• 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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• 제78권4호
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• pp.416-418
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• 2015

Mycobacterium shinjukuense is a novel species of nontuberculous mycobacteria (NTM) that was first reported in Japan in 2011. It is a slow-growing NTM pathogen that can cause chronic pulmonary infections. There are only a few reported cases of M. shinjukuense infections, all of which are from Japan. We reported a case of chronic lung disease caused by M. shinjukuense. The organism was identified by 16S rRNA, rpoB, and hsp65 gene sequencing. To the best of our knowledge, this was the first confirmed case of lung disease caused by M. shinjukuense outside of Japan.

• 식물분류학회지
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• 제51권1호
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• pp.109-114
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• 2021

Veronica nakaiana Ohwi (Plantaginaceae) is an endemic taxon on Ulleungdo Island, Korea. We report the second complete chloroplast genome sequence of V. nakaiana. Its genome size is 152,319 bp in length, comprising a large single-copy of 83,195 bp, a small single-copy of 17,702 bp, and a pair of inverted repeat regions of 25,711 bp. The complete genome contains 115 genes, including 51 protein-coding genes, four rRNA genes, and 31 tRNA genes. When comparing the two chloroplast genomes of V. nakaiana, 11 variable sites are recognized: seven SNPs and four indels. Two substitutions in the coding regions are recognized: rpoC2 (synonymous substitution) and rpl22 (nonsynonymous substitution). In nine noncoding regions, one is in the tRNA gene (trnK-UUU), one is in the intron of atpF, and seven are in the intergenic spacers (trnH-GUG~psbA, trnK-UUU, rps16~trnQ-UUG, trnC-GCA~petN, psbZ~trnG-GCC, ycf3~trnS-GGA, ycf4~cemA, and psbB~psbT). The data provide the level of genetic variation in V. nakaiana. This result will be a useful resource to formulate conservation strategies for V. nakaiana, which is a rare endemic species in Korea.

• 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.

• 한국어병학회지
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• 제32권2호
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• pp.69-80
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• 2019

We performed MLSA (multilocus sequence analysis) and phenotypic characterization of Aliivibrio species isolated from walleye pollock (Gadus chalcogrammus) maintained in 3 different facilities of Gangwon Province, the east coast of Korea. Of 38 Aliivibrio species identified by 16S rDNA sequences, 12 strains were randomly selected and MLSA was conducted with 5 house-keeping genes (gapA, gyrB, pyrH, recA and rpoA) and 16S rDNA gene. Phylogenetic analysis and homology of the concatenated sequences (4,580 bp) with other Vibrionaceae genera revealed that 4 strains (GNGc16.1, YYGc16.1, YYGc16.2, GSGc18.1) were identified as Aliivibrio logei and one strain (GSGc16.1) as A. wodanis. One strain (GSGc17.1) was tentatively identified as A. logei, but needs further analysis because it did not belong to the same clade with A. logei type strain. 6 strains (GSGc17.2, GNGc16.2, GSGc16.2, GSGc17.3, GSGc18.2, GSGc17.4) need further investigation as potential novel species. Either phenotypic characterization or 16S rDNA sequence alone did not provide enough information for identification of Aliivibrio strains at the species level. A. logei and A. wodanis are generally known as non-pathogenic bacteria, but also known as opportunistic or secondary pathogens of cold water fishes. Cares should be taken to prevent potential outbreaks due to these bacteria, although there was no outbreaks during the sampling period.

• Journal of Microbiology and Biotechnology
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• 제21권4호
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• pp.421-429
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• 2011

For precise identification of a Lactobacillus K1 isolate, LC-MS/MS analysis of the putative surface layer protein was performed. The results obtained from LTQ-FT-ICR mass spectrometry confirmed that the analyzed protein spot is the surface layer protein originating from Lb. helveticus species. Moreover, the identified protein has the highest similarity with the surface layer protein from Lb. helveticus R0052. To evaluate the proteomic study, multilocus sequence analysis of selected housekeeping gene sequences was performed. Combination of 16S rRNA sequencing with partial sequences for the genes encoding the RNA polymerase alpha subunit (rpoA), phenylalanyl-tRNA synthase alpha subunit (pheS), translational elongation factor Tu (tuf), and Hsp60 chaperonins (groEL) also allowed to classify the analyzed isolate as Lb. helveticus. Further classification at the strain level was achieved by sequencing of the slp gene. This gene showed 99.8% identity with the corresponding slp gene of Lb. helveticus R0052, which is in good agreement with data obtained by nano-HPLC coupled to an LTQ-FT-ICR mass spectrometer. Finally, LC-MS/MS analysis of surface layer proteins extracted from three other Lactobacillus strains proved that the proposed method is the appropriate molecular tool for the identification of S-layer-possessing lactobacilli at the species and even strain levels.

• Tuberculosis and Respiratory Diseases
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• 제78권4호
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• pp.432-435
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• 2015

This is a report of the first South Korean case of a lung disease caused by Mycobacterium simiae. The patient was a previously healthy 52-year-old female. All serial isolates were identified as M. simiae by multi-locus sequencing analysis, based on hsp65, rpoB, 16S-23S rRNA internal transcribed spacer, and 16S rRNA fragments. A chest radiography revealed deterioration, and the follow-up sputum cultures were persistently positive, despite combination antibiotic treatment, including azithromycin, ethambutol, and rifampin. To the best of our knowledge, this is the first confirmed case of a lung disease caused by M. simiae in South Korea.

• The Plant Pathology Journal
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• 제37권2호
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• pp.137-151
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• 2021

The present study describes the bacterial blight of walnut, caused by Xanthomonas arboricola pv. juglandis (Xaj) in the northern Gyeongbuk province, Korea. Disease symptoms that appear very similar to anthracnose symptoms were observed in walnut trees in June 2016. Pathogens were isolated from disease infected leaves, fruits, shoots, bud, flower bud of walnut, and cultured onto yeast dextrose carbonate agar plates. Isolated bacteria with bacterial blight symptoms were characterized for their nutrient utilization profiles using Biolog GN2 and Vitek 2. In addition, isolates were subjected to physiological, biochemical, and morphological characterizations. Furthermore, isolates were identified using 16S rDNA sequence analysis, and multi-locus sequence analysis using atpD, dnaK, efp, and rpoD. To confirm pathogenicity, leaves, fruits, and stems of 3-year-old walnut plants were inoculated with bacterial pathogen suspensions as a foliar spray. One week after inoculation, the gray spots on leaves and yellow halos around the spots were developed. Fruits and stems showed browning symptoms. The pathogen Xaj was re-isolated from all symptomatic tissues to fulfill Koch's postulates, while symptoms were not appeared on control plants. On the other hand, the symptoms were very similar to the symptoms of anthracnose caused by Colletotrichum gloeosporioides. When walnut plants were inoculated with combined pathogens of Xaj and C. gloeosporioides, disease symptoms were greater in comparison with when inoculated alone. Xaj population size was more in the month of April than March due to their dormancy in March, and sensitive to antibiotics such as oxytetracycline and streptomycin, while resistant to copper sulfate.

• International Journal of Oral Biology
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• 제39권4호
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• pp.207-213
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• 2014

Antimicrobial actions of reactive oxygen/nitrogen species (ROS/RNS) derived from products of NADPH oxidase and inducible nitric oxide (NO) synthase in host phagocytes inactivate various bacterial macromolecules. To cope with these cytotoxic radicals, pathogenic bacteria have evolved to conserve systems necessary for detoxifying ROS/RNS and repairing damages caused by their actions. In response to these stresses, bacteria also induce expression of molecular chaperones to aid in ameliorating protein misfolding. In this study, we explored the function of a newly identified chaperone Spy, that is localized exclusively in the periplasm when bacteria exposed to conditions causing spheroplast formation, in the resistance of Salmonella Typhimurium to ROS/RNS. A spy deletion mutant was constructed in S. Typhimurium by a PCR-mediated method of one-step gene inactivation with ${\lambda}$ Red recombinase, and subjected to ROS/RNS stresses. The spy mutant Salmonella showed a modest decrease in growth rate in NO-producing cultures, and no detectable difference of growth rate in $H_2O_2$ containing cultures, compared with that of wild type Salmonella. Quantitative RT-PCR analysis showed that spy mRNA levels were similar regardless of both stresses, but were increased considerably in Salmonella mutants lacking the flavohemoglobin Hmp, which are incapable of NO detoxification, and lacking an alternative sigma factor RpoS, conferring hypersusceptibility to $H_2O_2$. Results demonstrate that Spy expression can be induced under extreme conditions of both stresses, and suggest that the protein may have supportive roles in maintaining proteostasis in the periplasm where various chaperones may act in concert with Spy, thereby protecting bacteria against toxicities of ROS/RNS.

• 대한방사선치료학회지
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• 제30권1_2호
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• pp.27-34
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• 2018

목 적 : 폐의 우측후사방향 선량전달시, Carbon Side Rail과 환자 고정기구인 Vac-lok이 미치는 영향을 보고자 한다. 대상 및 방법 : Vac-lok의 오른쪽 부분을 10, 20, 30 mm 두께로 제작하였다. 측정은 유리선량계를 이용하여 측정하였고, 측정점은 팬텀 우측 폐의 center Point를 기준으로 좌, 우, 하, 상 방향 각각 A, B, C, D Point로 설정 하였다. 각 point에 유리선량계를 삽입한 후 couch의 Side Rail을 외측(Out)으로 뺀 후 vac-lok을 놓지 않은 no vac-lok, 그리고 10, 20, 30 mm의 vac-lok 위에 팬텀을 세팅하였다. 중심점에 6 MV 광자선을 조사야 $10{\times}10cm^2$, SAD 100 cm, 겐트리 각도 $225^{\circ}$로 하여 300 MU/min 선량률과 100 MU 조사선량을 전달하였다. 측정은 5회씩 실시하였고, 마찬가지로 Side Rail을 내측(In)으로 넣은 후 각 point에 대해서도 같은 조건으로 5 회씩 측정하여 평균값을 산출하였다. 결 과 : side rail에 따라서는 중심점, A, B, C, D Point 각각 -11.8 %, -12.3 %, -4.1 %, -12.3 %, -7.3 %의 선량 감소를 보였다. Side-Rail-Out에서 10 mm vac-lok의 경우 약 -0.9 %가 감소되었고, 20 mm vac-lok 사용 시 약 -2.0 %, 30 mm vac-lock 사용 시 약 -3.0 %가 감소되었다. Side-Rail-In에서 10 mm vac-lok의 경우 약 -1.0 %가 감소되었고, 20 mm vac-lok 사용 시 약 -2.1 %, 30 mm vac-lok 사용 시 약 -3.0 %가 감소되었다. Side-Rail-In 상태의 no vac-lok 선량 값을 기준으로 Side-Rail-Out 상태의 10, 20, 30 mm vac-lok을 사용할 때, side rail에 대한 선량 감소에 더하여 중심점에서는 약 -0.9 %, -1.8 % -2.4 %, A point에서는 -0.5 %, -1.6 %, -2.1 %, B point에서는 약 -0.9 %, -2.0 %, -3.2 %, C Point에서는 -1.0 %, -2.1 %, -3.1 %, D point에서는 약 -1.0 %, -1.6 %, -3.1 %의 추가적인 선량 감소를 나타냈다. 결 론 : 폐를 비롯한 우측후사방향 방사선 치료 시 side rail에 대해 주의를 기울이고, vac-lok 제작 시 vaclok 두께에 대해 관심을 갖는다면 더 나은 치료 효과를 기대해 볼 수 있으리라 사료된다.