• Title/Summary/Keyword: Circular RNA

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Complete genome sequence of Lactobacillus koreensis 26-25, a ginsenoside converting bacterium, isolated from Korean kimchi (김치에서 분리한 진세노사이드 전환 능력이 있는 Lactobacillus koreensis 26-25의 유전체 서열 분석)

  • Kim, Ju-Hyeon;Liu, Qing-Mei;Srinivasan, Sathiyaraj;Kim, Myung Kyum;Kim, Sang Yong;Wee, Ji-Hyang;Im, Wan-Taek
    • Korean Journal of Microbiology
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    • v.54 no.4
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    • pp.477-479
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    • 2018
  • A Gram-positive, rod-shaped, ivory colored, and motile, Lactobacillus koreensis 26-25 was isolated from Korean kimchi. Strain 26-25 showed the ability of conversion from major ginsenosides into minor ginsenosides for which whole genome was sequenced. The whole genome sequence of Lactobacillus koreensis 26-25 consisted of one circular chromosome comprised of 3,006,812 bp, with a DNA G + C content of 49.23%. The whole genome analysis of strain 26-25 showed many glycosides hydrolase genes, which may contribute to identify the genes responsible for transformation of major ginsenosides into minor ginsenosides for its high pharmacological effects.

Complete genome sequence of Niabella ginsenosidivorans BS26T, a ginsenoside-converting bacterium, isolated from compost (퇴비에서 분리한 진세노사이드 전환능력이 있는 Niabella ginsenosidivorans BS26T 의 유전체 서열 분석)

  • Lee, Young-Woo;Siddiqi, Muhammad Zubair;Liu, Qing-Mei;Kim, Dae-Cheol;Im, Wan-Taek
    • Korean Journal of Microbiology
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    • v.54 no.4
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    • pp.465-467
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    • 2018
  • An orange-colored, rod-shaped strain, designated Niabella ginsenosidivorans $BS26^T$, was isolated from compost. Strain $BS26^T$ showed the ability to convert major ginsenosides to minor ginsenosides, and its whole genome was sequenced. The whole genome of N. ginsenosidivorans $BS26^T$ consists of a single circular chromosome of 5,627,734 bp with 44.48% G + C content. Based on the complete genome sequence of strain $BS26^T$, we found several glycosides hydrolase-encoding genes that might involve in the conversion of major ginsenosides into minor ginsenoside and deliberate its strong pharmacological effects.

Safety Assessment of Lactiplantibacillus (formerly Lactobacillus) plantarum Q180

  • Kwon, Yoo Jin;Chun, Byung Hee;Jung, Hye Su;Chu, Jaeryang;Joung, Hyunchae;Park, Sung Yurb;Kim, Byoung Kook;Jeon, Che Ok
    • Journal of Microbiology and Biotechnology
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    • v.31 no.10
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    • pp.1420-1429
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    • 2021
  • The safety of the probiotic strain Q180, which exerts postprandial lipid-lowering effects, was bioinformatically and phenotypically evaluated. The genome of strain Q180 was completely sequenced, and single circular chromosome of 3,197,263 bp without any plasmid was generated. Phylogenetic and related analyses using16S rRNA gene and whole-genome sequences revealed that strain Q180 is a member of Lactiplantibacillus (Lp., formerly Lactobacillus) plantarum. Antimicrobial resistance (AMR) genes were bioinformatically analyzed using all Lp. plantarum genomes available in GenBank, which showed that AMR genes are present differently depending on Lp. plantarum strains. Bioinformatic analysis demonstrated that some mobile genetic elements such as prophages and insertion sequences were identified in the genome of strain Q180, but because they did not contain harmful genes such as AMR genes and virulence factor (VF)- and toxin-related genes, it was suggested that there is no transferability of harmful genes. The minimum inhibition concentrations of seven tested antibiotics suggested by the European Food Safety Authority guidelines were slightly lower than or equal to the microbiological cut-off values for Lp. plantarum. Strain Q180 did not show hemolytic and gelatinase activities and biogenic amine-producing ability. Taken together, this study demonstrated the safety of strain Q180 in terms of absence of AMR genes and VF- and toxin-related genes as a probiotic strain.

Effects of taurine supplementation in low fish meal diets for red seabream (Pagrus major) in low water temperature season

  • Gunathilaka, G.L.B.E.;Kim, Min-Gi;Lee, Chorong;Shin, Jaehyeong;Lee, Bong-Joo;Lee, Kyeong-Jun
    • Fisheries and Aquatic Sciences
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    • v.22 no.10
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    • pp.23.1-23.10
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    • 2019
  • Background: Taurine is a conditional essential amino acid for fish. A study was conducted to investigate the compensating effect of supplemental taurine in diets for red seabream (Pagrus major) on impaired growth performance by fish meal (FM) replacement with soybean meal (SM) at low water temperature (14.15 ± 1.95 ℃). Methods: A FM-based diet was considered as a high FM diet and three other experimental diets were formulated to replace FM with SM by 20, 35, or 50% (HFM, SM20, SM35, or SM50, respectively) without taurine and other four diets were formulated by adding 1% taurine to the diets (HFM-T, SM20-T, SM35-T, or SM50-T, respectively). Triplicate groups of fish (108.9 ± 1.58 g/fish) were distributed into 24 polyvinyl circular tanks (215 L) with 20 fish per tank and fed one of the diets to satiation for 20 weeks. Results: Growth performance and feed utilization of red seabream were significantly improved by the dietary taurine supplementation. SM20-T and SM35-T diets increased fish growth that are comparable to HFM diet. Feed intake, feed conversion ratio, and protein efficiency ratio of fish fed SM20-T and SM35-T diets were not significantly different from those of HFM group. Dietary taurine supplementation in each FM replaced group numerically increased innate immunity of the fish. Lysozyme and superoxide dismutase activities were significantly decreased in fish fed SM35, SM50, and SM50-T diets compared to those of fish fed HFM diet while they were not significantly lower in SM20, SM20-T, SM35, and SM35-T groups. Glutathione peroxidase activity was significantly lower in fish group fed SM50 diet while SM50-T group did not significantly lower compared to that of HFM group. The relative expression level of hepatic IGF-1 mRNA was improved in fish fed taurine-supplemented diets compared to their respective SM diets. Conclusions: Growth performance and feed utilization of red seabream can be accelerated or restored by 1% taurine supplementation when they are fed high level of SM up to 35% in diets during low water temperature season.

Characterization of the Novel Marine Bacterium Planococcus sp. 107-1T (신종 해양미생물 Planococcus sp. 107-1T의 분류학적 특성 분석)

  • Kim, Dong-Gyun;Jung, Hyun-Kyoung;Kim, Young-Ok;Kong, Hee Jeong;Nam, Bo-Hye;Kim, Ju-Won;Kim, Young-Sam
    • Korean Journal of Fisheries and Aquatic Sciences
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    • v.55 no.5
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    • pp.612-624
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    • 2022
  • A novel Gram-positive, motile, non-spore forming aerobic marine bacterium, designated 107-1T was isolated from tidal mud collected in Gyehwa-do, South Korea. Cells of strain 107-1T were short rod or coccoid, oxidase negative, catalase positive and grew at 10-40℃ (with optimum growth at 25-30℃). It utilized menaquinones MK-7 and 8 as its respiratory quinones and its major fatty acids were anteiso-C15:0 (37.9%), iso-C16:0 (14.9%), and iso-C14:0 (10.8%). Phylogenetic analysis based on 16S rRNA gene sequences revealed a distinct clade containing strain 107-1T and close species Planococcus ruber CW1T(98.52% sequence similarity), P. faecalis KCTC 33580T(97.67%), P. kocurii ATCC 43650T(97.48%), P. donghaensis DSM 22276T(97.47%), and P. halocryophilus DSM 24743T(97.37%). Strain 107-1T contains one circular chromosome (3,513,248bp in length) with G+C content of 44.6 mol%. Estimated ranges for genome to genome distance, average nucleotide identity, and average amino acid identity comparing strain 107-1T with close taxa were 20.3-34.8%, 77.9-86.9%, and 73.6-92.8%, respectively. Based on polyphasic analysis, strain 107-1T represents a novel species belonging to the genus Planococcus.

Evaluation of Construction Operation and Design Properties of CLSM for Corrugated Pipe in Underground (파형강관을 이용한 지하매설물용 뒤채움재 설계 및 시공성 평가)

  • Lee Kwan-Ho;Park Jae-Heon
    • International Journal of Highway Engineering
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    • v.8 no.2 s.28
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    • pp.63-74
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    • 2006
  • During the construction of circular underground pipe, the non-proper compaction along the pipe and the decrease of compaction efficiency have been the main problems to induce the failure of underground pipe or facility. The use of CLSM (controlled low strength materials) should be one of the possible applications to overcome those problems. In this research, the full-scaled field test and the numeric analysis using PENTAGON-3D FEM program were carried out for three different cases on the change of backfill materials, including the common sand, the soil from construction site, and the CLSM. From the full-scaled test in field, the use of in-situ CLSM as backfill materials reduced the vertical and lateral deformation of the pipe, as well as the deformation of the ground surface. The main reason for reducing the deformation would be the characteristics of the CLSM, especially self-leveling and self-hardening properties. The measured earth pressure at the surround of the corrugated pipe using the CLSM backfills was the smaller than the other cases, and the absolute value was almost zero. Judging from the full-scaled field test and FEM analysis, the use of CLSM as backfill materials should be one of the best choices reducing the failure of the underground pipes.

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Melanogenesis regulatory constituents from Premna serratifolia wood collected in Myanmar

  • WOO, SO-YEUN
    • Proceedings of the Plant Resources Society of Korea Conference
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    • 2019.04a
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    • pp.21-22
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    • 2019
  • Melanin is a mixture of pigmented biopolymers synthesized by epidermal melanocytes that determine the skin, eye, and hair colors. Melanocytes produce two different kinds of melanin, eumelanin (dark brown/black insoluble pigments found in dark skin and dark hair and pheomelanin (lighter red/yellow). The biological role of melanin is to prevent skin damage by ultraviolet (UV) radiation. However, the overproduction or deficiency of melanin synthesis could lead to serious dermatological problems, which include melasma, melanoderma, lentigo, and vitiligo. Therefore, regulating melanin production is important to prevent the pigmentation disorders. Myanmar has a rich in natural resources. However, the chemical constituents of these natural resources in Myanmar have not been fully investigated. In the effort to search for compounds with anti-melanin deposition activity from Myanmar natural resources, five plants were collected in Myanmar. Extracts of these collected five plants were tested for anti-melanin deposition activity against a mouse melanoma cell line (B16-F10) induced with ${\alpha}$-melanocyte-stimulating hormone (${\alpha}$-MSH) and 3-isobutyl-1-methylxanthine (IBMX), and their anti-melanin deposition activities were compared with the positive control, arbutin. Among the tested extracts, the CHCl3 extracts of the Premna serratifolia (syn: P. integrifolia) wood showed anti-melanin deposition activities with IC50 values of $81.3{\mu}g/mL$. Hence, this study aims to identify secondary metabolites with anti-melanin deposition activity from P. serratifolia wood of Myanmar. P. serratifolia belongs to the Verbenaceae family and is widely distributed in near western sea coast from South Asia to South East Asia, which include India, Malaysia, Vietnam, Cambodia, and Sri Lanka. People in Tanintharyi region located in the southern part of Myanmar utilize the P. serratifolia, Sperethusa crenulata, Naringi crenulata, and Limonia acidissima as Thanaka, traditional cosmetics in Myanmar. Thanaka is applied in the form of paste onto skins to make it smooth and clear, as well as to prevent wrinkles, skin aging, excessive facial oil, pimples, blackheads, and whiteheads. However, the chemical constituents responsible for their cosmetic properties are yet to be identified. Moreover, the chemical constituents of P. serratifolia was almost uncharacterized. Investigation of the P. serratifolia chemical constituents is thus an attractive endeavor to discover new anti-melanin deposition active compounds. The investigation of the chemical constituents of the active CHCl3 extract of P. serratifolia led to isolation of four new lignoids, premnan A (1), premnan B (2), taungtangyiol C (3), and 7,9-dihydroxydolichanthin B (4), together with premnan C (5) (assumed to be an artifact), one natural newlignoid,(3R,4S)-4-(1,3-benzodioxol-5-ylcarbonyl)-3-[(R)-1-(1,3-benzo dioxol-5-yl)-1-hydroxy methyl]tetrahydro-2-furanone (6), and five known compounds (7-11)1,2). The structures of all isolated compounds were determined on the basis of their spectroscopic data and by comparison with the reported literatures. The absolute configurations of 1-3 and 5 were also determined by optical rotation and circular dichroism (CD) data analyses1). The anti-melanin deposition activities of all the isolated compounds were evaluated against B16-F10 cell line. 7,9-Dihydroxydolichanthin B (4) and ($2{\alpha},3{\alpha}$)-olean-12-en-28-oic acid (11) showed strong anti-melanin deposition activities with IC50 values of 18.4 and $11.2{\mu}M$, respectively, without cytotoxicity2). On the other hand, compounds 1-3, 5, and 7 showed melanogenesis enhancing activities1). To better understand their anti-melanin deposition mechanism, the effects of 4 and 11 on tyrosinase activities were investigated. The assay indicated that compounds 4 and 11 did not inhibit tyrosinase. Furthermore, we also examined the mRNA expression of microphthalmia-associated transcription factor (MITF), tyrosinase (TYR), tyrosinase-related protein-1 (TRP-1), and tyrosinase-related protein-2 (TRP-2). Compounds 4 and 11 down-regulated the expression of Tyr and Mitf mRNAs, respectively. Although the P. serratifolia wood has been used as traditional cosmetics in Myanmar for centuries, there are no scientific evidences to support its effectiveness as cosmetics. Investigation of the anti-melanin deposition activity of the chemical constituents of P. serratifolia thus provided insight into the effectiveness of the P. serratifolia wood as a cosmetic agent.

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