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System Identification of the Arabidopsis Plant Circadian System
Mathias Foo,David E. Somers,김판준 한국물리학회 2015 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.66 No.4
The circadian system generates an endogenous oscillatory rhythm that governs the daily activitiesof organisms in nature. It offers adaptive advantages to organisms through a coordination of theirbiological functions with the optimal time of day. In this paper, a model of the circadian systemin the plant Arabidopsis (species thaliana) is built by using system identification techniques. Priorknowledge about the physical interactions of the genes and the proteins in the plant circadian systemis incorporated in the model building exercise. The model is built by using primarily experimentallyverifieddirect interactions between the genes and the proteins with the available data on mRNAand protein abundances from the circadian system. Our analysis reveals a great performance of themodel in predicting the dynamics of the plant circadian system through the effect of diverse internaland external perturbations (gene knockouts and day-length changes). Furthermore, we found thatthe circadian oscillatory rhythm is robust and does not vary much with the biochemical parametersexcept those of a light-sensitive protein P and a transcription factor TOC1. In other words, thecircadian rhythmic profile is largely a consequence of the network’s architecture rather than itsparticular parameters. Our work suggests that the current experimental knowledge of the geneto-protein interactions in the plant Arabidopsis, without considering any additional hypotheticalinteractions, seems to suffice for system-level modeling of the circadian system of this plant and topresent an exemplary platform for the control of network dynamics in complex living organisms.
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System identification of circadian clock in plant Arabidopsis thaliana
Mathias Foo,Hee Young Yoo,Pan-Jun Kim 제어로봇시스템학회 2013 제어로봇시스템학회 국제학술대회 논문집 Vol.2013 No.10
The use of mathematical models in describing the dynamics of circadian clock in the plant Arabidopsis thaliana is gaining popularity. Models used to describe the plant circadian clock are usually derived from laws of physics and they comprise complex nonlinear ordinary differential equations. In this paper, we build mathematical models of the core loop of plant circadian clock using system identification techniques. This core loop involves two main genes (proteins), i.e. LHY/CCA1 and TOC1. Models obtained using system identification techniques are usually simple, sufficient to describe the relevant dynamics of the system and often are able to provide physical interpretation about the system. The obtained models through system identification can be useful for control design and prediction in the event for which we want to do phenotype manipulation and for understanding the behaviour of the system respectively.
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Sugary interfaces mitigate contact damage where stiff meets soft
Hee Young Yoo,Mihaela Iordachescu,Jun Huang,EliseHennebert,Sang sik Kim,Sangchul Rho,MathiasFoo,PatrickFlammang,HongboZeng,DaeheeHwang,J. Herbert Waite,Dong Soo Hwang 한국당과학회 2017 한국당과학회 학술대회 Vol.2017 No.01
The byssal threads of the fan shell Atrina pectinata are non-living functional materials intimately associated with living tissue, which provide an intriguing paradigm of bionic interface for robust load-bearing device. An interfacial load-bearing protein (A. pectinata foot protein-1, apfp-1) with L-3,4-dihydroxyphenylalanine (DOPA)-containing and mannose binding domains has been characterized from Atrina’s foot. apfp-1 was localized at the interface between stiff byssus and the soft tissue by immunochemical staining and confocal Raman imaging, implying that apfp-1 is an interfacial linker between the byssus and soft tissue, that is, the DOPA-containing domain interacts with itself and other byssal proteins via Fe3+–DOPA complexes, and the mannose-binding domain interacts with the soft tissue and cell membranes. Both DOPA- and sugar-mediated bindings are reversible and robust under wet conditions. This work shows the combination of DOPA and sugar chemistry at asymmetric interfaces is unprecedented and highly relevant to bionic interface design for tissue engineering and bionic devices.
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