• Korean Journal of Plant Taxonomy
• /
• v.51 no.1
• /
• pp.109-114
• /
• 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
• /
• v.38 no.2
• /
• pp.93-110
• /
• 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.

• Journal of fish pathology
• /
• v.32 no.2
• /
• pp.69-80
• /
• 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
• /
• v.21 no.4
• /
• pp.421-429
• /
• 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
• /
• v.78 no.4
• /
• pp.432-435
• /
• 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
• /
• v.37 no.2
• /
• pp.137-151
• /
• 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
• /
• v.39 no.4
• /
• pp.207-213
• /
• 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.

• The Journal of Korean Society for Radiation Therapy
• /
• v.30 no.1_2
• /
• pp.27-34
• /
• 2018

Purpose : To evaluate the effect of carbon couch side rail and vacuum immobilization device in case of lung RPO irradiation. Materials and Methods : The 10, 20, 30 mm thickness of vac-lok's right side were obtained. To measure of doses, glass dosimeters were used and measured reference point is left lung center at the phantom. A, B, C, and D points are left, right, down, and up directions based on the center point. In the state of Side-Rail-Out, place the without vac-lok, with the thickness of 10, 20, and 30 mm vac-lok. After the glass dosimeters was inserted in center, A, B, C, and D points, 100 MU of 6 MV X-ray were irradiated to the referenced center point in the condition of $10{\times}10cm^2$ field size, SAD 100 cm, gantry angle 225, 300 MU/min dose rate. Five measurements were made for each point. In the state of Side-Rail-In, five measurement were made for each point under the same conditions. The average is measured on each of the five Side-Rail-Out and Side-Rail-In measurements. Results : In the presence of side rail, the dose reduction ratio was -11.8 %, -12.3 %, -4.1 %, -12.3 %, -7.3 % for each A, B, C, and D points. In the state of Side-Rail-Out, the dose reduction ratio for the using 10 mm thickness of vac-lok was -0.9 % than without vac-lok. The dose reduction ratio for the using 20 mm thickness of vac-lok was -2.0 %, for the using 30 mm thickness of the vac-lok was -3.0 % than without vac-lok. In the state of Side-Rail-In, the dose reduction ratio for the using 10 mm thickness of vac-lok was -1.0 % than without vac-lok. The dose reduction ratio for the using 20 mm vac-lok was -2.1 %, for the using 30 mm vac-lok was -3.0 % than without vac-lok. Based on the value of no vac-lok dose in the Side-Rail-In state, The dose reduction ratios for the using 10 mm, 20 mm and 30 mm thickness of vac-loks In the Side-Rail-Out that the center point were -12.7 %, -13.7 %, -14.2 % and -12.8 %, -13.8 %, -14.5 % respectively at point A. The dose reduction ratios for the same conditions to the B point were -4.9 %, -6.1 %, -7.1 % and -13.4 %, -14.4 %, -15.5 % respectively at point C. The dose reduction ratios for the same conditions to the D point were -8.4 %, -9.0 %, -10.4 % respectively. Conclusion : The attenuation was caused by presence of side rails and thickness of vac-lok. Pay attention to these attenuation factors, making it a more effective radiation therapy.

• Tuberculosis and Respiratory Diseases
• /
• v.69 no.3
• /
• pp.201-206
• /
• 2010

Nontuberculous mycobacterial (NTM) diseases are increasing worldwide. However NTM lung disease in organ transplant recipients has been rarely reported. Here, we report 2 cases of NTM lung disease in heart transplant recipients. A 37-year-old man, who had undergone a heart transplant one year previous, was admitted to hospital due to a cough. Chest CT scan showed multiple centrilobular nodules in both lower lungs. In his sputum, M. abscessus was repeatedly identified by rpoB gene analysis. The patient improved after treatment with clarithromycin, imipenem, and amikacin. An additional patient, a 53-year-old woman who had undergone a heart transplant 4 years prior and who suffered from bronchiectasis, was admitted because of purulent sputum. The patient's chest CT scan revealed aggravated bronchiectasis; M. intracellulare was isolated repeatedly in her sputum. Treatment was successfully completed with clarithromycin, ethambutol, and ciprofloxacin. NTM lung disease should be considered as a potential opportunistic infection in organ transplant recipients.

• Tuberculosis and Respiratory Diseases
• /
• v.74 no.4
• /
• pp.187-190
• /
• 2013

We report a rare case of lung disease caused by Mycobacterium lentiflavum in a previously healthy woman. A 54-year-old woman was referred to our hospital due to chronic cough and sputum. A computed tomography scan of the chest revealed bilateral bronchiectasis with bronchiolitis in the right middle lobe and the lingular division of the left upper lobe. Nontuberculous mycobacteria were isolated twice from three expectorated sputum specimens. All isolates were identified as M. lentiflavum by multilocus sequence analysis based on rpoB, hsp65, and 16S rRNA fragments. To the best of our knowledge, this is the first documented case of M. lentiflavum lung disease in an immunocompetent adult in Korea.