• ALGAE
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• 제38권2호
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• pp.93-110
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• 2023

Progress in phylogenomic analysis has led to a considerable re-evaluation of former cyanobacterial system, with many new taxa being established at different nomenclatural levels. The family Geminocystaceae is among cyanobacterial taxa recently described on the basis of polyphasic approach. Within this family, there are six genera: Geminocystis, Cyanobacterium, Geminobacterium, Annamia, Picocyanobacterium, and Microcrocis. The genus Geminocystis previously encompassed two species: G. herdmanii and G. papuanica. Herein, a new species G. urbisnovae was proposed under the provision of the International Code of Nomenclature for algae, fungi, and plants (ICN). Polyphasic analysis was performed for five strains from the CALU culture collection (St. Petersburg State University, Russian Federation), and they were assigned to the genus Geminocystis in accordance with high 16S rRNA gene similarity to existing species, as well as because of proximity to these species on the phylogenetic trees reconstructed with RaxML and Bayes methods. Plausibility of their assignment to a separate species of the genus Geminocystis was substantiated with smaller cell size; stenohaline freshwater ecotype; capability to complementary chromatic adaptation of second type (CA2); distinct 16S rRNA gene clustering; sequences and folding of D1-D1' and B box domains of the 16S-23S internal transcribed spacer region. The second objective pursued by this communication was to provide a survey of the family Geminocystaceae. The overall assessment was that, despite attention of many researchers, this cyanobacterial family has been understudied and, especially in the case of the crucially important genus Cyanobacterium, taxonomically problematic.

• 대한임상검사과학회지
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• 제45권2호
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• pp.48-53
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• 2013

Recently, the isolation rate of nontuberculous mycobacteria (NTM) in clinical laboratories and the incidence of NTM infections are on the increase in Korea, but there have been only a few studies that reveal the general aspect of NTM isolation or species distribution. Therefore, this study was performed to examine the species identification by PCR-restriction fragment length polymorphism analysis (PRA, PCR-RFLP), and the clinical significance of mycobacterial cultures. PRA was used during the novel region of the rpoB gene and was developed for rapid and precise identification of mycobacteria to the species level. From January 2012 to April 2012, we examined pre-identified nontuberculous mycobacteria (60 species in 3 hospital of Busan-Kyeongnam area). We confirmed 4 (6.6%) Mycobacterium tuberculosis (MTB) and 56 (93.4%) NTM from 60 pre-identified NTM species by multiplex PCR (MolecuTech $MTB-ID^R$ V3, YD Diagnostics, Korea) and PRA (Myco-ID, YD Diagnostics, Korea). The distribution of 56 NTM species were M. intracellulare type I 15 (26.7%), M. avium 14 (25%), M. abscessus 11 (19.5%), M. kansasii type I 3 (5.4%), M. pulveris 2 (3.6%), M. intracellulare type, M. chelonae, M. kansasii type V, M. gallinarum, M. wolinskyi. Respectively, 1 (1.8%) and 6 (10.7%) species were not identified.

• 식물병연구
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• 제24권2호
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• pp.138-144
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• 2018

In December 2016, stem rot symptoms were observed on Persian buttercup (Ranunculus asiaticus) plants in Chilgok, Gyeongbuk, Korea. In the early stage of the disease, several black spots appeared on the stem of infected plants. As the disease progressed, the infected stem cleaved and wilted. The causal agent was isolated from a lesion and incubated on Reasoner's 2A (R2A) agar at $25^{\circ}C$. Total genomic DNA was extracted for phylogenetic analysis. Based on the 16S rRNA gene analysis, the isolated strain was found to belong to the genus Pseudomonas. To identify the isolated bacterial strain at the species level, the nucleotide sequences of the gyrase B (gyrB) and RNA polymerase D (rpoD) genes were obtained and compared with the sequences in the GenBank database. As the result, the causal agent of the stem rot disease was identified as Pseudomonas marginalis. To determine the pathogenicity of the isolated bacterial strain, it was inoculated into the stem of healthy R. asiaticus plant, the inoculated plant showed a lesion with the same characteristics as the naturally infected plant. Based on these results, this is the first report of bacterial stem rot on R. asiaticus caused by P. marginalis in Korea.

• 식물병연구
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• 제22권3호
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• pp.158-167
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• 2016

육묘장과 재배포장의 애호박에서 새롭게 발생한 병원균의 특성을 분석하여 동정하였다. 병징은 잎에 수침상의 병반과 강한 노란색의 둘레무리를 가진 점무늬, 꽃에서 갈색 병반, 열매에 노란색의 점무늬였다. 잎의 점무늬로부터 분리된 세균은 박과작물 8개의 식물체, 흑종호박, 애호박, 쥬키니호박, 풋호박, 참박, 참외, 멜론, 오이에 병원성이 있었지만 수박과 밤호박에서는 병을 일으키지 못했다. 분리세균은 다발모를 가진 막대형으로 그람음성이며 King's B 배지에서 형광성이었으며, LOPAT 1a 그룹에 속했다. 그들의 Biolog 기질이용성은 Biolog database의 P. syringae pv. syringae 이용성과 유사하였다. 16S rRNA 유전자 염기서열을 이용한 계통수와 4개의 항존유전자(gapA, gltA, gyrB, rpoD)의 염기서열과 PAMDB에 있는 P. syringae균주들의 염기서열을 이용한 MLST는 애호박 분리균주들이 P. syringae pv. syringae 균주들과 동일한 그룹(clade)으로 그룹화되었고, MLST 계통수에서 애호박 분리균주들의 그룹(clade)은 genomospecies 1에 속하였다. 표현형적, 유전적 특성은 애호박 분리균이 P. syringae pv. syringae임을 제시하였다.

• Journal of Microbiology and Biotechnology
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• 제33권2호
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• pp.167-179
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• 2023

The rifampicin-resistant strain E9-302 of Edwardsiella ictaluri strain 669 (WT) was generated by continuous passage on BHI agar plates containing increasing concentrations of rifampicin. E9-302 was attenuated significantly by 119 times to zebrafish Danio rerio compared to WT in terms of the 50% lethal dose (LD₅₀). Zebrafish vaccinated with E9-302 via intraperitoneal (IP) injection at a dose of 1 × 10³ CFU/fish had relative percentage survival (RPS) rates of 85.7% when challenged with wild-type E. ictaluri via IP 14 days post-vaccination (dpv). After 14 days of primary vaccination with E9-302 via immersion (IM) at a dose of 4 × 10⁷ CFU/ml, a booster IM vaccination with E9-302 at a dose of 2 × 10⁷ CFU/ml exhibited 65.2% RPS against challenge with wild-type E. ictaluri via IP 7 days later. These results indicated that the rifampicin-resistant attenuated strain E9-302 had potential as a live vaccine against E. ictaluri infection. A previously unreported amino acid site change at position 142 of the RNA polymerase (RNAP) β subunit encoded by the gene rpoB associated with rifampicin resistance was identified. Analysis of the whole-genome sequencing results revealed multiple missense mutations in the virulence-related genes esrB and sspH2 in E9-302 compared with WT, and a 189 bp mismatch in one gene, whose coding product was highly homologous to glycosyltransferase family 39 protein. This study preliminarily explored the molecular mechanism underlying the virulence attenuation of rifampicin-resistant strain E9-302 and provided a new target for the subsequent study of the pathogenic mechanism of E. ictaluri.

• 한국식품위생안전성학회지
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• 제27권4호
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• pp.466-472
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• 2012

식품 중 P. mirifica 원료 함유여부에 대한 판별법 마련을 위하여 식물의 종 동정에 일반적으로 사용되는 ribulose bisphosphate carboxylase (rbcL), RNA polymerase C (rpoC1), intergenic spacer (psbA-trnH) 및 second internal transcribed spacer (ITS2) 유전자부위를 선정하였다. 선정된 유전자부위를 증폭하기 위하여 일반 프라이머를 이용하였으며 각각 719 bp, 520 bp, 348 bp 및 507 bp의 PCR 산물을 확인하였다. 그리고 염기서열을 결정하고 유전자은행에 등록되어있는 염기서열과 유사성에 대한 분석한 결과 rbcL, rpoC1 및 psbA-trnH 부위는 상동성이 매우 높아 프라이머를 설계하기는 어려웠다. 그러나 ITS2의 경우 염기서열의 차이점이 있어 4종류의 프라이머를 설계하였다. 설계된 프라이머를 이용하여 P. mirifica, P. lobata, B. superba에 대한 PCR을 실시한 결과 SFI12-miri-6F/SFI12-miri-7R 및 SFI12-miri-6F/SFI12-miri-8R의 경우 P. lobata 와 B. superba에서 비 특이적 밴드가 없으며 P. mirifica에서 예상크기인 137 bp 및 216 bp를 확인할 수 있었다. 따라서 본 연구에서 개발된 P. mirifica을 판별할 수 있는 종 특이 프라이머는 식품가능원료 및 가공식품에 대한 적용할 수 있어 인터넷 쇼핑몰 등 시중에 불법적으로 유통되는 제품에 대한 안전관리에 활용도가 매우 클 것으로 기대된다.

• Journal of Microbiology
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• 제35권4호
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• pp.277-283
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• 1997

Promoters inducible by paraquat, a superocide-generating agent, were isolated from Escherichia coli using a promoter-probing plasmid pRS415 with promoterless lacA gene. Twenty one promoters induced by paraquat were selected and further characterized. From sequence analysis, thirteen of the promoters were mapped to their specific loci on the Escherichia coli chromosome. Several promoters were mapped to the upstream of known genes such as usgl, katG, and mglB, whose relationships with superoxide response have not been previously reported. Other promoters were mapped to the upstream region of unknown open reading frames. Downstream of HC 96 promoter are uncharacterized ORFs whose sequences are homologous to ABC-transporter subunits. Downstream of HC84 promoter is an ORF encoding a transcriptional regulator-like protein, which contains a LysR family-specific HTH (helix-turn-helix) DNA bindign motif. We investigated whether these promoters belong to the soxRS regulon. All promoters except HC96 were found to belong to the soxRS regulon. The HC96 promoter was significantly induced by paraquat in the soxRS deletion mutant strain. The basal transcription level of three promoters (HE43, HC71, HD94) significantly increased at the stationary phase, implying that they are regulated by RpoS. However, paraquat inducibility of all promoters disappeared in the stationary phase, suggesting that SoxRS regulatory system is active only in rapidly growing cells.

• Tuberculosis and Respiratory Diseases
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• 제76권1호
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• pp.30-33
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• 2014

We report the first Korean case of lung diseases caused by Mycobacterium abscessus subsp. bolletii in a previously healthy male, except for a previous history of pulmonary tuberculosis and bronchiectasis. All serial isolates are identified as M. abscessus subsp. bolletii by multi-locus sequence analysis based on the hsp65, rpoB, and 16S rRNA fragments. At the genetic level, the isolate has the erm(41) gene with a T28 sequevar, associated with clarithromycin resistance, and no rrl mutation. The isolate is resistant to clarithromycin. Although the symptoms and radiographic findings have improved after combination of antibiotics, the follow-up sputum cultures are persistently positive.

• Tuberculosis and Respiratory Diseases
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• 제74권5호
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• pp.215-221
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• 2013

Background: Nontuberculous mycobacteria (NTM) are considered opportunistic pathogens, and several species of NTM are associated with human diseases that typically involve the pulmonary, skin/soft tissue, or lymphatic systems; such infection may also cause disseminated diseases. Recent studies have reported increasing rates of NTM-induced disease worldwide. Methods: Respiratory samples are being analyzed for acid-fast bacilli (AFB) culture and NTM identification at Dankook University Hospital in Cheonan, Korea, from September 2005 to September 2011. Identification is performed by using polymerase chain reaction-restriction fragment length polymorphism analysis targeting a novel region of the rpoB gene. Results: A total of 25,133 specimens were received for AFB culture, of which 1,014 (4.0%) were NTM-positive. A total of 267 samples from 186 patients were tested for NTM identifications, and 232 samples from 157 patients were positive for NTM species. Among the patients who tested positive for NTM, 65.6% were men and the average age was 63.3 years. Mycobacterium avium complex, the most commonly detected NTM pathogen, was found in 65.9% of the 232 samples. The annual average percentage of NTM isolates from AFB culture-positive specimens was 31.3%: the highest rate was seen in 2011 (44.3%), followed by 2009 (37.4%) and 2010 (37.2%). An upward trend in NTM incidence was found during the study period. Conclusion: The prevalence of pulmonary NTM isolates continues to increase in Cheonan, suggesting that pulmonary NTM disease is becoming increasingly common.

• 대한의생명과학회지
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• 제15권4호
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• pp.295-300
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• 2009

Tuberculosis caused by Mycobacterium tuberculosis (MTB) still remains to be the most dreadful infectious disease affecting almost every country. In the present study, we developed a simple and rapid but accurate and sensitive assay method for detecting MTB using microplate hybridization assay. For this, a selective region of the rpoB gene was used to design PCR primers, and MTB and Mycobacterium genus-specific probe molecules. The specificity of the assay was confirmed using fifteen different mycobacterial reference strains and twelve different non-mycobacterial reference strains, and the sensitivity was determined to be 100 fg using genomic DNA of MTB reference strain, H37Rv. Subsequently, a total of 62 sputum samples with diverse smear scores and culture positive results were used to evaluate the kit performance. In brief, the specificity and the sensitivity of the assay were 100% and 98.4%, respectively.