• Journal of Species Research
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• v.11 no.4
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• pp.310-320
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• 2022

As a subset study to discover indigenous prokaryotic species in Korea, we isolated 20 bacterial strains and assigned them to the phyla Actinobacteria, Bacteroidota, Firmicutes, and Proteobacteria. From the high 16S rRNA gene sequence similarity (≥98.7%) and formation of a robust phylogenetic clades, we determined that each strain belonged to independent, predefined bacterial species. There are no official reports of these 20 species in Korea; therefore, 7 strains of the Actinobacteria, 2 strain of the Bacteroidota, 3 strains of the Firmicutes, and 8 strains of the Firmicutes are described in Korea for the first time. Gram reaction, colony and cell morphology, basic biochemical characteristics, and isolation sources are also described in the species description section.

• The Korean Journal of Mycology
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• v.51 no.1
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• pp.25-38
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• 2023

Three fungal strains belonging to the class Sordariomycetes were isolated from soil collected on Jeju Island and Gyeongsangbuk-do, Korea. They were identified as Diaporthe endophytica (KNU-JJ-1809), Faurelina indica (KNU-JJ-1830), and Trichoderma ivoriense (KNU-4-KH1). KNU-JJ-1809 produced beta conidia that were straight, curved, hyaline, smooth-walled, with a diameter of 16.5-25.0×0.6-1.7 ㎛. The conidia of strain KNU-JJ-1830 were hyaline to light green, thin, clavate, round, truncate base, had guttules at both ends, with a diameter of 2.5-5.2×1.7-3.8 ㎛. The conidia of strain KNU-4-KH1 were oblong or ellipsoidal, smooth-walled, greenish, with a diameter of 2.2-4.4×2.2-3.6 ㎛. Internal transcribed spacer regions, partial large subunit, translation elongation factor 1-alpha, β-tubulin, and calmodulin genes were used to confirm the strains, and their cultural and morphological characteristics. To our knowledge, this is the first report on D. endophytica, F. indica, and T. ivoriense in Korea.

• Geomechanics and Engineering
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• v.34 no.5
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• pp.507-527
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• 2023

Accurately estimation of the geo-mechanical parameters in Artificial Ground Freezing (AGF) is a most important scientific topic in soil improvement and geotechnical engineering. In order for this, one way is using classical and conventional constitutive models based on different theories like critical state theory, Hooke's law, and so on, which are time-consuming, costly, and troublous. The others are the application of artificial intelligence (AI) techniques to predict considered parameters and behaviors accurately. This study presents a comprehensive data-mining-based model for predicting the Young's Modulus of frozen sand under the triaxial test. For this aim, several single and hybrid models were considered including additive regression, bagging, M5-Rules, M5P, random forests (RF), support vector regression (SVR), locally weighted linear (LWL), gaussian process regression (GPR), and multi-layered perceptron neural network (MLP). In the present study, cell pressure, strain rate, temperature, time, and strain were considered as the input variables, where the Young's Modulus was recognized as target. The results showed that all selected single and hybrid predicting models have acceptable agreement with measured experimental results. Especially, hybrid Additive Regression-Gaussian Process Regression and Bagging-Gaussian Process Regression have the best accuracy based on Model performance assessment criteria.

• Geomechanics and Engineering
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• v.34 no.3
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• pp.303-316
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• 2023

With the development and utilization of urban underground space, the artificial ground freezing technology has been widely used in the construction of underground engineering in soft soil areas. The mechanical properties of soft clay changed greatly after freezing and thawing, which affected the seismic performance of underground structures. In this paper, a series of triaxial tests were carried out to study the dynamic response of the freezing-thawing clay under the seismic load considering different dynamic stress amplitudes and different confining pressures. The reduction factor of dynamic shear stress was determined to correct the amplitude of the seismic load. The deformation development mode, the stress-strain relationship and the energy dissipation behavior of the soft clay under the seismic load were analyzed. An empirical model for predicting accumulative plastic strain was proposed and validated considering the loading times, the confining pressures and the dynamic stress amplitudes. The relevant research results can provide a theoretical reference to the seismic design of underground structures in soft clay areas.

• Journal of Species Research
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• v.12 no.spc2
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• pp.15-22
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• 2023

During a comprehensive investigation of indigenous prokaryotic species in Korea, 20 and one bacterial strains assigned to the phyla Bacillota and Verrucomicrobiota, respectively, were isolated from diverse environmental habitats, including soil, mud, tidal flat, seawater, sand, sediment, brackish water, and healthy human urine. Based on their high 16S rRNA gene sequence similarities (>98.7%) and the formation of robust phylogenetic clades with their closest related reported species, each strain was assigned to an independent and predefined bacterial species. Since there were no published or official reports regarding these 21 isolates in Korea, they - 20 species of four families in two orders of the phylum Bacillota and one species of the phylum Verrucomicrobiota - have been reported as unrecorded species in Korea. In addition, Gram staining, colony and cell morphology, basic biochemical characteristic, isolation source, and strain ID of each species are also described in the species description sections.

• Journal of Species Research
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• v.12 no.spc2
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• pp.23-32
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• 2023

During screening for indigenous prokaryotic species in Republic of Korea in 2021, a total of 21 bacterial strains assigned to the phylum Bacteroidota were isolated from a variety of environmental habitats including pine cone, seaweed, soil, sea sediment, brackish water and moss. Based on the 16S rRNA gene sequence similarity value of more than 98.7% and formation of a robust phylogenetic clade with the type strain of the closest bacterial species, it was found that the 21 strains belong to independent and recognized bacterial species. There has been no official report that the identified 21 species have been isolated in Republic of Korea up to date. Therefore, 16 species in six genera of two families in the order Flavobacteriales, two species in two genera of two families in the order Cytophagales, one species in one genus of one family in the order Chitinophagales and two species in one genus of one family in the order Sphingobacteriales are proposed as unrecorded species of the phylum Bacteroidota isolated in Republic of Korea. Their Gram reaction, colony and cell morphology, basic phenotypic characteristics, isolation source, taxonomic status, strain ID and other information are described in the species descriptions.

• Journal of Species Research
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• v.13 no.1
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• pp.10-31
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• 2024

In this study, 11 strains of epilithic cyanobacteria belonging to six unrecorded species in Korea were isolated from gravel submerged in freshwater of seven collection sites in Korea. The morphological characteristics of the six species isolated in this study were consistent with the type strain of each species, and the similarity of the 16S rRNA gene sequences with the type strain of each species were 98.8-100%. In the phylogenetic tree using the 16S rRNA gene sequences, the 11 strains of these six species formed the same cluster as the strains of each species. The habitat of each previously reported species is mainly the soil surface, but all Korean strains appeared from the gravel submerged in freshwater. As a result of the morphological, ecological, and molecular analyses, these six species of cyanobacteria were identified as Geminocystis papuanica, Allocoleopsis franciscana, Ancylothrix terrestris, Klisinema persicum, Scytolyngbya timoleontis, and Shackletoniella antarctica, which were added as newly recorded species in Korea.

• Earthquakes and Structures
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• v.26 no.5
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• pp.327-336
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• 2024

Evaluation of tunnel performance in seismic-prone areas demands efficient means of estimating performance at different hazard levels. The present study introduces an innovative push-over analysis approach which employs the standard earthquake spectrum to simulate the performance of a tunnel. The numerical simulation has taken into account the lining and surrounding rock to calculate the rock-tunnel interaction subjected to a static push-over displacement regime. Elastic perfectly plastic models for the lining and hardening strain rock medium were used to portray the development of plastic hinges, nonlinear deformation, and performance of the tunnel structure. Separately using a computational algorithm, the non-linear response spectrum was approximated from the average shear strain of the rock model. A NATM tunnel in Turkey was chosen for parametric study. A seismic performance curve and two performance thresholds are introduced that are based on the proposed nonlinear seismic static loading approach and the formation of plastic hinges. The tunnel model was also subjected to a harmonic excitation with a smooth response spectrum and different amplitudes in the fully-dynamic phase to assess the accuracy of the approach. The parametric study investigated the effects of the lining stiffness and capacity and soil stiffness on the seismic performance of the tunnel.

• Microbiology and Biotechnology Letters
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• v.52 no.2
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• pp.195-199
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• 2024

Paraburkholderia phenoliruptrix T36S-14, identified as a potential plant growth-promoting bacterium, was isolated from the core microbiome of tomato rhizosphere soil. When assessed for its growth promotion, Strain T36S-14 demonstrated a notable 20% increase in the fresh weight of tomato seedlings. The strain possesses two circular chromosomes, one of 4,104,520 base pair (bp) (CP119873) and the other of 3,258,072 bp (CP119874), both exhibiting G+C contents of 63.5% and 62.7%, respectively. The chromosome comprises 6,319 protein-coding sequences, 65 transfer RNA genes, and 18 ribosomal RNA genes (5S: 6, 16S: 6, and 23S: 6). Additionally, P. phenoliruptrix T36S-14 produces siderophores that promote plant growth.

• The Korean Journal of Pesticide Science
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• v.18 no.4
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• pp.396-403
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• 2014

Ginseng (Panax ginseng C. A. Meyer) is an economically valuable pharmaceutical crop in Korea. In order to find promising biocontrol agents for soil-borne fungal pathogens which infect ginseng roots, we have isolated actinomycete, BK185 from soil. The isolate was investigated for the antifungal activity against to ginseng rot pathogens prior to testing genetic and chemical properties. The strain was identified as Streptomyces sp. using phylogenetic analysis based on 16S rRNA gene sequence. The most closely related species was S. sporoclivatus and S. geldanamycininus with high similarities (>99%). The isolate, BK185 showed positive reaction for PCR detection targeting biosynthetic gene clusters of PKS (Type-I polyketide synthase) and NRPS (Non-ribosomal polypeptide synthetase) genes. Major metabolite from the BK185 was analyzed by The LC/MS and identified to geldamycin, which was known to contained broad antibacterial, antifungal or anticancer activities. The results provide evidences that the strain, BK185 can be promising biocontrol agent for ginseng organic farming.