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Abstract
Recently, the number and heterogeneity of life science datasets published on the Web have increased significantly. However, biomedical scientists face numerous serious difficulties finding, using and publishing useful databases. To address these issues, the authors developed a Resource Description Framework-based database platform, called the RIKEN MetaDatabase (http://metadb.riken.jp), that allows biologists to develop, publish and integrate multiple databases easily. The platform manages the metadata of both research and individual data described using standardised vocabularies and ontologies, and has a simple browser-based graphical user interface to view data including tabular and graphical forms. The platform was released in April 2015, and 113 databases, including mammalian, plant, bioresource and image databases, with 26 ontologies have been published using this platform as of January 2017. This paper describes the technical knowledge obtained through the development and operation of the RIKEN MetaDatabase to accelerate life science data distribution.
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Affiliation(s)
- Norio Kobayashi
- Advanced Center for Computing and Communication (ACCC), BioResource Center, RIKEN CLST-JEOL Collaboration Center, RIKEN, Japan
| | - Satoshi Kume
- RIKEN Center for Life Science Technologies, RIKEN CLST-JEOL Collaboration Center, RIKEN Compass to Healthy Life Research Complex Program, RIKEN, Japan
| | - Kai Lenz
- Advanced Center for Computing and Communication (ACCC), RIKEN, Japan
| | - Hiroshi Masuya
- BioResource Center, Advanced Center for Computing and Communication (ACCC), RIKEN, Japan
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Ko DW, Yoon JK, Ahn JI, Lee M, Yang WS, Ahn JY, Lim JM. The importance of post-thaw subculture for standardizing cellular activity of fresh or cryopreserved mouse embryonic stem cells. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 31:335-343. [PMID: 28823125 PMCID: PMC5838338 DOI: 10.5713/ajas.17.0294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/08/2017] [Accepted: 08/07/2017] [Indexed: 12/25/2022]
Abstract
Objective Remarkable difference in cellular activity was found between early and late subpassaged embryonic stem cell (ESCs) lines, which can be created by subtle changes in cell manipulation protocol. This study subsequently examined whether post-thaw subculture of early subpassaged ESC lines could further affect the activity of the ESCs. Methods Fresh (as a control treatment) or cryopreserved F1 hybrid (B6CBAF1) early ESC lines (C57BL/6xCBA) of the 4 (P4) or the 19 passage (P19) were subcultured once, twice or six times under the same condition. The post-thaw survival of the ESCs was monitored after the post-treatment subculture and the ability of cell proliferation, reactive oxygen species (ROS) generation, apoptosis and mitochondrial ATP synthesis was subsequently examined. Results Regardless of the subculture number, P19 ESCs showed better (p<0.05) doubling time and less ATP production than P4 ESCs and such difference was not influenced by fresh or cryopreservation. The difference between P4 and P19 ESC lines became decreased as the post-treatment subculture was increased and the six times subculture eliminated such difference. Similarly, transient but prominent difference in ROS production and apoptotic cell number was detected between P4 and P19 ESCs only at the 1st subculture after treatment, but no statistical differences between two ESC lines was detected in other observations. Conclusion The results of this study suggest that post-thaw subculture of ESCs under the same environment is recommended for standardizing their cellular activity. The activity of cell proliferation ability and ATP synthesis can be used as parameters for quality control of ESCs.
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Affiliation(s)
- Dong Woo Ko
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jung Ki Yoon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong Il Ahn
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Myungook Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Woo Sub Yang
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Ji Yeon Ahn
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Jeong Mook Lim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea.,Research Institutes of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.,GreenBio Research Institute, Seoul National University, Pyeongchang 25354, Korea
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Liras A. Future research and therapeutic applications of human stem cells: general, regulatory, and bioethical aspects. J Transl Med 2010; 8:131. [PMID: 21143967 PMCID: PMC3014893 DOI: 10.1186/1479-5876-8-131] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 12/10/2010] [Indexed: 12/24/2022] Open
Abstract
There is much to be investigated about the specific characteristics of stem cells and about the efficacy and safety of the new drugs based on this type of cells, both embryonic as adult stem cells, for several therapeutic indications (cardiovascular and ischemic diseases, diabetes, hematopoietic diseases, liver diseases). Along with recent progress in transference of nuclei from human somatic cells, as well as iPSC technology, has allowed availability of lineages of all three germ layers genetically identical to those of the donor patient, which permits safe transplantation of organ-tissue-specific adult stem cells with no immune rejection. The main objective is the need for expansion of stem cell characteristics to maximize stem cell efficacy (i.e. the proper selection of a stem cell) and the efficacy (maximum effect) and safety of stem cell derived drugs. Other considerations to take into account in cell therapy will be the suitability of infrastructure and technical staff, biomaterials, production costs, biobanks, biosecurity, and the biotechnological industry. The general objectives in the area of stem cell research in the next few years, are related to identification of therapeutic targets and potential therapeutic tests, studies of cell differentiation and physiological mechanisms, culture conditions of pluripotent stem cells and efficacy and safety tests for stem cell-based drugs or procedures to be performed in both animal and human models in the corresponding clinical trials. A regulatory framework will be required to ensure patient accessibility to products and governmental assistance for their regulation and control. Bioethical aspects will be required related to the scientific and therapeutic relevance and cost of cryopreservation over time, but specially with respect to embryos which may ultimately be used for scientific uses of research as source of embryonic stem cells, in which case the bioethical conflict may be further aggravated.
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Affiliation(s)
- Antonio Liras
- Department of Physiology, School of Biological Sciences, Complutense University of Madrid, Spain.
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Masuya H, Makita Y, Kobayashi N, Nishikata K, Yoshida Y, Mochizuki Y, Doi K, Takatsuki T, Waki K, Tanaka N, Ishii M, Matsushima A, Takahashi S, Hijikata A, Kozaki K, Furuichi T, Kawaji H, Wakana S, Nakamura Y, Yoshiki A, Murata T, Fukami-Kobayashi K, Mohan S, Ohara O, Hayashizaki Y, Mizoguchi R, Obata Y, Toyoda T. The RIKEN integrated database of mammals. Nucleic Acids Res 2010; 39:D861-70. [PMID: 21076152 PMCID: PMC3013680 DOI: 10.1093/nar/gkq1078] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The RIKEN integrated database of mammals (http://scinets.org/db/mammal) is the official undertaking to integrate its mammalian databases produced from multiple large-scale programs that have been promoted by the institute. The database integrates not only RIKEN's original databases, such as FANTOM, the ENU mutagenesis program, the RIKEN Cerebellar Development Transcriptome Database and the Bioresource Database, but also imported data from public databases, such as Ensembl, MGI and biomedical ontologies. Our integrated database has been implemented on the infrastructure of publication medium for databases, termed SciNetS/SciNeS, or the Scientists' Networking System, where the data and metadata are structured as a semantic web and are downloadable in various standardized formats. The top-level ontology-based implementation of mammal-related data directly integrates the representative knowledge and individual data records in existing databases to ensure advanced cross-database searches and reduced unevenness of the data management operations. Through the development of this database, we propose a novel methodology for the development of standardized comprehensive management of heterogeneous data sets in multiple databases to improve the sustainability, accessibility, utility and publicity of the data of biomedical information.
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