• Mycobiology
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• 제46권4호
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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.

• 생태와환경
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• 제50권3호
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• pp.305-313
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• 2017

기후변화로 잦아진 강우에 의해 염분 환경에 유입되는 담수생물의 영향을 파악해 보고자 하였다. 담수의 오염지표생물인 깔따구과의 실내 실험종인 C. riparius를 대상으로 염분 노출에 따른 스트레스 반응으로 생존율과 탈피율, 성장기간, 하순기절 기형을 분석하였고, 분자생물학적으로 스트레스 분자마커로 연구가 이루어진 HSP70 유전자 발현을 측정하였다. C. riparius의 생존율은 노출시간에 따라 감소하였으며 15 psu에서 4일이 경과하면 생존개체가 관찰되지 않았다. C. riparius의 pupation과 emergence는 15 psu 이상에서는 보이지 않았고 탈피의 성공은 10 psu에서 20% 이하였다. 또한 C. riparius의 성장지연은 pupation과 emergence 기간에서 잘 반영되어, 대조군과 5 psu에 비해 10 psu에서 4일이 늦어졌다. 염분 노출 96시간 후 관찰한 C. riparius 하순기절 형태 이상은 10 psu와 15 psu에서 소수 관찰되었다. C. riparius HSP70 유전자 발현은 대조군에 비해 5, 10 psu에서 약 2.5~4배 이상 발현량이 크게 증가하였다. 따라서 염분은 담수생물에게 매우 큰 스트레스를 제공하는 원인물질로 유해물질과 유사한 생태독성학적인 반응과 분자지표 반응을 보여주었다.

• 대한의생명과학회지
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• 제17권4호
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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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• 제26권2호
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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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• 제26권12호
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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.

• 대한수의학회지
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• 제51권4호
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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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• 제44권2호
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• pp.251-263
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• 1997

연구배경 : 다제내성결핵의 증가는 효과적인 결핵 치료를 어렵게 할 뿐만 아니라 결핵관리 사업에 큰 장애로 대두되고 있다. 따라서 다제내성결핵균의 내성획득 기전에 대한 이해와 조기진단 방법의 개발이 시급한 실정이다. 최근 분자생물학의 발달로 결핵균의 유전학적인 검검출방법은 기존 배양검사의 감수성에 필적하는 수준이며, 더 나아가 1차 약제인 INH와 RMP 등의 핵산 수준에서 내성기전에 대한 최근의 연구 결과는 더욱 새롭고 빠른 감수성 검사의 기틀을 마련할 것으로 생각된다. RMP에 대한 M. tuberculosis의 주 내성기전은 RNA polymerase $\beta$subunit (rpoB)의 돌연변이로 보고되고 있다. 방 법 : 본 실험에서 42예의 결핵균 배양검체 (RMP 내성 32예, 감수성 10예)를 선택하여 rpoB 유전자의 돌연변이를 분석하였다. 역교잡법(reverse hybridization)을 이용한 상용화된 INNO-LiPA Line Probe Assay (LiPA)를 이용하여 돌연변이 양상을 검사하고 직접염기서열 방법으로 분석한 결과와 비교하였다. 결 과 : LiPA에서 RMP 감수성균주는 S띠의 발색이 모두 나타났으며, 내성균주는 모두 R띠의 발색이냐 S띠의 소실이 나타나 내성임을 확인할 수 있었다. 내성균주 32예중 22예(68.8%)는 4개의 R띠중 하나의 소실이 있어 바로 돌연변이 양상을 확인할 수 있었으며 R5(S531L)형이 17예(77.3%)로 제일 많았다. LiPA에서 확인되지 않았던 10예는 직접염기서열 분석법으로 내성양상을 검사한 바, 총 11예와 점돌연변이와 1예의 염기결실을 확인하였다. 이중 S522W와 9염기쌍의 결실은 현재까지 보고된 바 없는 처음으로 보고되는 유형의 돌연변이었다. 결 론 : 한국인의 결핵균에서 RMP 내성의 주 기전은 rpoB 유전자의 돌연변이에 의한 RNA polymerase의 구조 변화에 기인하는 것을 알 수 있었고 직접염기서열 결정법으로 그 양상을 확인하였으며, LiPA법이 RMP 내성의 조기진단에 유용하게 이용될 수 있는 것으로 판단되었다.

• 한국잡초학회지
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• 제12권3호
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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.