• The Plant Pathology Journal
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• v.34 no.4
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• pp.297-307
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• 2018

The sugar beet cyst nematode, Heterodera schachtii is a well known pathogen on Chinese cabbage in the highland fields of Korea. However, a race of cyst forming nematode with close morphological resemblance to H. trifolii was recently isolated from the same Chinese cabbage fields. Morphological species differentiation between the two cyst nematodes is challenging, with only minor differences between them. Thus, this study described the newly intercepted H. trifolii population, and reviewed morphological and molecular characteristics conceivably essential in differentiating the two nematode species. A comparison of morphometric measurements of both infective juveniles and vulval cones of cysts showed significant differences between the two cyst nematodes. When total RNA and genomic DNA were extracted from a mixed field population, COI genes and ITS regions were clearly amplified with primers of the two Heterodera species, suggesting that Heterodera population collected from the Chinese cabbage field consisted of a mixture of two species. COI and ITS of H. trifolii were predominantly amplified from nucleotides prepared from H. trifolii monoxenic population whereas those of H. schachtii were strongly detected in H. schachtii monoxenic cultures. Thus, this study confirms the coexistence of the two species in some Chinese cabbage fields; and the presence of H. trifolii in Korea is reported here for the first time.

• Journal of Microbiology and Biotechnology
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• v.25 no.4
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• pp.431-438
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• 2015

Ever since the ban on antibiotic growth promoters (AGPs), the livestock death rate has increased owing to pathogenic bacterial infections. There is a need of developing AGP alternatives; however, the mechanisms by which AGP enhances livestock growth performance are not clearly understood. In this study, we fed 3-week-old swine for 9 weeks with and without AGPs containing chlortetracycline, sulfathiazole, and penicillin to investigate the effects of AGPs on swine gut microbiota. Microbial community analysis was done based on bacterial 16S rRNA genes using MiSeq. The use of AGP showed no growth promoting effect, but inhibited the growth of potential pathogens during the early growth stage. Our results showed the significant increase in species richness after the stabilization of gut microbiota during the post-weaning period (4-week-old). Moreover, the swine gut microbiota was divided into four clusters based on the distribution of operational taxonomic units, which was significantly correlated to the swine weight regardless of AGP treatments. Taxonomic abundance analysis indicated a negative correlation between host weight and the abundance of the family Prevotellaceae species, but showed positive correlation to the abundance of the family Spirochaetaceae, Clostridiaceae_1, and Peptostreptococcaeae species. Although no growth performance enhancement was observed, the use of AGP inhibited the potential pathogens in the early growth stage of swine. In addition, our results indicated the ecological succession of swine gut microbiota according to swine weight. Here, we present a characterization of swine gut microbiota with respect to the effects of AGPs on growth performance.

• Journal of Soil and Groundwater Environment
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• v.20 no.7
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• pp.121-134
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• 2015

Spatial and temporal changes in algal population in Yongdam reservoir and ecological factors that induced the changes in the size and composition of algal population were investigated by monthly sampling at ten locations in the reservoir. Nutritional state of the reservoir was identified to be phosphorus-limited with nitrogen to phosphorus (N : P) ratio much greater than 17 in most samples. Algal population was dominated by three taxonomic groups, diatoms, chlorophytes and cyanobacteria. Although explosive algal growth was not observed in the summer, algal population showed transition with time of the dominant algal type from diatoms in the winter to cyanobacteria in the summer. Chlorophyta was not the dominant group in the reservoir although they maintained relatively stable number of cells in the reservoir and showed increase in population from March to May. The application of statistical methods revealed that the factors inducing changes in cell number of each group were water temperature for diatoms and cyanobacteria and phosphorus concentration for chlorophyte. Fluctuation of cyanobacterial population was mainly observed near the inlet of tributaries while diatoms showed higher variation inside the reservoir.

• BMB Reports
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• v.45 no.8
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• pp.476-481
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• 2012

Flavodoxin (Fld) has been demonstrated to bind to ferredoxin-NADP$^+$ reductase A (FprA) in Pseudomonas putida. Two residues ($Phe^{256}$, $Lys^{259}$) of FprA are likely to be important for interacting with Fld based on homology modeling. Site-directed mutagenesis and pH-dependent enzyme kinetics were performed to further examine the role of these residues. The catalytic efficiencies of FprA-$Ala^{259}$ and FprA-$Asp^{259}$ proteins were two-fold lower than those of the wild-type FprA. Homology modeling also strongly suggested that these two residues are important for electron transfer. Thermodynamic properties such as entropy, enthalpy, and heat capacity changes of FprA-$Ala^{259}$ and FprA-$Asp^{259}$ were examined by isothermal titration calorimetry. We demonstrated, for the first time, that $Phe^{256}$ and $Lys^{259}$ are critical residues for the interaction between FprA and Fld. Van der Waals interactions and hydrogen bonding were also more important than ionic interactions for forming the FprA-Fld complex.

• Journal of Microbiology and Biotechnology
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• v.16 no.11
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• pp.1819-1825
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• 2006

Four naphthalene-degrading bacteria (Pseudomonas sp. strains O1, W1, As1, and G1) were isolated feom pollutant-contaminated sites. Examination of their substrate utilization and analyses of key naphthalene-catabolic regulatory genes revealed that the pathway and regulation of naphthalene-degradation in all four strains resemble those of NAH7 from P. putida G7. Superoxide anion production, superoxide dismutase activity, and catalase activity during their growth on naphthalene-amended medium increased significantly, compared with those with glucose-amended medium. Addition of ascorbate, an antioxidant, or ferrous iron ($Fe^{2+}$) increased the growth rates of all tested microorganisms on naphthalene. Northern blot and HPLC analyses showed that both nahA gene expression and naphthalene degradation increased under those conditions. Our data suggest that naphthalene degradation can impose severe oxidative stress, and defenses against oxidative stress would play an important role in the metabolism of naphthalene.

• Fisheries and Aquatic Sciences
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• v.15 no.2
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• pp.91-97
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• 2012

To isolate a nonylphenol (NP)-degrading bacterium, we isolated a single colony from the NP-degrading microbial consortium SW-3, which was previously isolated from an aqueous environment. Ten colonies that exhibited different cell morphologies were isolated and the strains were named SW-3-A, -B, -C, -D, -E, -F1, -F2, -G, -H, and -I. The ability of isolates to degrade NP was evaluated by kinetic analysis by the constant of NP degradation rate ($k_1$) and the half-life time of NP degradation ($t_{1/2}$). SW-3-F1, -F2, -G, and -I strains were superior at degrading NP. The $k_1$ and $t_{1/2}$ values of the four strains were sixfold higher and one-sixth lower, respectively, than those of the consortium strain. Additionally, SW-3-F1, -G, and -I strains were tested for their ability to degrade NP during coculture. NP degradation by coculture with a combination of all three strains was inferior to that of culture conducted with single isolates, suggesting that the three strains are antagonistic toward each other during NP degradation.

• Genomics & Informatics
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• v.21 no.1
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• pp.10.1-10.6
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• 2023

The fishes of the Chiasmodontidae family, known as swallower fishes, are species adapted to live in deep seas. Several studies have shown the proximity of this family to Tetragonuridae and Amarsipidae. However, the phylogenetic position of this clade related to other Pelagiaria groups remains uncertain even when phylogenomic studies are employed. Since the low number of published mitogenomes, our study aimed to assemble six new mitochondrial genomes of Chiasmodontidae from database libraries to expand the discussion regarding the phylogeny of this group within Scombriformes. As expected, the composition and organization of mitogenomes were stable among the analyzed species, although we detected repetitive sequences in the D-loop of species of the genus Kali not seen in Chiasmodon, Dysalotus, and Pseudoscopelus. Our phylogeny incorporating 51 mitogenomes from several families of Scombriformes, including nine chiasmodontids, recovered interfamilial relationships well established in previous studies, including a clade containing Chiasmodontidae, Amarsipidae, and Tetragonuridae. However, phylogenetic relationships between larger clades remain unclear, with disagreements between different phylogenomic studies. We argue that such inconsistencies are not only due to biases and limitations in the data but mainly to complex biological events in the adaptive irradiation of Scombriformes after the Cretaceous-Paleogene extinction event.

• Journal of Soil and Groundwater Environment
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• v.26 no.6
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• pp.130-143
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• 2021

Wetlands are one of the most representative groundwater dependent ecosystems(GDEs) that require access to groundwater on a permanent or intermittent basis to maintain their biological communities and ecological processes. In this study, the seasonal characteristics of the GDEs in Baekseok Reservoir Wetland were evaluated through the monitoring of the temporal and spatial community of benthic macroinvertebrates in the wetland. The appearance of benthic macroinvertebrates appearance was changed seasonally depending on environmental factors such temperature, precipitation and water level for their habitat and it also showed the clear spatial difference in the wetland. The scores of Diversity index(H'), Richness Index (R1) and the Ecological score of benthic macroinvertebrates (TESB/AESB) were relatively high at St.3 and 4(i.e., north area) where groundwater inflows into wetland(i.e., high ²²²Rn conc.). The statistical analysis (ANOVA test and PCA) investigated the correlation among the benthic macroinvertebrates' community, groundwater level, wetland water level and water quality. The results showed that the community of benthic macroinvertebrates at St. 3 and 4 in Baekseok Reservoir Wetlands was spatially dependent on groundwater level and groundwater inflow. The characterization and assessment of GDEs requires understanding the hydrological, biogeochemical and biological process and this study will provide information for characterization and assessment of GDEs.

• Journal of Microbiology and Biotechnology
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• v.24 no.8
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• pp.1096-1104
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• 2014

$\small{L}$-Asparaginase from gram-positive bacteria has been poorly explored. We conducted recombinant overexpression and purification of $\small{L}$-asparaginase from Staphylococcus sp. OJ82 (SoAsn) isolated from Korean fermented seafood to evaluate its biotechnological potential as an antileukemic agent. SoAsn was expressed in Escherichia coli BL21 (DE3) with an estimated molecular mass of 37.5 kDa, determined using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Consistent with asparaginases in gram-negative bacteria, size-exclusion chromatography determined SoAsn as a homodimer. Interestingly, the optimal temperature of SoAsn was $37^{\circ}C$ and over 90% of activity was retained between $37^{\circ}C$ and $50^{\circ}C$, and its thermal stability range was narrower than that of commercial E. coli $\small{L}$-asparaginase (EcAsn). Both SoAsn and EcAsn were active between pH 9 and 10, although their overall pH-dependent enzyme activities were slightly different. The $K_m$ value of SoAsn was 2.2 mM, which is higher than that of EcAsn. Among eight metals tested for enzyme activity, cobalt and magnesium greatly enhanced the SoAsn and EcAsn activity, respectively. Interestingly, SoAsn retained more than 60% of its activity under 2 M NaCl condition, but the activity of EcAsn was reduced to 48%. Overall, the biochemical characteristics of SoAsn were similar to those of EcAsn, but its kinetics, cofactor requirements, and NaCl tolerance differed from those of EcAsn.

• Journal of Crop Science and Biotechnology
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• v.10 no.4
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• pp.223-230
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• 2007

Vitellaria paradoxa commonly called shea is an important agro forestry and fruit-bearing species present in four agro-ecological zones of Cameroon. The goal of this work was the morphological characterization of certain populations of V. paradoxa which will serve as a necessary step for a subsequent genetic study of the species. Morphological observations related to 20 agronomic traits, studied on 8-13 trees selected from each of the eight shea populations across four different agro-ecological zones located in four provinces of Cameroon were studied. The study showed that there was a variation between the populations, related to the traits measured on the trunk, fruit, nut, and leaf. Three shapes of the tree(ball, broom, and trained), five shapes of the fruit(round, oblong, reversed pear, ovoid, and oblong), three colors of the nut(clear brown, dark brown, and blackish brown) were identified. The principal component analysis(PCA) carried out on the quantitative characters revealed 72% of the total variance expressed on the first and second main axis. This variation was essentially explained by the traits measured on the fruits and on the nuts. The analyses showed that only the traits of the fruits and the nuts were discriminative. The shea populations studied were structured into two distinct groups using these discriminative traits.