• The Plant Pathology Journal
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• v.40 no.1
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• pp.73-82
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• 2024

Gardenia (Gardenia jasminoides) is a popular and economically vital plant known for its ornamental and medicinal properties. Despite its widespread cultivation, there has been no documentation of plant viruses on gardenia yet. In the present study, gardenia leaves exhibiting symptoms of plant viral diseases were sampled and sequenced by both metatranscriptome and small RNA sequencing. As a consequence, bean common mosaic virus (BCMV) was identified in gardenia for the first time and named BCMV-gardenia. The full genome sequence of BCMV-gardenia is 10,054 nucleotides (nt) in length (excluding the poly (A) at the 3' termini), encoding a large polyprotein of 3,222 amino acids. Sequence analysis showed that the N-termini of the polyprotein encoded by BCMV-gardenia is less conserved when compared to other BCMV isolates, whereas the C-termini is the most conserved. Maximum likelihood phylogenetic analysis showed that BCMVgardenia was clustered closely with other BCMV isolates identified outside the leguminous plants. Our results indicated that the majority of BCMV-gardenia virus-derived small interfering RNAs (vsiRNAs) were 21 nt and 22 nt, with 21 nt being more abundant. The first nucleotide at the 5' termini of vsiRNAs derived from BCMV-gardenia preferred U and A. The ratio of vsiRNAs derived from sense (51.1%) and antisense (48.9%) strands is approaching, and the distribution of vsiRNAs along the viral genome is generally even, with some hot spots forming in local regions. Our findings could provide new insights into the diversity, evolution, and host expansion of BCMV and contribute to the prevention and treatment of this virus.

• Animal Bioscience
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• v.37 no.1
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• pp.28-38
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• 2024

Objective: Tibetan chickens, which have unique adaptations to extreme high-altitude environments, exhibit phenotypic and physiological characteristics that are distinct from those of lowland chickens. However, the mechanisms underlying hypoxic adaptation in the liver of chickens remain unknown. Methods: RNA-sequencing (RNA-Seq) technology was used to assess the differentially expressed genes (DEGs) involved in hypoxia adaptation in highland chickens (native Tibetan chicken [HT]) and lowland chickens (Langshan chicken [LS], Beijing You chicken [BJ], Qingyuan Partridge chicken [QY], and Chahua chicken [CH]). Results: A total of 352 co-DEGs were specifically screened between HT and four native lowland chicken breeds. Gene ontology and Kyoto encyclopedia of genes and genomes enrichment analyses indicated that these co-DEGs were widely involved in lipid metabolism processes, such as the peroxisome proliferator-activated receptors (PPAR) signaling pathway, fatty acid degradation, fatty acid metabolism and fatty acid biosynthesis. To further determine the relationship from the 352 co-DEGs, protein-protein interaction network was carried out and identified eight genes (ACSL1, CPT1A, ACOX1, PPARC1A, SCD, ACSBG2, ACACA, and FASN) as the potential regulating genes that are responsible for the altitude difference between the HT and other four lowland chicken breeds. Conclusion: This study provides novel insights into the molecular mechanisms regulating hypoxia adaptation via lipid metabolism in Tibetan chickens and other highland animals.

• Korean Journal of Mineralogy and Petrology
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• v.33 no.3
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• pp.165-173
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• 2020

The activity of living microorganism directly or indirectly affects to the biomineralization in sediments and rocks that display the unique biotic structure. Minerals in the biotic structures showed unique properties and bypass the thermodynamic and kinetic barriers. Therefore, investigations on the biotically induced microstructure is essential to identify the new mineral formation mechanism by analyzing crystal structures and morphology at a nano-scale. The significant implication as well as advantages of using scanning electron microscopy to characterize the biotic structures were discussed in this paper for the examples of hydrothermal vent area microbial mat and deep-sea ferromanganese crust sample.

• Journal of Soil and Groundwater Environment
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• v.22 no.5
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• pp.30-39
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• 2017

In this study, the predictive toxicity of barley Hordeum vulgare was estimated using a modified terrestrial biotic ligand model (TBLM) to account for the toxic effects of $CuOH^+$ and $CuCO_3(aq)$ generated at pH 7 or higher, and this was compared to that from the original TBLM. At pH values higher than 7, the difference in $EA_{50}\{Cu^{2+}\}$ (half maximal effective activity of $Cu^{2+}$) between the two models increased with increasing pH. As Mg concentration increased from 8.24 to 148 mg/L in the pH range of 5.5 to 8.5, the difference in $EA_{50}\{Cu^{2+}\}$ increased, and it reached its maximum at pH 8. The difference in $EC_{50}[Cu]_T$ (half maximal effective concentration of Cu) between the two models increased as dissolved organic carbon (DOC) concentration increased when pH was above 7. Thus, for soils with alkaline pH, the toxic effect of $CuOH^+$ and $CuCO_3(aq)$ are greater at higher salt and DOC concentrations. The acceptable Cu concentration in soil porewater can be estimated by the modified TBLM through deterministic method at pH levels higher than 7, while combination of TBLM and species sensitivity distribution through the probabilistic method could be utilized at pH levels lower than 7.

• Journal of Soil and Groundwater Environment
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• v.22 no.1
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• pp.49-58
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• 2017

Biotic ligand model (BLM) and species sensitivity distribution (SSD) were used to determine the site-specific Cu threshold concentration (5% hazardous concentration; HC5) in soil pore water. Model parameters for Cu-BLM were collected for six plants, one collembola, and two earthworms from published literatures. Half maximal effective concentration ($EC_{50}\{Cu^{2+}\}$), expressed as $Cu^{2+}$ activity, was calculated based on activities of major cations and the collected Cu-BLM parameters. The $EC_{50}\{Cu^{2+}\}$ varied from 2 nM to $251{\mu}M$ according to the variation in environmental factors of soil pore water (pH, major cation/anion concentrations) and the type of species. Hazardous activity for 5% (HA5) and HC5 calculated from SSD varied from 0.076 to $0.4{\mu}g/L$ and 0.4 to $83.4{\mu}g/L$, respectively. HA5 and HC5 significantly decreased with the increase in pH in the region with pH less than 7 due to the decrease in competition with $H^+$ and $Cu^{2+}$. In the region with pH more than 7, HC5 increased with the increase in pH due to the formation of complexes of Cu with inorganic ligands. In the presence of dissolved organic carbon (DOC), Cu and DOC form a complex, which decreases $Cu^{2+}$ activity in soil pore water, resulting in up to 292-fold increase in HC5 from 0.48 to $140{\mu}g/L$.

• Korean Journal of Environment and Ecology
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• v.22 no.5
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• pp.544-550
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• 2008

This study conducted a survey on the ecosystem of Wonju stream from May until November in 2004 and made an health assessment of Wonju stream using family biotic indices(FBI) and physical habitat assessment(PHA) of the aquatic insects. Through this survey, aquatic insects covering 8 orders, 37 families, 62 genuses, and 92 species were observed at 9 stations along Wonju stream. In terms of family biotic indices, it was confirmed that station 1,2 and 3 were maintaining the healthiest stream ecosystem with the value ranging from 4.55 to 4.82. In addition, station 2 was found to have the best habitat environment in the correlation between physical habitat assessment and family biotic indices with its value of 100 and 4.82, respectively. However, station 7 and 9 showed the lowest habitat environment with the value of 45, 6.17 and 45, 6.97, respectively. posing the need for improvement in PHA; further, station 7 and 9 showed inverted correlationship between PHA and FBI.

• Korean Journal of Medicinal Crop Science
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• v.11 no.5
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• pp.358-363
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• 2003

ScopoIamine and hyoscyamine which belong to tropane alkaloids are the pharmaceutically valuable anticholinergic drugs. In order to increase the productivities, the effects of elicitation were investigated during hairy root cultures of Scopolia. parviflora. Biotic elicitors originated from 3 fungi and 1 yeast were prepared as homogenate and supernatant and added to 3-week-old cultures. Both of homogenate and supernatant of Candida albicans elicitors increased the scopolamine production. The production of hyoscyamine was enhanced by homogenate of Fusarium solani and supernatant of C. albicans. Most of the other fungal elicitors were also improved on the tropane alkaloid production compared to non-treatment. Among the elicitors tested, C. albicans was proved the optimal biotic elicitor on tropane alkaloids production. These results will be served mass production of tropane alkaloids by large-scale production.

• Ocean and Polar Research
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• v.29 no.4
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• pp.339-348
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• 2007

In this work, we compared the characteristics of three benthic biotic indices (BPI, AMBI, BIBI) which indicates the health condition of benthic communities in Masan Bay, Korea where anthropogenic impacts have been concentrated. Also we evaluated the usefulness of these benthic indices and some problems if they were applied to the Korean coastal waters. For this we used the macrozoobenthos data collected using van Veen grab ($0.1\;m^2$) at 21 sites in Masan Bay in February and August 2004. Based on the BPI values, two stations in the inner bay were found in a very hard polluted condition and three stations in the middle bay were also in a highly polluted condition. Only one station located in the bay mouth was in a normal condition. The inner bay stations showed very high AMBI values (${\geq}5.0$), indicating a highly polluted condition. The bay mouth station was assessed in a moderately polluted condition. The overall BIBI values in Masan Bay were in the range between 1.0 and 3.0. The inner bay stations showed low BIBI values (${\leq}2.0$) in the severely degraded condition. The bay mouth station with high BIBI value over 3.0 was assessed as a normal condition. All three benthos indices showed that macrozoobenthic communities in the inner bay were in a seriously polluted condition all year round, and macrobenthic faunas in the bay mouth seemed in a bad healthy condition (slightly polluted) based on AMBI during summer season. These three benthic biotic indices showed the similar assessment result, and thus we consider that each of them is a useful tool for the assessment of coastal benthic ecosystems under the organic enrichment in sediment.

• Journal of the Korean Society of Environmental Restoration Technology
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• v.7 no.4
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• pp.52-60
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• 2004

In order to analysis of the water pollution of the Anyang stream(one of the biggest branch streams of the Han River) and its main tributaries, the geological and topographical and rainfall features in its basin were investigated. To do this, the water samples were collected 23 points of the upper, mid and down of Anyang stream and its tributaries and were analyzed based on the chemical methods, Korean Biotic Index(KBI) and Saprobien systems. The Anyang stream basin has a characteristic of topographical torrential heavy rainfall like a typical rainfall feature in Korea. The concentration and the outflow rate of rainfall is very different in seasonal, and water pollution in dry season is especially severe. After 1997, although the water quality status of stream has been improved gradually, the concentration of T-N and SS at the upstream is increased due to the deficiency of facility used for collecting wastewater released from industrial factories, livestock farms and residential areas. The mainstream of the Anyang stream is classified into the 5th grade water as polysaprobic water area according to Saprobien system and the biotic index is over 2.5 in overall. Most of tributaries have 1~3 grade water limit with ${\alpha}$- and ${\beta}$-mesosaprobic except the upper and mid streams of Samsung tributary, in which pollution status is the lowest part. Though Sambong tributary is ${\alpha}$-mesosaproboic, biotic index is low because of the appearance of abundant benthos animals in farming and fishing villages.

• Journal of Plant Biotechnology
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• v.38 no.2
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• pp.151-161
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• 2011

Plant proteomics is the large-scale studies of proteins, particularly on their structures and functions, governed by the physiological metabolism of plant cells. With the development of techniques and strategies in proteomics, proteomics approach is moving forward in systems biology handling sophisticated components of major signaling and biochemical pathways in plants responding to their environment. In Korea, pioneers in plant proteomics are trying to catch up with global trends in plant proteomics; these researchers are not only improving existing techniques in protein extraction but also developing new techniques in proteomics context. In the hot field of abiotic and biotic stress proteomics, 29 and 9 out of 74 papers have been published during the review period from 2005 to 2010, respectively. This present review article provides an overview on the output of Korean plant proteomers while paying special attention to both abiotic and biotic stress proteomics.