• Journal of Microbiology and Biotechnology
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• v.33 no.10
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• pp.1292-1298
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• 2023

PAMB 00755^T, a bacterial strain, was isolated from Korean fir leaves. The strain exhibits yellow colonies and consists of Gram-negative, non-motile, short rods or ovoid-shaped cells. It displays optimal growth conditions at 20℃, 0% NaCl, and pH 6.0. Results of 16S rRNA gene-based phylogenetic analyses showed that strain PAMB 00755^T was most closely related to Sphingomonas chungangi MAH-6^T (97.7%) and Sphingomonas polyaromaticivorans B2-7^T (97.4%), and ≤96.5% sequence similarity to other members of the genus Sphingomonas. The values of average nucleotide identity (79.9-81.3%), average amino acid identity (73.3-75.9%), and digital DNA-DNA hybridization (73.3-75.9%) were significantly lower than the threshold values for species boundaries; these overall genome-related indexes (OGRI) analyses indicated that the strain represents a novel species. Genomic analysis revealed that the strain has a 4.4-Mbp genome encoding 4,083 functional genes, while the DNA G+C content of the whole genome is 66.1%. The genome of strain PAMB 00755^T showed a putative carotenoid biosynthetic cluster responsible for its antioxidant activity. The respiratory quinone was identified as ubiquinone 10 (Q-10), while the major fatty acids in the profile were identified as C_18:1ω7c and/or C_18:1ω6c (summed feature 8). The major polar lipids of strain PAMB 00755^T were diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, and phosphatidylcholine. Based on a comprehensive analysis of genomic, phenotypic, and chemotaxonomic characteristics, we proposed the name Sphingomonas abietis sp. nov. for this novel species, with PAMB 00755^T as the type strain (= KCTC 92781^T = GDMCC 1.3779^T).

• The Plant Pathology Journal
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• v.38 no.2
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• pp.167-174
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• 2022

Pseudomonas amygdali is a hemibiotrophic phytopathogen that causes disease in woody and herbaceous plants. Complete genomes of four P. amygdali pathovars were comparatively analyzed to decipher the impact of genomic diversity on host colonization. The pan-genome indicated that 3,928 core genes are conserved among pathovars, while 504-1,009 are unique to specific pathovars. The unique genome contained many mobile elements and exhibited a functional distribution different from the core genome. Genes involved in O-antigen biosynthesis and antimicrobial peptide resistance were significantly enriched for adaptation to hostile environments. While the type III secretion system was distributed in the core genome, unique genomes revealed a different organization of secretion systems as follows: type I in pv. tabaci, type II in pv. japonicus, type IV in pv. morsprunorum, and type VI in pv. lachrymans. These findings provide genetic insight into the dynamic interactions of the bacteria with plant hosts.

• Journal of Species Research
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• v.9 no.4
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• pp.375-376
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• 2020

A type specimen is the specimen originally used to name a new species; thus, it is one of the most significant materials for taxonomic study. In our study on the inventory and management of endemic species in Korea, we checked the type materials for Pseudolysimachion pusanensis (Y. Lee) Y. Lee, combination name Veronica pusanensis Y. Lee, recorded as deposited at the herbaria of the Ewha Womans University and the National Institute of Biological Resources, and failed to find any specimens. Thus, we concluded that all type specimens of V. pusanensis have since been misplaced. According to articles 9.11 and 9.13 of the International Code of Nomenclature for algae, fungi, and plants, it is necessary to select a neotype if the holotype is missing and no other original material exists. Therefore, we designate the neotype maintained in the herbarium of the National Institute of Biological Resources of the Republic of Korea.

• Journal of Applied Biological Chemistry
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• v.42 no.3
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• pp.119-124
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• 1999

About two thirds of the naturally occurring antibiotics have been discovered from actinomycetes. Therefore, the probability of discovering further new antibiotics from actinomycetes is declining as many known metabolites are isolated repeatedly. However, various efforts leave been made in order to enhance the probability of discovering novel compounds. In the present study, we have developed new screening strategies based on the antibiotic biosynthetic pathway, and the genetic information, utilizing polymerase chain reaction. We have selected macrolide type polyketides. In order to divide the ansamycin group antibotic of macrolide type polyketides, we have selected 3-amino-5-hydroxybenzoic acid (AHBA) moiety which contains a biosynthetically unique structural element in the group as a target molecules. Oligonucleotide primers were designed to amplify DNA fragments of macrolide type polyketide synthase and AHBA synthase genes from fourteen actinomycetes species. This method was successfully applied to all three of the known macrolide type polyketide produccing actinomycetes tested. In addition, it also identified the presence of potential macrolide type polyketide producing genes from seven actinomycetes that were known to produce none of macrolide type polyketides, and AHBA biosynthetic genes in one actinomycetes. This technique is potentially useful for the screening of new antibiotices and cloning of their biosynthetic genes.

• Journal of Species Research
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• v.9 no.3
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• pp.218-220
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• 2020

A holotype is an element to which the name of a taxon is permanently attached and is key material that facilitates taxonomic research. However, type citation or designation errors due to typographical errors or inadvertent mistakes often exist. When reviewing recently published literature for the type specimens of vascular plants in the herbarium of the National Institute of Biological Resources, we observed that three species, Isoetes laosiensis, Isoetes coreana, and Huperzia jejuensis, had errors, and the actual holotype information and the type descriptions of the protologues did not match. The name Isoetes laosiensis had a collecting number error, while Isoetes coreana and Huperzia jejuensis had collector errors. According to Article 9.2 of the International Code of Nomenclature for algae, fungi, and plants (Shenzhen code), if a holotype designation in the protologue of the name of a taxon is found to contain errors such as collector, collecting number, and illustration errors, the errors are to be corrected. We, therefore, corrected the errors in holotypes of three species, with no alterations made to the intents of the original authors.

• Communications of the Korean Mathematical Society
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• v.24 no.2
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• pp.215-226
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• 2009

For a class of Holling type II food chain systems with biological and chemical controls, we give conditions of the local stability of prey-free periodic solutions and of the permanence of the system. Further, we show the system is uniformly bounded.

• Korean Journal of Microbiology
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• v.24 no.4
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• pp.406-410
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• 1986

The isolation and charateriation of a type II restriction endonuclease from Xanthomonas citri IFO 3835 were described. This enzyme (Xci I endonuclease) is an isoschizomer of Sal I endonuclease recognizing 5'-GTCGAC-3' and cleaving at the site indicated by the arrow. Unlike Sal I endonuclease, Xci I endonuclease requries a NaCl concentration of 50mM for its maximum activity.

• Journal of Species Research
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• v.7 no.1
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• pp.73-79
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• 2018

The review provides the information about 46 type specimens on 35 taxa of vascular plants from Korea (Fig. 1), kept in the Herbarium of the Komarov Botanical Institute of the Russian Academy of Sciences in addition to 150 taxa published before. Lectotype of Ligustrum patulum Palib is designated here.

• Korean Journal of Microbiology
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• v.28 no.4
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• pp.337-344
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• 1990

Slime sampless from 10 ratating biological contactor (RBC) plants in New Jersey were microscopically examined. Filamentous bacteria such as Type 1701, Type 0041, Type 021N, Nocardia, Beggiatoa, and Sphaerotilus, which are commonly present as suspended forms also were found in RBC slimes growing as attached forms. However, the abundance wwas much different from that of activated sludge. In RBC slimes, Beggiatoa was most frequently observed filamentous bacteria and Sphaerotilus, Type 0041, Type 1701, Type 021N and Nocardia were present in decreasing order of abundance. There were morphologically two different types of Behhiatia in RBC slimes. The statistical anaysis shows that filamentous bacterial poulations between the 100 cm inside and the outside the RBC were different in most cases with significant interactions between the location and stage.

• Korean Journal of Plant Taxonomy
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• v.43 no.2
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• pp.106-117
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• 2013

Using scanning electron microscope (SEM), we examined the trichomes on leaf and petiole and the epicuticular waxes on leaf surfaces for a total of 27 taxa representing two subtribes, Fragariinae and Potentillinae, of tribe Potentilleae (Rosaceae) in Korea. Four types of trichomes on adaxial and abaxial surface of leaves and petioles were identified. Type I (conical hirtellous) is the most common trichome type found in the majority of taxa in Fragariinae and Potentillinae. Type II (verruculose conical hirtellous) can be found only in Potentilla cryptotaeniae of sect. Conostylae of Potentillinae. Potentilla chinensis complex (sect. Conostylae) and P. egedii (sect. Letostylae) have type III trichome (crispate villous), while type IV (floccose villous) can be found in two species in sect. Conostylae, P. nivea and P. discolor. Both woolly hairs and conical hirtellous exist together in types III and IV. The same type of trichomes in leaves and petioles can be found across different subtribes and sections. In addition, different types of trichomes can be found even in a single species. Among the taxa which have type I trichome, the majority of subtribe Fragariinae and P. centrigrana and P. dickinsii complex have well developed epicuticular waxes on the surface of leaves. Sharing epicuticular waxes among the taxa across different subtribes appears to be correlated with their similar geographical distribution and ecological conditions. However, molecular phylogenetic study implies that the existence of epicuticular waxes could be also due to phylogenetic signal.