (2 strains), P. monteilii (1 strain), and P. putida (1 strain), and were tested for antibiotic resistance after determining the MIC of imipenem to be $${\geq_-}8{\mu}g/mL$$ using the AST-N225 card of Vitek II system. The imipenem-resistant genotypes were determined using PCR products amplified using specific ${\beta}-Lactamase$ gene primers. The MBL gene was identified in all four isolates. One strain of P. aeruginosa exhibited the VIM and SHV-1 type genes, while the other strain exhibited both VIM and OXA group II genes. According to the antimicrobial susceptibility test, the bacteria were more susceptible to amikacin than other antibiotics. DNA fingerprint analysis using ERIC-PCR to analyze the epidemiological relationship between strains estimated that both the P. aeruginosa isolates were similar, but exhibited different DNA band types. It is uncommon to find four strains of imipenem-resistant bacteria with different DNA band types in a single patient.

• Applied Microscopy
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• v.41 no.4
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• pp.229-234
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• 2011

The occurrence of nuclear inclusions has been reported in various plant groups from primitive ferns to higher flowering plants. Their presence within a group seems to be randomly distributed without any phylogenetic relationships among species. According to the current survey, nuclear inclusions have been widely documented in more than several hundreds of species from various families of plants. The morphology and internal structures of nuclear inclusions are diverse and at least five types of inclusions develop within plant nuclei; amorphous, crystalline, fibrous, lamellar, and tubular form. Among these types, crystalline inclusions are the ones that are the most frequently reported. The inclusions are not bound by membranes and appear to be related to the nucleoli, either spatially by a close association or by an inverse relationship in size during development. The idea that nuclear inclusions are of a proteinaceous nature has been widely accepted. Further link to nucleolar activity as a protein storing site has also been suggested based on the association between the nucleolus and nuclear inclusions. Various investigations of nuclear inclusions have revealed more information about their structural features, but characterizing their precise function and subunit complexity employing molecular analysis and 3-D reconstruction remains to be elucidated. Tilting and tomography of serial sections with appropriate image processing can provide valuable information on their subunit(s). The present review summarizes discussion about different nuclear inclusions in plants from previous works, giving special attention to their fine, ultrastructural morphology, function, and origin.

• Korean Journal of Environmental Biology
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• v.17 no.3
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• pp.321-330
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• 1999

Nematodes were isolated using silkwom trap through the investigation of 100 soil samples from various biotopes in Korea. The 30 nematode strains from soil and dead insects by the pathogenicity aganinst silkworms (Bombyx mori mori) and insect pests of Calliphora vomitoria, Pseufazetia separata, Palomena angulosa, and Melolontha incana. Mortailty of the silkworm larvae and pupae were as high as 100% by nematode infection, those of insect of pests were varied from 20 to 100%. The 30 strains of entemopathogenic nematodes were classified into five groups of Rhabditidae, Diplogatroidae, Heterorhabitidae, Steinernematidae, and Tylenchida by morphological criteria. The genetic relationships among the 30 nematode strains were analyzed by various RAPD bands with twenty primers. The 30 nematode strains were classified into six major subgroups on the basis of the genetic similarity coefficient of 0.853. The grouping by RAPD was agree with those of morphological taxa in discrimination of the higher group, however, was not completely agree in the subgroup. The family Steinernematidae belong to Rhabditida was clarified as closer to the Tylenchida, rather than the other Rhabditida of Heterorhabitidae, Rhabditidae, and Diplogatroidae in genetic distance valule. From the result of the morphological classification and RAPD of the genomic DNA showed that genetic relationship analysis furnish infurmation on phylogenetic classification and relationships of entomopathogenic nematodes. The application of genetic similarity will overcome the limitation of taxonomy and classification of morphologically simple nematode. Several primers were confirmed those utility of identification for individual nematode strains, the methods of molecular genetics secured the simplicity, rapidity and accuracy on the selection of entomopathogenic nematodes.

• Journal of Life Science
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• v.20 no.1
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• pp.119-123
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• 2010

Genetic variations of Chajogi (Perilla frutescens var. crispa) germplasms were investigated by using RAPD markers. Twenty-two Perilla frutescens var. crispa lines collected from various locations were subjected to RAPD analysis using 80 primers. Among them, only 22 primers showed polymorphic bands and these 22 primers provided a total of 224 bands consisting of 127 polymorphic and 97 monomorphioc bands. The polymorphic bands were subjected to phylogenetic analysis using the UPGMA method. From UPGMA, similarity co-efficiency of 22 Chajogi lines ranged from 0.72 to 0.94. The dendrogram of 22 lines obtained through the UPGMA method resulted in two groups (one major group and one minor group). Although the two groups were roughly consistent with growth phenotypes (period of flowering, period of maturity, stem length, number of branches, number of nodes, number of flower clusters and number of ovaries) in detail, much inconsistency also was present

• The Korean Journal of Mycology
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• v.37 no.1
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• pp.86-90
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• 2009

The C. militaris belongs to entomopathogenic fungi, which have their specific sequences in internal transcribed spacer regions (ITS1 and ITS2) depending on species. In this study, to identify the phylogenetic relationship of the strain hybrided by mating of C. militaris, we compared DNA sequences of ITS regions and 5.8S ribosomal DNA (rDNA) repeat unit of hybrid strain and its parental strains. The result revealed that hybrid strains are C. militaris species. In addition, cordycepins produced by hybrid strains and other strains of C. militaris were analyzed by HPLC with 20mM $KH_2PO_4$ of mobile phase and C-18 columns. The result indicated that the strain hybrided by mating produce higher concentration of phytochemical cordycepin than other C. militaris strains.

• Mycobiology
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• v.45 no.3
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• pp.160-171
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• 2017

Larvae of Bradysia agrestis, an insect vector that transports plant pathogens, were sampled from geographically isolated regions in Korea to identify their cutaneous fungal and bacterial flora. Sampled areas were chosen within the distribution range of B. agrestis; each site was more than 91 km apart to ensure geographical segregation. We isolated 76 microbial (fungi and bacteria) strains (site 1, 29; site 2, 29; site 3, 18 strains) that were identified on the basis of morphological differences. Species identification was molecularly confirmed by determination of universal fungal internal transcribed spacer and bacterial 16S rRNA gene sequences in comparison to sequences in the EzTaxon database and the NCBI GenBank database, and their phylogenetic relationships were determined. The fungal isolates belonged to 2 phyla, 5 classes, and 7 genera; bacterial species belonged to 23 genera and 32 species. Microbial diversity differed significantly among the geographical groups with respect to Margalef's richness (3.9, 3.6, and 4.5), Menhinick's index (2.65, 2.46, and 3.30), Simpson's index (0.06, 0.12, and 0.01), and Shannon's index (2.50, 2.17, and 2.58). Although the microbial genera distribution or diversity values clearly varied among geographical groups, common genera were identified in all groups, including the fungal genus Cladosporium, and the bacterial genera Bacillus and Rhodococcus. According to classic principles of co-evolutionary relationship, these genera might have a closer association with their host insect vector B. agrestis than other genera identified. Some cutaneous bacterial genera (e.g., Pseudomonas) displaying weak interdependency with insect vectors may be hazardous to agricultural environments via mechanical transmission via B. agrestis. This study provides comprehensive information regarding the cutaneous microflora of B. agrestis, which can help in the control of such pests for crop management.

• Korean Journal of Plant Resources
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• v.19 no.1
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• pp.54-58
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• 2006

The genetic analyses of Acanthopanax senticosus Harms from Korea, China and Russia, were made by comparing the internal transcribed spacer (ITS) sequences of the nuclear ribosomal DNA. The ITS region of A. senticosus was amplified by polymerase chain reaction (PCR) using the universal primers and then directly sequenced. The length of the ITS region including 162 bp 5.85 rRNA gene ranged from 608 bp (for Korean and Chinese) to 611 bp (for Russian). The G+C content of ITS region were 60.20% for Korean and Chinese plants and 60.06% for Russian plants. Sequence comparisons indicated that ITS regions of A. senticosus from Korea and China were identical, whereas the ITS sequence of A. senticosus from Russia showed 99.2% homology with the plants from Korea. Variation in sequences were attributable to 5 bp substitution such as transversion or insertion events. These results suggested that A. senticosus Harms from Korea and China were closely related in phylogenetic relationship compared to Russian. In addition, A. senticosus Harms were more similar to Kalopanax pictus than A. sessiliflorus in their ITS sequences.

• Journal of Ginseng Research
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• v.44 no.4
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• pp.637-643
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• 2020

Background: Ginseng (Panax ginseng Meyer) is one of the world's most valuable medicinal plants with numerous pharmacological effects. Ginseng has been cultivated from wild mountain ginseng collections for a few hundred years. However, the genetic diversity of cultivated and wild ginseng populations is not fully understood. Methods: We developed 92 polymorphic microsatellite markers based on whole-genome sequence data. We selected five markers that represent clear allele diversity for each of their corresponding loci to elucidate genetic diversity. These markers were applied to 147 individual plants, including cultivars, breeding lines, and wild populations in Korea and neighboring countries. Results: Most of the 92 markers displayed multiple-band patterns, resulting from genome duplication, which causes confusion in interpretation of their target locus. The five high-resolution markers revealed 3 to 8 alleles from each single locus. The proportion of heterozygosity (H_e) ranged from 0.027 to 0.190, with an average of 0.132, which is notably lower than that of previous studies. Polymorphism information content of the markers ranged from 0.199 to 0.701, with an average of 0.454. There was no statistically significant difference in genetic diversity between cultivated and wild ginseng groups, and they showed intermingled positioning in the phylogenetic relationship. Conclusion: Ginseng has a relatively high level of genetic diversity, and cultivated and wild groups have similar levels of genetic diversity. Collectively, our data demonstrate that current breeding populations have abundant genetic diversity for breeding of elite ginseng cultivars.