Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli

Handle URI:
http://hdl.handle.net/10754/621259
Title:
Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli
Authors:
Sakata, Katsumi; Saito, Toshiyuki; Ohyanagi, Hajime; Okumura, Jun; Ishige, Kentaro; Suzuki, Harukazu; Nakamura, Takuji; Komatsu, Setsuko
Abstract:
Soybean (Glycine max) is sensitive to flooding stress, and flood damage at the seedling stage is a barrier to growth. We constructed two mathematical models of the soybean metabolic network, a control model and a flooded model, from metabolic profiles in soybean plants. We simulated the metabolic profiles with perturbations before and after the flooding stimulus using the two models. We measured the variation of state that the system could maintain from a state–space description of the simulated profiles. The results showed a loss of variation of state during the flooding response in the soybean plants. Loss of variation of state was also observed in a human myelomonocytic leukaemia cell transcriptional network in response to a phorbol-ester stimulus. Thus, we detected a loss of variation of state under external stimuli in two biological systems, regardless of the regulation and stimulus types. Our results suggest that a loss of robustness may occur concurrently with the loss of variation of state in biological systems. We describe the possible applications of the quantity of variation of state in plant genetic engineering and cell biology. Finally, we present a hypothetical “external stimulus-induced information loss” model of biological systems.
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Citation:
Sakata K, Saito T, Ohyanagi H, Okumura J, Ishige K, et al. (2016) Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli. Scientific Reports 6: 35946. Available: http://dx.doi.org/10.1038/srep35946.
Publisher:
Springer Nature
Journal:
Scientific Reports
Issue Date:
24-Oct-2016
DOI:
10.1038/srep35946
Type:
Article
ISSN:
2045-2322
Sponsors:
We thank Prof. M. Okamoto and Dr. T. Sekiguchi for supplying the Winbest-kit program, and Takumi Hidaka for editing analytical data. This study was supported by the Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (Grant Nos 26540157 and 16K00399), and partly supported by research grants from the Ministry of Education, Culture, Sports, Science and Technology, Japan for the RIKEN Centre for Life Science Technologies.
Additional Links:
http://www.nature.com/articles/srep35946
Appears in Collections:
Articles; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorSakata, Katsumien
dc.contributor.authorSaito, Toshiyukien
dc.contributor.authorOhyanagi, Hajimeen
dc.contributor.authorOkumura, Junen
dc.contributor.authorIshige, Kentaroen
dc.contributor.authorSuzuki, Harukazuen
dc.contributor.authorNakamura, Takujien
dc.contributor.authorKomatsu, Setsukoen
dc.date.accessioned2016-10-31T07:37:29Z-
dc.date.available2016-10-31T07:37:29Z-
dc.date.issued2016-10-24en
dc.identifier.citationSakata K, Saito T, Ohyanagi H, Okumura J, Ishige K, et al. (2016) Loss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimuli. Scientific Reports 6: 35946. Available: http://dx.doi.org/10.1038/srep35946.en
dc.identifier.issn2045-2322en
dc.identifier.doi10.1038/srep35946en
dc.identifier.urihttp://hdl.handle.net/10754/621259-
dc.description.abstractSoybean (Glycine max) is sensitive to flooding stress, and flood damage at the seedling stage is a barrier to growth. We constructed two mathematical models of the soybean metabolic network, a control model and a flooded model, from metabolic profiles in soybean plants. We simulated the metabolic profiles with perturbations before and after the flooding stimulus using the two models. We measured the variation of state that the system could maintain from a state–space description of the simulated profiles. The results showed a loss of variation of state during the flooding response in the soybean plants. Loss of variation of state was also observed in a human myelomonocytic leukaemia cell transcriptional network in response to a phorbol-ester stimulus. Thus, we detected a loss of variation of state under external stimuli in two biological systems, regardless of the regulation and stimulus types. Our results suggest that a loss of robustness may occur concurrently with the loss of variation of state in biological systems. We describe the possible applications of the quantity of variation of state in plant genetic engineering and cell biology. Finally, we present a hypothetical “external stimulus-induced information loss” model of biological systems.en
dc.description.sponsorshipWe thank Prof. M. Okamoto and Dr. T. Sekiguchi for supplying the Winbest-kit program, and Takumi Hidaka for editing analytical data. This study was supported by the Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (Grant Nos 26540157 and 16K00399), and partly supported by research grants from the Ministry of Education, Culture, Sports, Science and Technology, Japan for the RIKEN Centre for Life Science Technologies.en
dc.publisherSpringer Natureen
dc.relation.urlhttp://www.nature.com/articles/srep35946en
dc.rightsThis work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material.en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.titleLoss of variation of state detected in soybean metabolic and human myelomonocytic leukaemia cell transcriptional networks under external stimulien
dc.typeArticleen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
dc.identifier.journalScientific Reportsen
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.institutionMaebashi Institute of Technology, Maebashi 371-0816, Japanen
dc.contributor.institutionNational Institute of Radiological Sciences, Chiba 263-8555, Japanen
dc.contributor.institutionRIKEN Centre for Life Science Technologies, Yokohama 230-0045, Japanen
dc.contributor.institutionNational Agriculture and Food Research Organisation (NARO) Hokkaido Agricultural Research Centre, Sapporo 062-8555, Japanen
dc.contributor.institutionNARO Institute of Crop Science, Tsukuba 305-8518, Japanen
kaust.authorOhyanagi, Hajimeen
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.