• Molecules and Cells
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• v.44 no.3
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• pp.179-185
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• 2021

Vancomycin response regulator (VncR) is a pneumococcal response regulator of the VncRS two-component signal transduction system (TCS) of Streptococcus pneumoniae. VncRS regulates bacterial autolysis and vancomycin resistance. VncR contains two different functional domains, the N-terminal receiver domain and C-terminal effector domain. Here, we investigated VncR C-terminal DNA binding domain (VncRc) structure using a crystallization approach. Crystallization was performed using the micro-batch method. The crystals diffracted to a 1.964 Å resolution and belonged to space group P212121. The crystal unit-cell parameters were a = 25.71 Å, b = 52.97 Å, and c = 60.61 Å. The structure of VncRc had a helix-turn-helix motif highly similar to the response regulator PhoB of Escherichia coli. In isothermal titration calorimetry and size exclusion chromatography results, VncR formed a complex with VncS, a sensor histidine kinase of pneumococcal TCS. Determination of VncR structure will provide insight into the mechanism by how VncR binds to target genes.

• Journal of Radiation Protection and Research
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• v.23 no.2
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• pp.89-96
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• 1998

To assess the radioprotective effects of follicle stimulating hormone (FSH) on ovarian follicles, 3 week-old female mice were irradiated with 8.33 Gy of ${\gamma}$-ray (group R) and followed by 5 IU ip-injection of FSH (group RF). For control groups, 5 IU of saline (group C) or 5 IU of FSH (group F) was ip-injected. Ovaries were collected 0h, 6h, 12h, 14, 2d, 4d, and 8d after irradiation or saline/FSH injection, and followed by fixation in neutral buffered formalin for routine histochemistry. Immunohistochemistry was used to assess the status of follicles and DNA fragmentation was analyzed by agarose gel electrophoresis for total DNA. Staining specific for apoptotic follicles showed high intensity at 6h and 12h in group R and RF On the other hand, staining specific for proliferating follicles showed noticeably high intensity at 8d in group R and Rf. DNA fragmentation of 185bp increased with time in all experimental groups. Especially 370bp appeared at 6h in group R, then disappeared after 1d. In case of group RF, it appeared at 12h and disappeared after 1d. From the above results, the irradiated antral follicles become completely disappeared from 4d to 8d, and then new follicles started to grow again at 8d. FSH had delaying or suppressing effects on follicular atresia after irradiation. In addition, it became clear that radiation-induced follicular atresia was mediated by granulosa cell apoptosis.

• Journal of Gastric Cancer
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• v.13 no.4
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• pp.232-241
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• 2013

Purpose: Gastrokine 1 plays an important role in gastric mucosal defense. Additionally, the Gastrokine 1-miR-185-DNMT1 axis has been shown to suppress gastric carcinogenesis through regulation of epigenetic alteration. Here, we investigated the effects of Gastrokine 1 on DNA methylation and gastritis. Materials and Methods: Expression of Gastrokine 1, DNMT1, EZH2, and c-Myc proteins, and the presence of Helicobacter pylori CagA protein were determined in 55 non-neoplastic gastric mucosal tissue samples by western blot analysis. The CpG island methylation phenotype was also examined using six markers (p16, hMLH1, CDH1, MINT1, MINT2 and MINT31) by methylation-specific polymerase chain reaction. Histological gastritis was assessed according to the updated Sydney classification system. Results: Reduced Gastrokine 1 expression was found in 20 of the 55 (36.4%) gastric mucosal tissue samples and was closely associated with miR-185 expression. The Gastrokine 1 expression level was inversely correlated with that of DNMT1, EZH2, and c-Myc, and closely associated with the degree of gastritis. The H. pylori CagA protein was detected in 26 of the 55 (47.3%) gastric mucosal tissues and was positively associated with the expression of DNMT1, EZH2, and c-Myc. In addition, 30 (54.5%) and 23 (41.9%) of the gastric mucosal tissues could be classified as CpG island methylation phenotype-low and CpG island methylation phenotype-high, respectively. Reduced expression of Gastrokine 1 and miR-185, and increased expression of DNMT1, EZH2, and c-Myc were detected in the CpG island methylation phenotype-high gastric mucosa. Conclusions: Gastrokine 1 has a crucial role in gastric inflammation and DNA methylation in gastric mucosa.

• Parasites, Hosts and Diseases
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• v.36 no.2
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• pp.69-80
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• 1998

Subgenus classification of Acanthcmoeba remains uncertain. Twenty-three reference strains of Acanthnmoeba including 18 (neo)type-strains were subjected for classification at the subgenus level by riboprinting, PCR/RFLP analysis of 185 rRNA gene (rDNA) . On the dendrogram reconstructed on the basis of riboprint analyses, two type- strains (A. astronwxis and A. tubinshi) of morphological group 1 diverged early from the other strains and were quite distinct from each other. Four type-strains of morphological group 3. A. culbertsoni, A. polestinensis, A. healyi were considered taxonomically valid, but A. pustulosn was regarded as an invalid synonym of A. pclestinensis. Strains of morphological group 2 were classified into 6 subgroups. Among them, A. giulni which has an intron in its 185 rDNA was the most divergent from the remaining strains. Acanthcmoebc ccstellanii Castellani, A. quinc Vil3, A. Iugdunensis L3a. A. poIyphage Jones, A. trinngularis SH621, and A. cqstellanii Ma strains belonged to a subgroup, A. castellanii complex. However, A. quinc and A. Lugnunensis were regarded as synonyms of A. ccstellanii. The Chang strain could be regarded as A. hatchetti. Acanthcmoebo nauritaniensis, A. niuionensis, A. paranivionensis could be considered as synonyms of A. rhwsodes. Neff strain was regarded as A. polyphage rather than as A. castellanii. It is likely that riboprinting can be applied for rapid identification of Acnnthcmoebc isolated from the clinical specimens and environments.

• Journal of the korean society of oceanography
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• v.39 no.3
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• pp.172-185
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• 2004

LSU rDNA D1-D2 and SSU rDNA genes of 23 strains in seven Alexandrium (Halim) species, A. tamarense (Lebour) Balech, A. catenella (Whedon et Kofoid), A. fraterculus (Balech) Balech, A. affine (Inoue et Fukuyo) Balech, A. insuetum Balech, A. pseudogonyaulax (Biecheler) Horiguchi ex Yuki et Fukuyo and A. tamiyavanichii Balech, were sequenced and the data were used for molecular phylogenetic analysis. The sequence data revealed 11 and 7 ribotypes in the LSU rDNA D1-D2 region and 4 and 17 ribotypes in the SSU rDNA region of A. catenella and A. tamarense, respectively. Other Alexandrium species had also 1 to 5 ribotypes in the two regions. With the exception of CMC2 and CMC3 of A. catenella, all A. tamarense and A. catenella strains had a common ribotype, a functionally expressed rRNA gene (here termed type A), in both gene regions. In addition to the functionally expressed gene, several pseudogenes were obtained that were found to be good tools to analyze the population designation of regional isolates by grouping them according to shared ribotypes. From the phylogenetic analysis of the sequence data determined in this study and retrieved from GenBank, the genus Alexandrium was divided into 14 groups: 1) A. tamarense, 2) A. excavatum, 3) A. catenella, 4) Tasmanian A. tamarense, 5) A. affine (and/or A. concavum), 6) Thai A. tamarense, 7) A. tamiyavanichii, 8) A. fraterculus, 9) A. margalefii, 10) A. andersonii, 11) A. ostenfeldii, 12) A. minutum (or A. lusitanicum), 13) A. insuetum, and 14) A. pseudogonyaulax. The SSU rDNA gene sequence of A. fundyense was so similar to those of A. tamarense used in this study that the two species were difficult to discriminate each other. A. tamiyavanichii was closest to the A. tamarense strain isolated in Thailand and close to the long chain-forming species of A. affine and A. fraterculus. The phylogenetic tree showed that A. margalefii, A. andersonii, A. ostenfeldii, A. minutum and A. insuetum constituted the basal relative complex, and that A. pseudogonyaulax is an ancestral taxon in the genus Alexandrium.

• Korean Journal of Plant Resources
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• v.19 no.1
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• pp.161-168
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• 2006

To investigate the origin of backyeoncho (Opuntia ficus-indica var. saboten), we isolated 685 bp clone using ITS primer pairs. The rDNA consists of the genes coding for the partial 54 bp 185, 162 bp 5.8S, and partial 56 bp 26S. The coding regions are interrupted by two internal transcribed spacers, 193 bp ITS1 and 220 bp ITS2. The ITS2 of backnyeoncho in length was shorter than that previously registered in Cucurbitoideae plants. The GC contents was 66.8% in ITS1, and 67.7% in ITS2. The rDNA of backnyeoncho matched to the previously reported genes and showed a high similarity with the 95% identity with Pereskiopsis porteri (L708037). In the phylogenetic analysis, the backnyeoncho rDNA was clustered with Pereskiopsis porteri (L708037).

• Parasites, Hosts and Diseases
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• v.35 no.2
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• pp.127-134
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• 1997

Transmission electron microscopy of an ArGnthnmoebo isolate (KA/LS) from a contact lens case revealed bacterial endosymbionts within cytoplasm of the amoebae. The Acnnthamoebn isolate belonged to the morphological group ll. Based on the polymerase chain reaction (PCR) - restriction fragment leilgth polymorphism (RFLP) of 185 ribosomal RNA coding DNA (rDNA) , the isolate was identified as A. Iwnunensis. Strain typing by isoenzyme analysis using isorlectric focusing (IEF) and mitochondrial (Ent) DNA RFLP revealed that the isolate was closely related with KA/Ll , the most predominant type of isolates from contact lens storage casas, KA/E2, a clinical isolate, KA/W4, previou:fly reported to host endosymbionts. and L3a strains of A. Iwnunensis. The endosymbionts were similar to those of KA/W4 in a.jpects that they were randomly distributed in both trophozoites and cysts, and were rod-shaped bacteri3 measuring approximately 1.38 x 0.50 ㎛. But the number of endosymbionts per amoeba was significantly lower than that of KA/W4. They were neither limited by phagosomal membranes nor included in lacunae- like stnlcture.

• Ocean and Polar Research
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• v.26 no.1
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• pp.51-58
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• 2004

We isolated and identified culturable Arctic bacteria that had inhabited soils around the Korean Arctic Research Station Dasan located at Ny-Alsund, Svalbard, Norway $(79^{\circ}N,\;12^{\circ}E)$. The collected soils were diluted in distilled water; the diluted soil-water was spread on 3M petri-films at Dasan Station. The petri-films were transported to the laboratory at KORDI, and cultured at $4^{\circ}C$. Colonies grown on the petri-films were subsequently cultured on nutrient agar plates at $4^{\circ}C$ every 7 days. The pure colonies were inoculated into nutrient liquid media, genomic DNA was extracted, and phylogenetic analysis was performed on the basis of 165 rDNA sequences. A total of 227 strains of bacteria were isolated. Among them, 16S rDNA sequences of 185 strains were identical with those of known strains isolated in this study, and 42 strains were finally identified. Phylogenetic analysis using 16S rDNA indicated that the 30 strains belonged to Pseudomonas, 7 strains to Arthrobacter, two strains to Flavobacterium, and the remaining to Achromobacter, Pedobacter, and Psychrobacter. Among the 42 strains, 14 bacteria produced protease: they were 6 strains of Pseudomonax, 4 strains of Arthrobater, an Achromobacter strain, 2 strains of Flavobacterium, and a Pedohacter strain. We expect these Arctic bacteria can be used for screening to develop new industrial enzymes that are active at low temperatures.

• Journal of Plant Biology
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• v.39 no.3
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• pp.185-188
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• 1996

Randomly amplified polymorphic DNAs were employed to study the genetic variation and gene introgression in potato dihaploids (2n=24) which were generated after interspecific pollination of tetraploid cultivars (2n=4X=48, Solanum tuberosum cv Irish Cobbler, Superior and Dejima) by haploid inducer clones (2n=2X=24, Solanum phureja 1.22, Hes-5 and Hes-6). Genetic variation and DNA marker segregation among dihaploids were observed. Most dihaploids contain S. tuberosum specific RAPD markers but haploid inducer-specific RAPD markers were also found in some dihaploids. Of six different arbitrary 10-mer oligonucletide primers which showed polymorphism betwen tetraploid cultivars and haploid inducers used, three generated amplification products which seemed to be derived from the S. phureja parent. Our results indicate that chromosomes of dihaploids may not be pure S. tuberosum and the dihaploids may not be produced by parthenogenesis.

• ALGAE
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• v.37 no.3
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• pp.185-204
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• 2022

The genus Coolia A. Meunier 1919 has a global distribution and is a common member of epiphytic dinoflagellate assemblages in neritic ecosystems. Coolia monotis is the type species of the genus and was the only known species for 76 years. Over the past few decades, molecular characterization has unveiled two species complexes that group morphologically very similar species, so their limits are often unclear. To provide new knowledge on the biogeography and species composition of the genus Coolia, 16 strains were isolated from Bahía de La Paz, Gulf of California. The species were identified by applying morphological and molecular approaches. The morphometric characteristics of all isolated Coolia species were consistent with the original taxa descriptions. Phylogenetic analyses (large subunit [LSU] rDNA D1 / D2 and internal transcribed spacer [ITS] 1 / 5.8S / ITS2) revealed a species assemblage comprising Coolia malayensis, C. palmyrensis, C. tropicalis, and the C. cf. canariensis lineage. This is the first report of Coolia palmyrensis and C. cf. canariensis in Mexico and C. tropicalis in the Gulf of California. Our results strengthen the biogeographical understanding of these potentially harmful epiphytic dinoflagellate species.