• Mycobiology
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• v.46 no.4
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• pp.361-369
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• 2018

The rice blast fungus, Magnaporthe oryzae, is an important pathogen of rice plants. It is well known that genes encoded in the genome have different evolutionary histories that are related to their functions. Phylostratigraphy is a method that correlates the evolutionary origin of genes with evolutionary transitions. Here we applied phylostratigraphy to partition total gene content of M. oryzae into distinct classes (phylostrata), which we designated PS1 to PS7, based on estimation of their emergence time. Genes in individual phylostrata did not show significant biases in their global distribution among seven chromosomes, but at the local level, clustering of genes belonging to the same phylostratum was observed. Our phylostrata-wide analysis of genes revealed that genes in the same phylostratum tend to be similar in many physical and functional characteristics such as gene length and structure, GC contents, codon adaptation index, and level of transcription, which correlates with biological functions in evolutionary context. We also found that a significant proportion of genes in the genome are orphans, for which no orthologs can be detected in the database. Among them, we narrowed down to seven orphan genes having transcriptional and translational evidences, and showed that one of them is implicated in asexual reproduction and virulence, suggesting ongoing evolution in this fungus through lineage-specific genes. Our results provide genomic basis for linking functions of pathogenicity factors and gene emergence time.

• Korean Journal of Ecology and Environment
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• v.50 no.3
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• pp.305-313
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• 2017

We investigate that the impact of freshwater organism exposed to the salinity environment by the frequent rainfall following climate change. To evaluate the stress response following salinity exposure, we assessed the survival rate, molting success rate, the developmental period and mouthpart deformities in Chironomus riparius. In addition, we measured the molecular responses of biomarker gene, gene expression of heat shock protein 70 (HSP70) in C. riparius exposed to salinity after 96 hour. The C. riparius survival rates were showed on time dependent manner and not observed survival organisms above 15 psu at day 4. The pupation and emergence of C. riparius were not seen above 15 psu, and the molting success rate was less than 20% at 10 psu. The developmental retardation of C. riparius was well observed in the pupation and emergence period and was delayed by 4 days at 10 psu compared to the control and 5 psu. The mouthpart deformities after salinity exposure at 96 or 72 hour were observed at 10 psu and 15 psu. The expression of C. riparius HSP70 level was significantly increased exposure to 5 psu and 10 psu. Thus, salinity has been caused to be various ecotoxicological and molecular stress responses on freshwater organisms similar to harmful substances such as EDCs and so on.

• Biomedical Science Letters
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• v.17 no.4
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• pp.297-304
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• 2011

Influenza A virus of the Orthomyxoviridae family is a contagious respiratory pathogen that continues to evolve and burden in the human public health. It is able to spread efficiently from human to human and have the potential to cause pandemics with significant morbidity and mortality. It has been estimated that every year about 500 million people are infected with this virus, causing about approximately 0.25 to 0.5 million people deaths worldwide. Influenza A viruses are classified into different subtypes by antigenicity based on their hemagglutinin (HA) and neuraminidase (NA) proteins. The sudden emergence of influenza A virus subtypes and access for epidemiological analysis of this subtypes demanded a rapid development of specific diagnostic tools. Also, rapid identification of the subtypes can help to determine the antiviral treatment, because the different subtypes have a different antiviral drug resistance patterns. In this study, our aim is to detect influenza A virus subtypes by using real-time nucleic acid sequence based amplification (NASBA) which has high sensitivity and specificity through molecular beacon. Real-time NASBA is a method that able to shorten the time compare to other molecular diagnostic tools and is performed by isothermal condition. We selected major pandemic influenza A virus subtypes, H3N2 and H5N1. Three influenza A virus gene fragments such as HA, NA and matrix protein (M) gene were targeted. M gene is distinguished influenza A virus from other influenza virus. We designed specific primers and molecular beacons for HA, NA and M gene, respectively. In brief, the results showed that the specificity of the real-time NASBA was higher than reverse transcription polymerase chain reaction (RT-PCR). In addition, time to positivity (TTP) of this method was shorter than real-time PCR. This study suggests that the rapid detection of neo-appearance pandemic influenza A virus using real-time NASBA has the potential to determine the subtypes.

• Toxicological Research
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• v.26 no.2
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• pp.137-147
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• 2010

Pulmonary fibrosis is a common consequence of many lung diseases and a leading cause of morbidity and mortality. The molecular mechanisms underlying the development of pulmonary fibrosis remain poorly understood. One model used successfully to study pulmonary fibrosis over the past few decades is the bleomycin-induced pulmonary fibrosis model. We aimed to identify the genes associated with fibrogenesis using an Affymetrix GeneChip system in a bleomycin-induced rat model for pulmonary fibrosis. To confirm fibrosis development, several analyses were performed, including cellular evaluations using bronchoalveolar lavage fluid, measurement of lactate dehydrogenase activity, and histopathological examinations. Common aspects of pulmonary fibrosis such as prolonged inflammation, immune cell infiltration, emergence of fibroblasts, and deposition of extracellular matrix and connective tissue elements were observed. Global gene expression analysis revealed significantly altered expression of genes ($\geq$ 1.5-fold, p < 0.05.) in a time-dependent manner during the development of pulmonary fibrosis. Our results are consistent with previous results of well-documented gene expression. Interestingly, the expression of triggering receptor expressed on myeloid cells 2 (Trem2), secreted phosphoprotein 1 (Spp1), and several proteases such as Tpsab1, Mcpt1, and Cma1 was considerably induced in the lung after bleomycin treatment, despite little evidence that they are involved in pulmonary fibrogenesis. These data will aid in our understanding of fibrogenic mechanisms and contribute to the identification of candidate biomarkers of fibrotic disease development.

• Journal of Microbiology and Biotechnology
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• v.26 no.12
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• pp.2224-2227
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• 2016

Shigella sonnei harboring $bla_{CTX-M-55}$ was isolated outside of Asia for the first time. The $bla_{CTX-M-55}$ gene was found to be downstream of ISEcp-1 and located in a ~130 kb conjugative plasmid belonging to the I1 incompatibility group. The strain was recovered from a 7-year-old Ecuadorian girl with watery diarrhea who had not travelled abroad. Recent local data describe the emergence of $bla_{CTX-M-55}$ and other variants typically found in Asia in the Andean Region, suggesting that increased travel of humans and trade relationships with Asian countries are influencing the current Ecuadorian bacterial resistance situation.

• Korean Journal of Veterinary Research
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• v.51 no.4
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• pp.267-275
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• 2011

Methicillin-resistant Staphylococcus (S.) aureus (MRSA) is one of the most important nosocomial pathogens worldwide and the emergence of this strain has become a major clinical problem. In this study, we investigated the prevalence of MRSA and their genetic characteristics in 69 S. aureus isolated from humans and animals. In human isolates, higher antimicrobial resistance rates were observed against penicillin (80.6%), followed by erythromycin (11.9%) and tetracycline (9.0%). All of them were susceptible to clindamycin, enrofloxacin, novobiocin, pirlimycin, trimethoprim/sulfamethoxazole and vancomycin. The resistance patterns in animal isolates were similar to those of human isolates. Two (2.9%) MRSA strains were isolated from human (n = 1) and animal (n = 1), and these isolates were confirmed as carrying the mecA gene. One isolate originating from human was resistant to 7 drugs and the other isolate derived from animal was resistant to 11 drugs. Staphylococcal cassette chromosome mec (SCCmec) variant IIIB was identified in animal isolate but SCCmec type of an isolate from human was not exactly determined. Two MRSA isolates showed unrelated PFGE pattern between them. Our results indicated although the frequency of MRSA isolates from humans and animals was low, a continuous surveillance and monitoring should be called for to prevent the contamination and spread of MRSA in the community. To our knowledge, this is the first time that SCCmec type variant IIIB was detected from animals in Korea.

• Tuberculosis and Respiratory Diseases
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• v.44 no.2
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• pp.251-263
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• 1997

Background : The emergence of multidrug-resistant strains of Mycobacterium tuberculosis presents a significant challange to the treatment and control of tuberculosis, and there is an urgent need to understand the mechanisms by which strains acquire multidrug resistance. Recent advances in molecular methods for the detection of M. tuberculosis genetic targets have approached the sensitivity of culture. Furthermore the prospect of determining resistance in mycobacteria at the nucleic acid level particulary to first-line drugs like rifampin, isoniazid has provided a glimps of the next generation of sensitivity test for M. tuberculosis. Previous studies in RMP resistant M. tuberculosis have shown that mutation in $\beta$subunit of RNA polymerase is main mechanism of resistance. Method : In this study, rpoB gene for the $\beta$subunit of RNA polymerase from M. tuberculosis of 42 cultured samples (32 were RMP resistant and 10 were sensitive cases) were isolated and characterised the mutations. Direct sequencing data were compared with the results of INNO-LiPA Line Probe Assay (LiPA, Innogenetics, Belgium), commercial RMP resistance detecting kit using reverse hybridization method. Results : All of the RMP resistant samples were revealed the presence of mutation by LiPA. In 22 samples (68.8%) out of 32 RMP resistant cases, the mutation types were confirmed by the positive signal at one of 4 mutation bands in the strip. The most frequent type was R5 (S531L) which were 17 cases (77.3%). Results of direct sequencing were identified the exact characteristics of 8 mutations which were not confirmed by LiPA. S522W type point mutation and 9 base pair deletion at codon 513~515 were new identified mutations for the first time. Conclusion : Mutations in rpoB gene is the main mechanism of RMP resistance in M. tuberculosis and LiPA is a very useful diagnostic tool for the early diagnosis of RMP resistance in M. tuberculosis.

• Korean Journal of Weed Science
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• v.12 no.3
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• pp.261-270
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• 1992

Many herbicides that are applied at the soil before weed emergence inhibit plant growth soon after weed germination occurs. Plant growth has been known as an irreversible increase in size as a result of the processes of cell divison and cell enlargement. Herbicides can influence primary growth in which most new plant tissues emerges from meristmatic region by affecting either or both of these processes. Herbicides which have sites of action during interphase($G_1$, S, $G_2$) of cell cycle and cause a subsequent reduction in the observed frequency of mitotic figures can be classified as an inhibitor of mitotic entry. Those herbicides that affect the mitotic sequence(mitosis) by influencing the development of the spindle apparatus or by influencing new cell plate formation should be classified as causing disruption of the mitotic sequence. Sulfonylureas, imidazolinones, chloroacetamides and some others inhibit plant growth by inhibiting the entry of cell into mitosis. The carbamate herbicides asulam, carbetamide, chlorpropham and propham etc. reported to disrupt the mitotic sequence, especially affecting on spindle function, and the dinitroaniline herbicides trifluralin, nitralin, pendimethalin, dinitramine and oryzalin etc. reported to disrupt the mitotic sequence, particularly causing disappearence of microtubles from treated cells due to inhibition of polymerization process. An inhibition of cell enlargement can be made by membrane demage, metabolic changes within cells, or changes in processes necessary for cell yielding. Several herbicides such as diallate, triallate, alachlor, metolachlor and EPTC etc. reported to inhibit cell enlargement, while 2, 4-D has been known to disrupt cell enlargement. One potential danger inherent in the use of soil acting herbicides is that build-up of residues could occur from year to year. In practice, the sort of build-up that would be disastrous is unikely to occur for substances applied at the correct soil concentration. Crop injury caused by soil applied herbicides can be minimized by (1) following the guidance of safe use of herbicides, particularly correct dose at correct time in right crop, (2) by use of safeners which protect crops against injury without protecting any weed ; interactions between herbicides and safeners(antagonists) at target sites do occur probably from the following mechanisms (1) competition for binding site, (2) circumvention of the target site, and (3) compensation of target site, and another mechanism of safener action can be explained by enhancement of glutathione and glutathione related enzyme activity as shown in the protection of rice from pretilachlor injury by safener fenclorim, (3) development of herbicide resistant crops ; development of herbicide-resistant weed biotypes can be explained by either gene pool theory or selection theory which are two most accepted explanations, and on this basis it is likely to develop herbicide-resistant crops of commercial use. Carry-over problems do occur following repeated use of the same herbicide in an extended period of monocropping, and by errors in initial application which lead to accidental and irregular overdosing, and by climatic influence on rates of loss. These problems are usually related to the marked sensitivity of the particular crops to the specific herbicide residues, e.g. wheat/pronamide, barley/napropamid, sugarbeet/ chlorsulfuron, quinclorac/tomato. Relatively-short-residual product, succeeding culture of insensitive crop to specific herbicide, and greater reliance on postemergence herbicide treatments should be alternatives for farmer practices to prevent these problems.