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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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    • 제56권1호
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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.

Hepatotoxicity and nephrotoxicity of saponin-enriched extract of Asparagus cochinchinensis in ICR mice

  • Sung, Ji Eun;Choi, Jun Young;Kim, Ji Eun;Lee, Hyun Ah;Yun, Woo Bin;Park, Jin Ju;Kim, Hye Ryeong;Song, Bo Ram;Kim, Dong Seob;Lee, Chung Yeoul;Lee, Hee Seob;Lim, Yong;Hwang, Dae Youn
    • Laboraroty Animal Research
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    • 제33권2호
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    • pp.57-67
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    • 2017
  • The inhibitory effects of Asparagus cochinchinensis against inflammatory response induced by lipopolysaccharide (LPS), substance P and phthalic anhydride (PA) treatment were recently reported for some cell lines and animal models. To evaluate the hepatotoxicity and nephrotoxicity of A. cochinchinensis toward the livers and kidneys of ICR mice, alterations in related markers including body weight, organ weight, urine composition, liver pathology and kidney pathology were analyzed in male and female ICR mice after oral administration of 150, 300 and 600 mg/kg body weight/day saponin-enriched extract of A. cochinchinensis (SEAC) for 14 days. The saponin, total flavonoid and total phenol levels were found to be 57.2, 88.5 and 102.1 mg/g in SEAC, respectively, and the scavenging activity of SEAC gradually increased in a dose-dependent manner. Moreover, body and organ weight, clinical phenotypes, urine parameters and mice mortality did not differ between the vehicle and SEAC treated group. Furthermore, no significant alterations were measured in alkaline phosphatase (ALP), alanine aminotransferase (ALT), aspartate aminotransferase (AST), lactate dehydrogenase (LDH), blood urea nitrogen (BUN) and the serum creatinine (Cr) in the SEAC treated group relative to the vehicle treated group. Moreover, the specific pathological features induced by most toxic compounds were not observed upon liver and kidney histological analysis. Overall, the results of the present study suggest that SEAC does not induce any specific toxicity in the livers and kidneys of male and female ICR mice at doses of 600 mg/kg body weight/day.

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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    • 제44권5호
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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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    • 제14권3호
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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.

In vivo role of a redox protein against $H_2O_2-induced$ cell death

  • Park, Jin-Ho;Kim, Jong-Cheol;Lee, Jung-Ro;Jang, Ho-Hee;Moon, Jeong-Chan;Kim, Sun-Young;Lee, Sun-Yong;Lim, Chae-Oh;Lee, Kyun-Oh;Lee, Sang-Yeol
    • 한국식물생명공학회:학술대회논문집
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    • 한국식물생명공학회 2005년도 추계학술대회 및 한일 식물생명공학 심포지엄
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    • pp.136-136
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    • 2005
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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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    • 제24권4호
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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.