• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.323-330
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• 2009

Nontuberculous mycobacteria (NTM) are a major cause of opportunistic infections in immunocompromised patients, making the reliable and rapid identification of NTM to the species level very important for the treatment of such patients. Therefore, this study evaluated the usefulness of the novel target genes tuf and tmRNA for the identification of NTM to the species level, using a PCRrestriction fragment length polymorphism analysis (PRA). A total of 44 reference strains and 17 clinical isolates of the genus Mycobacterium were used. The 741 bp or 744 bp tuf genes were amplified, restricted with two restriction enzymes (HaeIII/MboI), and sequenced. The tuf gene-PRA patterns were compared with those for the tmRNA (AvaII), hsp65 (HaeIII/HphI), rpoB (MspI/HaeIII), and 16S rRNA (HaeIII) genes. For the reference strains, the tuf gene-PRA yielded 43 HaeIII patterns, of which 35 (81.4%) showed unique patterns on the species level, whereas the tmRNA, hsp65, rpoB, and 16S rRNA-PRAs only showed 10 (23.3%), 32 (74.4%), 19 (44.2%), and 3 (7%) unique patterns after single digestion, respectively. The tuf gene-PRA produced a clear distinction between closely related NTM species, such as M. abscessus (557-84-58) and M. chelonae (477-84-80-58), and M. kansasii (141-136-80-63-58-54-51) and M. gastri (141-136-117-80-58-51). No difference was observed between the tuf-PRA patterns for the reference strains and clinical isolates. Thus, a diagnostic algorithm using a tuf gene-targeting PRA is a promising tool with more advantages than the previously used hsp65, rpoB, and 16S rRNA genes for the identification of NTM to the species level.

• ALGAE
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• v.31 no.2
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• pp.155-165
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• 2016

Green microalgae from the class Chlorophyceae represent a major biodiversity component of eukaryotic algae in continental water. Identification and classification of this group through morphology is a hard task, since it may present cryptic species and phenotypic plasticity. Despite the increasing use of molecular methods for identification of microorganisms, no single standard barcode marker is yet established for this important group of green microalgae. Some available studies present results with a limited number of chlorophycean genera or using markers that require many different primers for different groups within the class. Thus, we aimed to find a single marker easily amplified and with wide coverage within Chlorophyceae using only one pair of primers. Here, we tested the universality of primers for different genes (tufA, ITS, rbcL, and UCP4) in 22 strains, comprising 18 different species from different orders of Chlorophyceae. The ITS primers sequenced only 3 strains and the UCP primer failed to amplify any strain. We tested two pairs of primers for rbcL and the best pair provided sequences for 10 strains whereas the second one provided sequences for only 7 strains. The pair of primers for the tufA gene presented good results for Chlorophyceae, successfully sequencing 21 strains and recovering the expected phylogeny relationships within the class. Thus, the tufA marker stands out as a good choice to be used as molecular marker for the class.

• Computers and Concrete
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• v.7 no.2
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• pp.191-202
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• 2010

A laboratory investigation was conducted to characterize the constitutive property behavior of Cor-Tuf, an ultra-high-performance composite concrete. Mechanical property tests (hydrostatic compression, unconfined compression (UC), triaxial compression (TXC), unconfined direct pull (DP), uniaxial strain, and uniaxial-strain-load/constant-volumetric-strain tests) were performed on specimens prepared from concrete mixtures with and without steel fibers. From the UC and TXC test results, compression failure surfaces were developed for both sets of specimens. Both failure surfaces exhibited a continuous increase in maximum principal stress difference with increasing confining stress. The DP tests results determined the unconfined tensile strengths of the two mixtures. The tensile strength of each mixture was less than the generally assumed tensile strength for conventional strength concrete, which is 10 percent of the unconfined compressive strength. Both concretes behaved similarly, but Cor-Tuf with steel fibers exhibited slightly greater strength with increased confining pressure, and Cor-Tuf without steel fibers displayed slightly greater compressibility.

• Journal of Species Research
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• v.11 no.4
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• pp.266-277
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• 2022

The current surveys of Ulva in the subtidal area around Jeju Island give a chance to discover unrecorded green algal species of the Korean macroalgal flora. As a result of this investigation, we found Ulva adhaerens Matusmoto & Shimada, inhabiting the subtidal regions, up to 15 m deep, and conducted the DNA barcoding on plastid rbcL-3P and tufA regions with describing the morphological characteristics. Our specimens of U. adhaerens forms a monophyletic clade with the Japanese type specimen and U. piritoka Ngāti Kuri, Heesch & W.A. Nelson from New Zealand exhibiting each 0.3% sequence divergences, respectively, in the plastid rbcL-3P. The genetic variation of U. adhaerens clade is 1.0-3.9% in rbcL-3P and 4.8-9.8% in tufA to each Ulva species, including the generic type, U. lactuca Linneaus. The morphology of Korean U. adhaerens specimens is identical to the type specimens of U. adhaerens from Japan having the development of rhizoidal filaments from both of the cell layers of the distromatic blade and the extension of rhizoidal clumps with adhesive trait between blades by extended rhizoidal clumps at the basal blades. The thallus attachment to substrate is by numerous minute discoidal plates made up of rhizoids originating from the inner part of distromatic blades in basal. Although there are still some problems to resolve the relationship between U. adhaerens and U. piritoka in the rbcL dataset and the phylogenetic pattern of the Group II intron of rbcL, we propose the new record of U. adhaerens in Korean macroalgal flora based on the morphological characteristics of Korean specimens. Continued study of the genus Ulva by morphological and molecular assessment will delimit the species of Ulva, elucidate the relationships between them, and uncover the species diversity.

• ALGAE
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• v.35 no.4
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• pp.349-359
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• 2020

Specimens of Umbraulva with greenish iridescent were collected in the subtidal zone of Jeju Island, Korea. To investigate these collections, plastid rbcL and tufA sequencing of six greenish iridescent specimens, including four Umbraulva japonica, were analyzed. Phylogenetic analysis of a concatenated multigene alignment found that the greenish iridescent specimens belonged to a yet undescribed taxon in the genus Umbraulva. We herein propose the name Um. yunseulla sp. nov. for this specimens. Juveniles of Um. yunseulla sp. nov. resemble the generitype Um. japonica in appearance, showing globular to subglobular and funnel-shaped habits, but the blades of this new species are not split longitudinally like those of Um. japonica. Although the multigene phylogenetic tree showed the polyphyletic clade of Umbraulva with respect to the genus Ryuguphycus, Um. yunseulla sp. nov. formed a clade with Um. japonica and Um. amamiensis by weak bootstrap support. These findings, Um. yunseulla sp. nov., highlight the importance of studying the biodiversity of subtidal habitats from Jeju Island, Korea and further emphasize the need for investigations of macroalgae in the mesophotic zone around the Korean peninsula.

• ALGAE
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• v.34 no.4
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• pp.253-266
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• 2019

Several species classified to the genus Ulva are primarily responsible for causing green tides all over the world. For almost two decades, green tides have been resulted in numerous ecological problems along the eastern coast of Jeju Island, Korea. In order to characterize the species of Ulva responsible for causing the massive blooms on Jeju Island, we conducted DNA barcoding of tufA and rbcL sequences on 183 specimens of Ulva from eight sites on Jeju Island. The concatenated analysis identified five bloom-forming species: U. australis, U. lactuca, U. laetevirens, U. ohnoi and a novel species, U. pseudo-ohnoi sp. nov. Among them, U. australis, U. lactuca, and U. laetevirens caused to the blooms coming mainly from the substratum. U. ohnoi and U. pseudo-ohnoi sp. nov. were causative the free-floating blooms. Four species, except U. australis, are characterized by marginal teeth. A novel species, U. pseudo-ohnoi sp. nov., is clearly diverged from the U. lactuca, U. laetevirens, and U. ohnoi clade in the concatenated maximum likelihood analysis. Accurate species delimitation will contribute to a management of massive Ulva blooms based on this more comprehensive knowledge.

• Journal of Fisheries and Marine Sciences Education
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• v.29 no.1
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• pp.234-241
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• 2017

Morphological and molecular information about two microfilamentous endophytic algae of the Grateloupia lanceolata or Bryopsis sp. from Korea is given. Of two endophytes, Phaeophila dendroides is endophytic in Grateloupia lanceolata. It is green in color and composed of uniseriate branched filaments with long setae. Each cell had several pyrenoids. Undulate or twisted Phaeophila-type hair developed from vegetative cells. Dilabifilum arthropyreniae is endophytic in Bryopsis sp. The frond of this species consists of frequently irregular, branching uniseriate filaments. Each cell had a single pyrenoid without hairs. Sporangia were not observed. The ends of the filaments were curved. In the phylogenetic tree, based on tufA and ITS sequences, these two species are nested in the same clade as Phaeophila dendroides and Dilabifilum arthropyreniae, respectively. In this study, these two species are newly recorded in the Korean marine algal flora, based on the morphological and molecular data.

• ALGAE
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• v.30 no.3
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• pp.197-205
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• 2015

The genus of leafy green algae, Prasiola Meneghini, includes marine, terrestrial, and freshwater species. A total of 11 species and one variety have been identified in China, Korea, and Japan. In Korea, Prasiola formosana var. coreana has been reported in Muncheon, North Korea, while a different type of Prasiola species has been reported in South Korea. The South Korean species has been found growing along a small stream originating from Chodanggul Cave, a limestone cave in Samcheok, Gangwon Province. Here, we revised the morphological characteristics of the South Korean Prasiola species and analyzed plastid rbcL, psaB, and tufA genes to clarify its identity. Although the external and anatomical morphologies varied among individuals, our results were very similar to previous reports. Plastid three genes sequences of the South Korean specimens were identical to those of P. japonica collected from Japan as well as to published sequences of P. yunnanica from China. A short rbcL-3P sequence (196 bp) from P. formosana var. coreana, which was identified in the type specimen, was also identical to a sequence from P. japonica. These Prasiola species and variety from Korea, Japan, and China are all distributed in areas characterized by limestone bedrock. Based on morphological, phylogenetic, and distributional features, the South Korean Prasiola species is regarded herein as P. japonica. Here, we also propose to synonymize P. formosana var. coreana and P. yunnanica with P. japonica.

• Pediatric Infection and Vaccine
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• v.21 no.3
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• pp.219-224
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• 2014

Invasive infection of the Streptococcus bovis group in a neonate is rare. In cases reported to date, the pathogen of neonatal S. bovis infections is usually Streptococcus gallolyticus subsp. pasteurianus (S. bovis biotype II/2). Streptococcus lutetiensis (S. bovis biotype II/1) was identified using 16S rRNA and tuf gene sequence analysis of the isolates from blood and cerebrospinal fluid (CSF) of a fever-presenting 28-day-old male. Blood culture analysis was performed using automatic equipment (VITEK 2) and identified Streptococcus infantarius supsp. infantarius, yet we were unable to get accurate results from the CSF culture. The fever subsided on the second day of hospitalization, and the patient was discharged without neurologic complication after 14 days of antibiotic therapy. In this case, we were able to accurately identify the pathogen using molecular genetic methods. To our knowledge, this is the first case of late onset neonatal bacteremia and meningitis caused by S. lutetiensis.

• Journal of Microbiology and Biotechnology
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• v.31 no.8
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• pp.1154-1162
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• 2021

The transcriptional capacities of target genes are strongly influenced by promoters, whereas few studies have focused on the development of robust, high-performance and cross-species promoters for wide application in different bacteria. In this work, four novel promoters (P_k.rtufB, P_k.r1, P_k.r2, and P_k.r3) were predicted from Ketogulonicigenium robustum and their inconsistency in the -10 and -35 region nucleotide sequences indicated they were different promoters. Their activities were evaluated by using green fluorescent protein (gfp) as a reporter in different species of bacteria, including K. vulgare SPU B805, Pseudomonas putida KT2440, Paracoccus denitrificans PD1222, Bacillus licheniformis and Raoultella ornithinolytica, due to their importance in metabolic engineering. Our results showed that the four promoters had different activities, with P_k.r1 showing the strongest activity in almost all of the experimental bacteria. By comparison with the commonly used promoters of E. coli (tufB, lac, lacUV5), K. vulgare (Psdh, Psndh) and P. putida KT2440 (JE111411), the four promoters showed significant differences due to only 12.62% nucleotide similarities, and relatively higher ability in regulating target gene expression. Further validation experiments confirmed their ability in initiating the target minCD cassette because of the shape changes under the promoter regulation. The overexpression of sorbose dehydrogenase and cytochrome c551 by P_k.r1 and P_k.r2 resulted in a 22.75% enhancement of 2-KGA yield, indicating their potential for practical application in metabolic engineering. This study demonstrates an example of applying bioinformatics to find new biological components for gene operation and provides four novel promoters with broad suitability, which enriches the usable range of promoters to realize accurate regulation in different genetic backgrounds.