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Development of bioinformatics and multi-omics analyses in organoids

  • Doyeon Ha;JungHo Kong;Donghyo Kim;Kwanghwan Lee;Juhun Lee;Minhyuk Park;Hyunsoo Ahn;Youngchul Oh;Sanguk Kim
    • BMB Reports
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    • v.56 no.1
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    • pp.43-48
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    • 2023
  • Pre-clinical models are critical in gaining mechanistic and biological insights into disease progression. Recently, patient-derived organoid models have been developed to facilitate our understanding of disease development and to improve the discovery of therapeutic options by faithfully recapitulating in vivo tissues or organs. As technological developments of organoid models are rapidly growing, computational methods are gaining attention in organoid researchers to improve the ability to systematically analyze experimental results. In this review, we summarize the recent advances in organoid models to recapitulate human diseases and computational advancements to analyze experimental results from organoids.

Nucleocapsid Amino Acids 211 to 254, in Particular, Tetrad Glutamines, are Essential for the Interaction Between the Nucleocapsid and Membrane Proteins of SARS-Associated Coronavirus

  • Fang, Xiaonan;Ye, Lin-Bai;Zhang, Yijuan;Li, Baozong;Li, Shanshan;Kong, Lingbao;Wang, Yuhua;Zheng, Hong;Wang, Wei;Wu, Zhenghui
    • Journal of Microbiology
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    • v.44 no.5
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    • pp.577-580
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    • 2006
  • GST pull-down assays were used to characterize the SARS-CoV membrane (M) and nucleocapsid (N) interaction, and it was found that the amino acids 211-254 of N protein were essential for this interaction. When tetrad glutamines (Q) were replaced with glutamic acids (E) at positions of 240-243 of the N protein, the interaction was disrupted.

Isolation and Culture Properties of a Thermophilic Agarase-Producing Strain, Microbulbifer sp. SD-1

  • Kim, Do-Kyun;Jang, Yu-Ri;Kim, Kyoung-Hoon;Lee, Mi-Nan;Kim, A-Ra;Jo, Eun-Ji;Byun, Tae-Hwan;Jeong, Eun-Tak;Kwon, Hyun-Ju;Kim, Byung-Woo;Lee, Eun-Woo
    • Fisheries and Aquatic Sciences
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    • v.14 no.3
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    • pp.186-191
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    • 2011
  • An agar-degrading enzyme-producing strain was isolated from seawater. The isolate was identified as Microbulbifer sp. SD-1 by 16S rRNA sequencing analysis. The optimal pH and temperature for growth were 6.0 and $30^{\circ}C$, respectively, and growth was possible at pH 9.0 and $60^{\circ}C$. The isolate required 5% NaCl for optimal growth and showed 45% growth activity without NaCl. Agar concentrations of 0-0.4% in the medium did not affect growth. Thin-layer chromatography analysis revealed that this strain could degrade agar into a monosaccharide and oligosaccharide, which may have industrial applications.

Cloning and Characterization of a Novel ${\alpha}$-Amylase from a Fecal Microbial Metagenome

  • Xu, Bo;Yang, Fuya;Xiong, Caiyun;Li, Junjun;Tang, Xianghua;Zhou, Junpei;Xie, Zhenrong;Ding, Junmei;Yang, Yunjuan;Huang, Zunxi
    • Journal of Microbiology and Biotechnology
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    • v.24 no.4
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    • pp.447-452
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    • 2014
  • To isolate novel and useful microbial enzymes from uncultured gastrointestinal microorganisms, a fecal microbial metagenomic library of the pygmy loris was constructed. The library was screened for amylolytic activity, and 8 of 50,000 recombinant clones showed amylolytic activity. Subcloning and sequence analysis of a positive clone led to the identification a novel gene (amyPL) coding for ${\alpha}$-amylase. AmyPL was expressed in Escherichia coli BL21 (DE3) and the purified AmyPL was enzymatically characterized. This study is the first to report the molecular and biochemical characterization of a novel ${\alpha}$-amylase from a gastrointestinal metagenomic library.

Production of curdlan with agro-industrial byproduct by Agrobacterium sp. ATCC 31749

  • Jeong, Dae-Yeong;Kim, Hyeon-Suk;Seo, Hyeong-Pil;Lee, Nam-Gyu;Kim, Ji-Mo;Lee, Jin-U
    • 한국생물공학회:학술대회논문집
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    • 2000.04a
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    • pp.251-254
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    • 2000
  • Effect of carbon sources including agro-industrial byproduct on cell growth and production of curdlan by Agrobacterium sp. ATCC 31749 was investigated. Maximal production of curdlan was obtained when the carbon source was sucrose. The conversion rate of curdlan from 2% (w/v) sucrose was 59%. Glucose, mannose and maltose were also found to be good carbon sources for production of curdlan. Production of curdlan increased up to 3% (w/v) glucose as the carbon source and then decrease as the concentration of glucose increased. The major components of agro-industrial byproduct (AIB) were glucose, maltose, and maltose, and maltotriose. Agrobacterium sp.ATCC 31749 utilized up to 25% (v/v) AIB and produced curdlan with 29.8g/1.

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Antioxidant Effects of Isoflavones from the Stem Bark of Cudrania tricuspidata

  • Lee, Jin-Hwan;Lee, Byong-Won;Kim, Jin-Hyo;Seo, Woo-Duck;Jang, Ki-Chang;Park, Ki-Hun
    • Journal of Applied Biological Chemistry
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    • v.48 no.4
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    • pp.193-197
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    • 2005
  • Isoflavones 4'-O-methylalpinumisoflavone (1) and 5, 7, 4'-trihydroxy-6,8-diprenylisoflavone (2) were isolated from stem bark of Cudrania tricuspidata (Carr.) Bureau. These compounds were the first reported from this plant. Antioxidant activities 1 and 2 were evaluated by measuring their ability to scavenge DPPH and ABTS radicals. Diprenylisoflavone 2 showed strong scavenging activity against ABTS ($IC_{50}\;=\;16.3\;{\mu}M$), three-fold higher compared to genistein, which do not possess prenylated group which indicates strong scavenging activity against ABTS radical of isoflavone 2 was due to prenyl group.