82 results on '"Shiono K"'
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2. The application of LS-PIV to a small irregular river for inbank and overbank flows
- Author
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Gunawan, B., Sun, X., Sterling, M., Shiono, K., Tsubaki, R., Rameshwaran, P., Knight, D.W., Chandler, J.H., Tang, X., and Fujita, I.
- Published
- 2012
- Full Text
- View/download PDF
3. Flow Characteristics in Vegetated Compound Channels
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Sun, X, Shiono, K, Huang, T L, Fu, X Y, and Proceedings of the 34th World Congress of the International Association for Hydro-Environment Research and Engineering: 33rd Hydrology and Water Resources Symposium and 10th Conference on Hydraulics in Water Engineering
- Published
- 2011
4. Influence of One-line Vegetation on the Edge of Floodplain on Velocity and Boundary Shear Stress Distributions in Compound Channel
- Author
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Terrier, B, Peltier, Y, Shiono, K, Paquier, A, Riviere, N, and Proceedings of the 34th World Congress of the International Association for Hydro-Environment Research and Engineering: 33rd Hydrology and Water Resources Symposium and 10th Conference on Hydraulics in Water Engineering
- Published
- 2011
5. Longitudinal Dispersion Processes in the Upper Tamar Estuary
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West, J. R., Uncles, R. J., Stephens, J. A., and Shiono, K.
- Published
- 1990
6. A numerical study of the complex flow structure in a compound meandering channel
- Author
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Universitat Politècnica de València. Departamento de Ingeniería Rural y Agroalimentaria - Departament d'Enginyeria Rural i Agroalimentària, Moncho Esteve, Ignacio José, García-Villalba, Manuel, MUTO Y., SHIONO K., Palau-Salvador, Guillermo, Universitat Politècnica de València. Departamento de Ingeniería Rural y Agroalimentaria - Departament d'Enginyeria Rural i Agroalimentària, Moncho Esteve, Ignacio José, García-Villalba, Manuel, MUTO Y., SHIONO K., and Palau-Salvador, Guillermo
- Abstract
[EN] In this study, we report large eddy simulations of turbulent flow in a periodic compound meandering channel for three different depth conditions: one in-bank and two overbank conditions. The flow configuration corresponds to the experiments of Shiono and Muto (1998). The predicted mean streamwise velocities, mean secondary motions, velocity fluctuations, turbulent kinetic energy as well as mean flood flow angle to meandering channel are in good agreement with the experimental measurements. We have analyzed the flow structure as a function of the inundation level, with particular emphasis on the development of the secondary motions due to the interaction between the main channel and the floodplain flow. Bed shear stresses have been also estimated in the simulations. Floodplain flow has a significant impact on the flow structure leading to significantly different bed shear stress patterns within the main meandering channel. The implications of these results for natural compound meandering channels are also discussed.
- Published
- 2018
7. Mathematical modelling of bed shear stress and depth averaged velocity for emergent vegetation on floodplain in compound channel
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Shiono, K., Rameshwaran, P., Shiono, K., and Rameshwaran, P.
- Abstract
A mathematical model is used to predict velocity and bed shear stress in a compound channel flow. Model parameters such as non-dimensional eddy viscosity and secondary flow term in the mathematical model based on Shiono and Knight Method (SKM) are reconsidered using the UK-FCF data. The turbulent shear stresses obtained by three turbulence models are compared with those in the FCF data and the results are no significant differences between them. The concept of the secondary flow in the SKM is redundant through the data analysis as a result a new one is introduced in representing the shear stress in the momentum equation. The shear stress is now expressed by three mechanisms of momentum transfer between the main channel and the floodplain. The analytical solutions to the SKM are used to predict velocity and bed shear stress with the new concept of the shear stress. An effect of various parameters in the SKM to the distributions of velocity and bed shear stress is also investigated.
- Published
- 2015
8. Influence of vegetation to boundary shear stress in open channel for overbank flow
- Author
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Terrier, B., Robinson, S., Shiono, K., Paquier, André, Ishigaki, T., Hydrologie-Hydraulique (UR HHLY), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), Loughborough University, and Bundesanstalt für Wasserbau
- Subjects
DRAG FORCE ,[SDE]Environmental Sciences ,Ingenieurwissenschaften (620) ,COMPOUND CHANNEL ,BOUNDARY SHEAR STRESS - Abstract
International audience; In rivers, flooding can be attributed to the effects of increased flow resistance due to riparian vegetation. Simply removing vegetation from river banks cannot be considered as a solution to aid flood mitigation, because vegetation plays a vital role in river environment. The flow structure in a compound channel with vegetation along edge of river bank is still not well understood. To better apprehend the influence of flow resistance of such vegetation to flow structure and boundary shear stress, laboratory experiments were carried out at Loughborough University. The experiments were conducted in a 12 m long, 0.306 m wide compound channel. The channel had a single line of emergent 3 mm diameter rods with 35 mm diameter brush bristles along the edge of the floodplain. The rods were spaced at rod distance to diameter ratios of L/d=8 and L/d=16. These ratios are compatible with those of trees in the River Thames. Boundary shear stress was measured using a Preston tube and velocity using a Pitot tube. The velocity distribution showed velocity dip caused by the presence of brushes. The boundary shear stress significantly decreased when compared with that of without brushes. The drag force of brushes was estimated from the force balance using weight component and boundary shear force. The drag force in-creases almost linearly with water depth. Stage discharge curves exhibited unexpected behaviour from other researcher findings (Sun and Shiono 2009).
- Published
- 2010
9. Turbulent structures in the flow through compound meandering channels
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Moncho-Esteve, I., Palau-Salvador, G., Shiono, K., Muto, Yasunori, and Bundesanstalt für Wasserbau
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Ingenieurwissenschaften (620) - Abstract
River engineering Numerical modelling in river engineering
- Published
- 2010
10. Solving open channel flow problems with a simple lateral distribution model
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Knight, Donald, Tang, Xiaonan, Sterling, M., Shiono, K., Mc Gahey, C., and Bundesanstalt für Wasserbau
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InformationSystems_GENERAL ,GeneralLiterature_INTRODUCTORYANDSURVEY ,ComputerApplications_MISCELLANEOUS ,ComputingMilieux_COMPUTERSANDEDUCATION ,Ingenieurwissenschaften (620) ,GeneralLiterature_MISCELLANEOUS - Abstract
Keynote Lectures
- Published
- 2010
11. Investigations on the establishment of uniform flow in compound channel flumes
- Author
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Terrier, B., Proust, Sébastien, Bousmar, D., Shiono, K., Riviere, N., Paquier, André, Loughborough University, Hydrologie-Hydraulique (UR HHLY), Centre national du machinisme agricole, du génie rural, des eaux et forêts (CEMAGREF), MINISTERE WALLON DE L'EQUIPEMENT ET DES TRANSPORTS CHATELET BEL, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA), and Kuratorium für Forschung im Küsteningenieurwesen (KFKI)
- Subjects
NUMERICAL MODELLING ,CEMAGREF ,Wasserbau (627) ,FLOW DEVELOPMENT ,HHLY ,[SDE]Environmental Sciences ,Ingenieurwissenschaften (620) ,HHLYMFO ,UNIFORM FLOW ,STRAIGHT COMPOUND CHANNEL - Abstract
International audience; There has been recently increasing concern about the uniformity of flow at measuring sections in straight compound channel experiments. Experiments have been usually carried out with the same total head at the inlet of the main channel and floodplain and as a result the velocities entering into the main channel and onto the floodplain are also the same. As flow enters onto the floodplain, the floodplain discharge exceeds the discharge for a uniform flow condition, hence mass transfer towards the main channel progressively occurs along the flume until flow becomes uniform for both main channel and floodplain. This paper investigates the influence of relative depth on the length required for a uniform flow condition to be achieved in compound channel flumes. The quasi one-dimensional model, the Independent Sub-Sections Method (ISM), the two-dimensional model Telemac 2D and a three-dimensional numerical model have been used to simulate the experiments conducted at LMFA (France) and at UCL (Belgium). The ISM has been subsequently used to investigate more upstream conditions at the LMFA and their resulting flow developments in relation to the flume length. The results show that as the relative depth increases, the length required for uniform flow condition increases and can even exceed the actual length of some of the experimental flumes studied in literature.
- Published
- 2008
12. An Integrated and Novel Approach to Estimating the Conveyance Capacity of the River Blackwater
- Author
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Gunawan, Budi, Sun, X., Sterling, M., Knight, D. W., Shiono, K., Chandler, J. H., Rameshwaran, P., Wright, N. G., Sellin, R. H. J., Tang, X., Fujita, I., and Kuratorium für Forschung im Küsteningenieurwesen (KFKI)
- Subjects
Wasserbau (627) ,Ingenieurwissenschaften (620) - Abstract
Source: ICHE Conference Archive - https://mdi-de.baw.de/icheArchive
- Published
- 2008
13. Water Surface and Velocity Measurement-River and Flume
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Chandler, J. H., primary, Ferreira, E., additional, Wackrow, R., additional, and Shiono, K., additional
- Published
- 2014
- Full Text
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14. Modelling of overbank flow structures in meandering channels
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Rameshwaran, P., Shiono, K., Rameshwaran, P., and Shiono, K.
- Abstract
Overbank flow in a meandering channel displays a complex coherent flow structure resulting from the interplay between the floodplain and main channel flows. Understanding and modeling such coherent flow structure are of great importance for addressing river engineering and management issues where the design solutions are required to retain natural channel features and to maintain a balance between environmental, ecological and amenity issues. In recent years, numerical models have increasingly been used for river flow modeling in order to understand their flow behavior. The main aim of this paper is to predict and investigate the overbank flow behavior in the physical model of meandering channels using three-dimensional (3D) numerical model. The performance of the model is first assessed by comparing predicted results with the limited experimental data. The experiment data were obtained from a 1:5 scale physical model of the River Blackwater and a flume study in Loughborough University. The predicted distributions of the streamwise velocity, secondary vectors, turbulent parameters and bed shear stress are used to investigate the coherent flow structures along the channel, in both the horizontal and inclined floodplain cases and main channel mobile sand bed case. The results show that the three-dimensional model predicts the coherent flow structures reasonably well.
- Published
- 2011
15. Discharge estimation in small irregular river using LSPIV
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Sun, X., Shiono, K., Chandler, J.H., Rameshwaran, P., Sellin, R.H.J., Fujita, I., Sun, X., Shiono, K., Chandler, J.H., Rameshwaran, P., Sellin, R.H.J., and Fujita, I.
- Abstract
This paper reports on an estimation method used to quantify discharge in the small irregular channel of the River Blackwater, using large-scale particle image velocimetry (LSPIV). The test reach (250 m 3 60 m) consists of relatively straight and multiple meander channels, with a bankfull depth of 0.90 m and a base width of 4.25 m. Water surface velocities were measured by LSPIV at three sections along the river. Acoustic Doppler velocimeter (ADV) was also used on two occasions to measure velocity profiles for the validation of water surface velocities of LSPIV. In addition to this field work, velocity data derived from a 1:5 physical model of the river were available to compare with the field data. A comparison between the LSPIV data and ADV data was made and agreement was confirmed. The discharge correction factor method was suggested to estimate the discharge in the river. Discharge correction factors of 0.90–1.05 and 1.10–1.15 were proposed for inbank and overbank flow conditions respectively.
- Published
- 2010
16. The effect of floodplain roughness on flow structures, bedforms and sediment transport rates in meandering channels with overbank flows: Part I
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Shiono, K., Chan, Tony L., Spooner, Jake, Rameshwaran, P., Chandler, J. H., Shiono, K., Chan, Tony L., Spooner, Jake, Rameshwaran, P., and Chandler, J. H.
- Abstract
Studies were carried out to understand the effect of floodplain roughness on flow structures, sediment transport rates and bedforms in a mobile meandering channel with overbank flows. Three floodplain roughnesses were examined in this study. Flow structures and bedforms were measured using a three component laser Doppler anemometer (LDA) system and digital photogrammetry, respectively. Comparisons of flow structures and bedforms between different floodplain rougheness are made. Considerable changes in the flow structure and bed form were observed. In particular, multiple secondary flow cells along the meandering channel occur at deeper water depths as the floodplain roughness increases. These cells also cause a series of wavy bedforms along the meandering channel. This paper is separated into two parts. Part I concentrates, in detail, on the flow structure with bedforms in the meandering channel for overbank flow as to change of floodplain roughness. The sister paper, Part II, concentrates on bed form formation during flood, sediment transport rates and flow resistance in the main channel and floodplain.
- Published
- 2009
17. The Modelling of Compound Channel Flow: Physical Model of River Blackwater
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Altinakar, M. S, Kokpinar, M. A., Aydin, I., Cokgor, S., Kirkgoz, S., Rameshwaran, P., Sun, X., Shiono, K., Chandler, J. H., Sellin, R. H. J., Altinakar, M. S, Kokpinar, M. A., Aydin, I., Cokgor, S., Kirkgoz, S., Rameshwaran, P., Sun, X., Shiono, K., Chandler, J. H., and Sellin, R. H. J.
- Abstract
This paper compares results derived from a physical model representing the River Blackwater, to numerical simulation using both a two-dimensional (2D) and three-dimensional (3D) model. The 2D model solves the shallow water depth-averaged continuity and Navier-Stokes equations with the depth-averaged form of the k −ε turbulence model for free surface flow. The 3D model solves the three-dimensional Reynolds-averaged continuity and Navier-Stokes equations with the renormalization group (RNG) k −ε turbulence model for steady-state flow. The model results are evaluated against the experimental data obtained from a 1:5 scale physical model of the River Blackwater, located at the UK Flood Channel Facility. The predicted distributions of the streamwise velocity, secondary vectors and bed shear stress are used to investigate the flow processes along the channel. The 2D and 3D model results show that the three-dimensional model predicts the flow fields much better than the two-dimensional model.
- Published
- 2008
18. Hydrodynamic behaviour of a two-stage channel with horizontal and inclined floodplains: a numerical investigation
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Wang, S. S. Y., Kawahara, M., Holz, K. P., Tsujimoto, T., Toda, Y., Rameshwaran, P., Shiono, K., Sun, X., Chandler, J. H., Sellin, R. H. J., Wang, S. S. Y., Kawahara, M., Holz, K. P., Tsujimoto, T., Toda, Y., Rameshwaran, P., Shiono, K., Sun, X., Chandler, J. H., and Sellin, R. H. J.
- Abstract
This paper presents the hydrodynamic behaviour of the two-stage River Blackwater model with horizontal and inclined floodplains using two-dimensional (2D) and threedimensional (3D) numerical models. The 2D model solves the shallow water depth-averaged continuity and Navier-Stokes equations with the depth-averaged form of the k −ε turbulence model for free surface flow. The 3D model solves the three-dimensional Reynoldsaveraged continuity and Navier-Stokes equations with the renormalization group (RNG) k −ε turbulence model for steady-state flow. The performance of the models is assessed by comparing predicted results with the experimental data obtained from a 1:5 scale physical model of the River Blackwater, located at the UK Flood Channel Facility. The predicted model results are used to investigate the flow processes along the channel in both the horizontal and inclined floodplain cases.
- Published
- 2008
19. An integrated and novel approach to estimating the conveyance capacity of the River Blackwater
- Author
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Wang, S. S. Y., Kawahara, M., Holz, K. P., Tsujimoto, T., Toda, Y., Gunawan, B., Sun, X., Sterling, M., Knight, D. W., Shiono, K., Chandler, J. H., Rameshwaran, P., Wright, N. G., Sellin, R. H. J., Tang, X., Fujita, I., Wang, S. S. Y., Kawahara, M., Holz, K. P., Tsujimoto, T., Toda, Y., Gunawan, B., Sun, X., Sterling, M., Knight, D. W., Shiono, K., Chandler, J. H., Rameshwaran, P., Wright, N. G., Sellin, R. H. J., Tang, X., and Fujita, I.
- Abstract
This paper presents a number of complex issues associated with the methodology and preliminary analysis of velocity and discharge measurements using various techniques applied to the River Blackwater, UK. An ADCP deployment procedure was adapted in order to take into account the difficulties of using such equipment in small rivers. The velocity profile in the middle of main channel has been measured using both ADCP and ADV, and averaged over a time scale of 800 s and 300 s respectively, to obtain a stable value. A discrepancy of approximately 6.8% was observed in the mean streamwise velocity between both measurements. A good agreement between surface velocity measurements using PIV and ADCP in cross-sections located in straight and meandering reaches of the river was observed. Finally, several numerical models have been benchmarked against a physical scale model of the river.
- Published
- 2008
20. Measuring a dynamic and flooding river surface by close range digital photogrammetry
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Chandler, J. H., Wackrow, R., Sun, X., Shiono, K., Rameshwaran, P., Chandler, J. H., Wackrow, R., Sun, X., Shiono, K., and Rameshwaran, P.
- Abstract
Current state of the art computational fluid dynamics (CFD) and in particular, river flow modelling, require accurate estimation of the “free surface” in order to accurately predict the three dimensional flow field along a river. Such models are increasingly important for management of river basins and mitigation of river floods as the incidence of extreme rainfall events increases, causing widespread flooding, disruption and loss of life. To increase the accuracy of such flow models, it has become necessary to calibrate model outputs using field data, demanding improved measurement of the flow field along rivers.A substantial and funded research project being conducted at Loughborough University is developing image based river measurement methods using a combination of Particle Image Velocimetry (PIV) and close range photogrammetry (CRP). This paper will report on the use of digital close range photogrammetry to measure the dynamic topographic water surface exhibited by real and flooding rivers.A pair of Nikon D80 (10 Mega-pixel) digital cameras have been purchased, each equipped with a variables zoom lens (f: 18-70mm). The two cameras have been synchronized using two cables connected via a single relay operated switch, tests demonstrating that the accuracy of synchronization is better than 100th of a second. The cameras are mounted on two standard camera tripods, providing convergent and stereoscopic coverage of the river reach, which is between 10 and 20m distant. In initial tests, conventional photogrammetric control was provided using temporary targeted points, coordinated using a Reflectorless Total Station. Subsequent work is being conducted on a semi-engineered river at Farnborough, in the UK, where fixed targets have been permanently installed and coordinated to be in position necessary for the two year duration of the project.Imagery is being processed using the Leica Photogrammetry System (LPS); commercial software which provides the ability to automatica
- Published
- 2008
21. Flow characteristics in meandering channels with non-mobile and mobile beds for overbank flows
- Author
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Shiono, K., Spooner, J., Chan, T., Rameshwaran, P., Chandler, J., Shiono, K., Spooner, J., Chan, T., Rameshwaran, P., and Chandler, J.
- Abstract
Experiments were conducted in meandering channels with non-mobile and mobile beds to measure flow rates, velocities, turbulent kinetic energies, bedforms and sediment transport rates for overbank flows. The behaviour of bedform in meandering channels with overbank flows was observed using digital photogrammetry, with velocity measurements taken with a Laser Doppler Anemometer. The bedform structure and velocity distributions along the meandering channel were obtained for bank full flow and three overbank flow depths. Important interactions between the flow structure and bedform were observed along the meandering channel. The sediment transport rates collected during the experiment showed three phases; an increase in the sediment transport rate up to the bankfull level, a small decrease as the flow goes overbank up to a relative depth ratio of 0.3 and then an increase again for higher flow depths. The regions of higher turbulent kinetic energy were identified. The total energy losses due to friction, secondary flow and interfacial turbulence in the lower layer flow of the main channel were compared in both the non-mobile and mobile bed cases.
- Published
- 2008
22. Quasi two-dimensional model for straight overbank flows through emergent vegetation on floodplains
- Author
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Rameshwaran, P., Shiono, K., Rameshwaran, P., and Shiono, K.
- Abstract
The paper presents a quasi two-dimensional (2D) model calculating depth-averaged velocity and bed shear stress in a straight compound channel with a vegetated floodplain. The model numerically solves the depth-averaged Navier–Stokes equation for the streamwise motion of flow (quasi 2D). Reduction in volume of water due to vegetation is modelled as porosity. Drag force due to vegetation is modelled as an additional momentum sink term in the Navier–Stokes equation. Estimation methods for model parameters—drag coefficient, shading factor, porosity, friction factor, eddy viscosity and advection term—are discussed. The predictive capability of the model is assessed against experimental data with regard to distributions of depth-averaged velocity, bed shear stress, transverse shear stress and stage-discharge. The results show that the quasi 2D model reproduces a reasonable simulation of the flow field.
- Published
- 2007
23. Inter-comparison of CFD codes using data from a large-scale physical model
- Author
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Gourbesville, P. et al, Naden, P., Rameshwaran, P., Wilson, C. A. M. E., Malki, R., Egarr, D. A., Shukla, D. R., Shiono, K., Gourbesville, P. et al, Naden, P., Rameshwaran, P., Wilson, C. A. M. E., Malki, R., Egarr, D. A., Shukla, D. R., and Shiono, K.
- Published
- 2006
24. Computer modelling of two-stage meandering channel flows
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Rameshwaran, P., Shiono, K., Rameshwaran, P., and Shiono, K.
- Published
- 2003
25. PIV and LDA measurements of secondary flow in a meandering channel for overbank flow
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Ishigaki, T., Shiono, K., Rameshwaran, P., Ishigaki, T., Shiono, K., and Rameshwaran, P.
- Published
- 2002
26. Various Spatiotemporal Expression Profiles of Anther-Expressed Genes in Rice
- Author
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Hobo, T., primary, Suwabe, K., additional, Aya, K., additional, Suzuki, G., additional, Yano, K., additional, Ishimizu, T., additional, Fujita, M., additional, Kikuchi, S., additional, Hamada, K., additional, Miyano, M., additional, Fujioka, T., additional, Kaneko, F., additional, Kazama, T., additional, Mizuta, Y., additional, Takahashi, H., additional, Shiono, K., additional, Nakazono, M., additional, Tsutsumi, N., additional, Nagamura, Y., additional, Kurata, N., additional, Watanabe, M., additional, and Matsuoka, M., additional
- Published
- 2008
- Full Text
- View/download PDF
27. Cardiovascular pharmacology of nicardipine in animals.
- Author
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Takenaka, T., Asano, M., Shiono, K., Shibasaki, M., and Inagaki, O.
- Abstract
The haemodynamic, antianginal and antihypertensive effects of nicardipine, a vascular selective calcium antagonist, were studied in experimental animals. In the canine isolated coronary artery, nicardipine relaxed potassium-induced contraction and suppressed 3,4- diaminopyridine-induced rhythmic contractions more effectively than nifedipine, verapamil or diltiazem. In anaesthetised rats, nicardipine prevented the elevation of ST segment induced by intracoronary injection of methacholine. In anaesthetised dogs, nicardipine produced a greater vasodilatation in vertebral, carotid, and coronary vessels than in mesenteric, femoral, and renal vessels and did not affect myocardial oxygen consumption. In conscious monkeys, nicardipine given intravenously lowered blood pressure and gave rise to reflex tachycardia but did not prolong the A-V conduction time. Nicardipine given orally lowered blood pressure in spontaneously hypertensive rats (SHR), renal hypertensive rats (RHR), and deoxycorticosterone acetate/salt hypertensive rats (DOCA/Salt), as well as in normotensive rats. Long-term treatment with nicardipine given orally for 12 weeks effectively lowered high blood pressure in the three types of hypertensive rats, reduced cardiac hypertrophy in SHR and DOCA/Salt rats, and prevented mortality from stroke in DOCA/Salt rats. Combined treatment with nicardipine and a beta-adrenoceptor blocking agent (indenolol) showed an antihypertensive effect similar to that obtained with nicardipine alone. Conscious renal hypertensive dogs given repeated oral administration of nicardipine for 14 days did not develop tolerance to the hypotensive activity of nicardipine. Under the same conditions, tolerance to hydralazine developed within 4 days. [ABSTRACT FROM AUTHOR]
- Published
- 1985
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28. Increased acute myocardial infarction mortality following the 1995 Great Hanshin-Awaji earthquake in Japan.
- Author
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Ogawa, K, Tsuji, I, Shiono, K, and Hisamichi, S
- Abstract
This study examined the factors affecting mortality from acute myocardial infarction (AMI) following the 1995 Great Hanshin-Awaji earthquake.
- Published
- 2000
29. A computerised geologic mapping system based on logical models of geologic structures.
- Author
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Sakamoto M., Masumoto S., Shiono K., Wadatsumi K., Sakamoto M., Masumoto S., Shiono K., and Wadatsumi K.
- Abstract
The basic framework is described of a computerised mapping system called "cigma". The system is based on a mathematical formulation of geological concepts. It consists of the following 6 subsystems: input of geological data set; inference of stratigraphic sequence; construction of logical models of geological structures; determination of 3-D geological boundary surfaces; construction of 3-D solid model of geological structures; and graphical presentation., The basic framework is described of a computerised mapping system called "cigma". The system is based on a mathematical formulation of geological concepts. It consists of the following 6 subsystems: input of geological data set; inference of stratigraphic sequence; construction of logical models of geological structures; determination of 3-D geological boundary surfaces; construction of 3-D solid model of geological structures; and graphical presentation.
30. Inter-comparison of CFD codes using data from a large-scale physical model
- Author
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Naden, P., Rameshwaran, P., Wilson, Catherine, Malki, R., Shukla, D. R., Shiono, K., Naden, P., Rameshwaran, P., Wilson, Catherine, Malki, R., Shukla, D. R., and Shiono, K.
31. Imaging the snorkel effect during submerged germination in rice: Oxygen supply via the coleoptile triggers seminal root emergence underwater.
- Author
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Shiono K, Koshide A, Iwasaki K, Oguri K, Fukao T, Larsen M, and Glud RN
- Abstract
Submergence during germination impedes aerobic metabolisms and limits the growth of most higher plants. However, some wetland plants including rice can germinate under submerged conditions. It has long been hypothesized that the first elongating shoot tissue, the coleoptile, acts as a snorkel to acquire atmospheric oxygen (O
2 ) to initiate the first leaf elongation and seminal root emergence. Here, we obtained direct evidence for this hypothesis by visualizing the spatiotemporal O2 dynamics during submerged germination in rice using a planar O2 optode system. In parallel with the O2 imaging, we tracked the anatomical development of shoot and root tissues in real-time using an automated flatbed scanner. Three hours after the coleoptile tip reached the water surface, O2 levels around the embryo transiently increased. At this time, the activity of alcohol dehydrogenase (ADH), an enzyme critical for anaerobic metabolism, was significantly reduced, and the coleorhiza covering the seminal roots in the embryo was broken. Approximately 10 h after the transient burst in O2 , seminal roots emerged. A transient O2 burst around the embryo was shown to be essential for seminal root emergence during submerged rice germination. The parallel application of a planar O2 optode system and automated scanning system can be a powerful tool for examining how environmental conditions affect germination in rice and other plants., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Shiono, Koshide, Iwasaki, Oguri, Fukao, Larsen and Glud.)- Published
- 2022
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32. Abscisic acid is required for exodermal suberization to form a barrier to radial oxygen loss in the adventitious roots of rice (Oryza sativa).
- Author
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Shiono K, Yoshikawa M, Kreszies T, Yamada S, Hojo Y, Matsuura T, Mori IC, Schreiber L, and Yoshioka T
- Subjects
- Abscisic Acid pharmacology, Lignin, Oxygen, Plant Roots genetics, Oryza genetics
- Abstract
To acclimate to waterlogged conditions, wetland plants form a barrier to radial oxygen loss (ROL) that can enhance oxygen transport to the root apex. We hypothesized that one or more hormones are involved in the induction of the barrier and searched for such hormones in rice. We previously identified 98 genes that were tissue-specifically upregulated during ROL barrier formation in rice. The RiceXPro database showed that most of these genes were highly enhanced by exogenous abscisic acid (ABA). We then examined the effect of ABA on ROL barrier formation by using an ABA biosynthesis inhibitor (fluridone, FLU), by applying exogenous ABA and by examining a mutant with a defective ABA biosynthesis gene (osaba1). FLU suppressed barrier formation in a stagnant solution that mimics waterlogged soil. Under aerobic conditions, rice does not naturally form a barrier, but 24 h of ABA treatment induced barrier formation. osaba1 did not form a barrier under stagnant conditions, but the application of ABA rescued the barrier. In parallel with ROL barrier formation, suberin lamellae formed in the exodermis. These findings strongly suggest that ABA is an inducer of suberin lamellae formation in the exodermis, resulting in an ROL barrier formation in rice., (© 2021 The Authors. New Phytologist © 2021 New Phytologist Foundation.)
- Published
- 2022
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33. Complete root specimen of plants grown in soil-filled root box: sampling, measuring, and staining method.
- Author
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Koyama T, Murakami S, Karasawa T, Ejiri M, and Shiono K
- Abstract
Background: Detailed datasets containing root system and its architecture in soil are required to improve understanding of resource capture by roots. However, most of the root study methods have paid little attention to make and preserve whole root specimens. This study introduces root system sampling equipment that makes the entire root specimen with minimum impairment and without displacement of the spatial arrangement of the root system in root boxes. The objectives are to assess: whether the equipment can rapidly sample the entire root system; whether root surface area is measurable from a scanned digital image of the root specimen; and whether staining of the entire root specimens would provide multidimensional visual information on the interaction between soil and physiological function of root system architecture (RSA). For validation, we examined the root response of two soybean cultivars to arbuscular mycorrhizal (AM) inoculation and the effect of waterlogging stress on the physiological activity of buckwheat RSA., Results: The root boxes allowed soybean and buckwheat plants to grow uniformly across the replications. Both species showed significant differences between cultivars and/or among treatments in shoot and root traits. The equipment enabled to sample the whole-root specimens of soybean and buckwheat, where the tips of the fine roots were alive (diameter < 0.2 mm). Also, the whole root specimens of soybean were made in about 7 min. The root surface area calculated from the scanned soybean specimens showed a significant correlation with that calculated from the roots spread out in water (a common method). Staining of the soybean root specimens enabled us to observe the localized root proliferation induced by AM colonization. Moreover, staining of the buckwheat root specimens made it possible to examine the respiratory activity of each root at different depths., Conclusions: The present method realized: fast and accurate production of the whole root specimen and precise calculation of the specimens' root surface area. Moreover, staining of the root specimens enabled analyzing the interaction between soil and physiological function of RSA. The evaluation of root traits, using our methods, will contribute to developing agronomic management and breeding program for sustainable food production., (© 2021. The Author(s).)
- Published
- 2021
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34. A barrier to radial oxygen loss helps the root system cope with waterlogging-induced hypoxia.
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Ejiri M, Fukao T, Miyashita T, and Shiono K
- Abstract
Internal aeration is crucial for root growth under waterlogged conditions. Many wetland plants have a structural barrier that impedes oxygen leakage from the basal part of roots called a radial oxygen loss (ROL) barrier. ROL barriers reduce the loss of oxygen transported via the aerenchyma to the root tips, enabling long-distance oxygen transport for cell respiration at the root tip. Because the root tip does not have an ROL barrier, some of the transferred oxygen is released into the waterlogged soil, where it oxidizes and detoxifies toxic substances (e.g., sulfate and Fe
2+ ) around the root tip. ROL barriers are located at the outer part of roots (OPRs). Their main component is thought to be suberin. Suberin deposits may block the entry of potentially toxic compounds in highly reduced soils. The amount of ROL from the roots depends on the strength of the ROL barrier, the length of the roots, and environmental conditions, which causes spatiotemporal changes in the root system's oxidization pattern. We summarize recent achievements in understanding how ROL barrier formation is regulated and discuss opportunities for breeding waterlogging-tolerant crops., (Copyright © 2021 by JAPANESE SOCIETY OF BREEDING.)- Published
- 2021
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35. Some Accessions of Amazonian Wild Rice ( Oryza glumaepatula ) Constitutively Form a Barrier to Radial Oxygen Loss along Adventitious Roots under Aerated Conditions.
- Author
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Ejiri M, Sawazaki Y, and Shiono K
- Abstract
A barrier to radial oxygen loss (ROL), which reduces the loss of oxygen transported via the aerenchyma to the root tips, enables the roots of wetland plants to grow into anoxic/hypoxic waterlogged soil. However, little is known about its genetic regulation. Quantitative trait loci (QTLs) mapping can help to understand the factors that regulate barrier formation. Rice ( Oryza sativa ) inducibly forms an ROL barrier under stagnant conditions, while a few wetland plants constitutively form one under aerated conditions. Here, we evaluated the formation of a constitutive ROL barrier in a total of four accessions from two wild rice species. Three of the accessions were wetland accessions of O. glumaepatula , and the fourth was a non-wetland species of O. rufipogon . These species have an AA type genome, which allows them to be crossed with cultivated rice. The three O. glumaepatula accessions (W2165, W2149, and W1183) formed an ROL barrier under aerated conditions. The O. rufipogon accession (W1962) did not form a constitutive ROL barrier, but it formed an inducible ROL barrier under stagnant conditions. The three O. glumaepatula accessions should be useful for QTL mapping to understand how a constitutive ROL barrier forms. The constitutive barrier of W2165 was closely associated with suberization and resistance to penetration by an apoplastic tracer (periodic acid) at the exodermis but did not include lignin at the sclerenchyma.
- Published
- 2020
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36. Groups of multi-cellular passage cells in the root exodermis of Echinochloa crus-galli varieties lack not only suberin lamellae but also lignin deposits.
- Author
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Ejiri M and Shiono K
- Subjects
- Echinochloa metabolism, Lignin metabolism, Oxygen metabolism, Plant Roots metabolism, Wetlands
- Abstract
Passage cells are frequently found in the exodermis and the endodermis of the roots. Because passage cells lack an apoplastic diffusion barrier, they are thought to provide pathways for the transport of nutrients and the entrance of endomycorrhizal fungi. Exodermal passage cells possess Casparian strips but not suberin lamellae. So far, exodermal passage cells have not been associated with a particular internal structure. In some wetland plants, the outer part of the root (i.e., epidermis, exodermis, and sclerenchyma) of emerging lateral root primordia has an oxygen leaky zone called a window. The exodermis at the window site also lacks suberin lamellae, but it remains unclear whether the exodermis at the window site also lacks Casparian strips. Here, we report that several of the exodermal cells in the window of Echinochloa crus-galli grown under aerated or deoxygenated stagnant agar nutrient solution also lack lignin, which is a major constituent of Casparian strips. The sclerenchyma cells that form part of the window also lacked lignin deposits. Sites at which lateral root primordia developed were highly permeable to an apoplastic tracer (periodic acid). These observations indicate that windows consist of a novel type of passage cell at the exodermis that lacks lignin as well as suberin lamellae.
- Published
- 2020
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37. Prevention of Radial Oxygen Loss Is Associated With Exodermal Suberin Along Adventitious Roots of Annual Wild Species of Echinochloa .
- Author
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Ejiri M and Shiono K
- Abstract
Internal aeration is crucial for root growth under waterlogged conditions. Some wetland plants have a structural barrier that impedes oxygen leakage from the basal part of roots called a radial oxygen loss (ROL) barrier. The ROL barrier reduces loss of oxygen transported via the aerenchyma to the root tips, enabling root growth into anoxic soil. The roots of some plants develop an ROL barrier under waterlogged conditions, while they remain leaky to oxygen under well-drained or aerated conditions. The main components of the inducible ROL barrier are thought to be suberin and lignin deposited at the outer cellular space (apoplast) in the outer part of roots. On the other hand, a few wetland plants including a species of Echinochloa form a constitutive ROL barrier, i.e., it is formed even in the absence of waterlogging. However, little is known about the components of constitutive ROL barriers. An ROL barrier is considered to be a characteristic of wetland species because it has not been found in any non-wetland species so far. Here, we examined whether Echinochloa species from non-waterlogged fields also form an inducible or constitutive ROL barrier. We found that three species of Echinochloa from non-waterlogged fields constitutively developed an ROL barrier under aerated conditions. Over 85% of their root exodermis cells were covered with suberin lamellae and had well-developed Casparian strips. These substances inhibited the infiltration of an apoplastic tracer (periodic acid), suggesting that the ROL barrier can also prevent the entry of phytotoxic compounds from the soil. Unlike the other Echinochloa species, E. oryzicola , which mainly inhabits rice paddies, was found to lack a constitutive ROL barrier under aerated conditions. Although close to 90% of its sclerenchyma was well lignified, it leaked oxygen from the basal part of roots. A high percentage (55%) of the root exodermis cells were not fortified with suberin lamellae. These results suggest that suberin is an important component of constitutive ROL barriers.
- Published
- 2019
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38. Camera Calibration for Water-Biota Research: The Projected Area of Vegetation.
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Wackrow R, Ferreira E, Chandler J, and Shiono K
- Subjects
- Endoscopes, Equipment Design, Photogrammetry methods, Photogrammetry standards, Water chemistry, Aquatic Organisms physiology, Photogrammetry instrumentation, Plants anatomy & histology
- Abstract
Imaging systems have an indisputable role in revealing vegetation posture under diverse flow conditions, image sequences being generated with off the shelf digital cameras. Such sensors are cheap but introduce a range of distortion effects, a trait only marginally tackled in hydraulic studies focusing on water-vegetation dependencies. This paper aims to bridge this gap by presenting a simple calibration method to remove both camera lens distortion and refractive effects of water. The effectiveness of the method is illustrated using the variable projected area, computed for both simple and complex shaped objects. Results demonstrate the significance of correcting images using a combined lens distortion and refraction model, prior to determining projected areas and further data analysis. Use of this technique is expected to increase data reliability for future work on vegetated channels.
- Published
- 2015
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39. Femtosecond laser processing with a holographic line-shaped beam.
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Hasegawa S, Shiono K, and Hayasaki Y
- Subjects
- Equipment Design, Equipment Failure Analysis, Reproducibility of Results, Sensitivity and Specificity, Surface Properties radiation effects, Holography instrumentation, Imaging, Three-Dimensional instrumentation, Lasers, Molecular Imprinting instrumentation, Tin Compounds chemistry, Tin Compounds radiation effects
- Abstract
Line-shaped femtosecond pulses are well-suited to large-area machining with high throughput in laser cutting, peeling, and grooving of materials. First, we demonstrated the single-shot fabrication of a line structure in a glass surface using a line-shaped pulse generated by a holographic cylindrical lens displayed on a liquid-crystal spatial light modulator. We found the line structure was uniform and smooth near the ends because of the ability to precisely control the intensity distribution and to achieve single-shot fabrication. Second, we demonstrated a line-shaped beam deformed three-dimensionally for showing the potential of holographic line-shaped beam processing. Third, we demonstrated laser peeling of an indium tin oxide film. We found that little debris around the fabricated area was observed, because the debris was removed by the beam itself. Last, we demonstrated laser grooving of stainless steel. We found the swelling of the surface included upwardly growing nanogratings, although many line-shaped pulse irradiations were given. The swelling was caused by the depositions of the debris on the top of the nanogratings.
- Published
- 2015
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40. Ethylene Biosynthesis Is Promoted by Very-Long-Chain Fatty Acids during Lysigenous Aerenchyma Formation in Rice Roots.
- Author
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Yamauchi T, Shiono K, Nagano M, Fukazawa A, Ando M, Takamure I, Mori H, Nishizawa NK, Kawai-Yamada M, Tsutsumi N, Kato K, and Nakazono M
- Subjects
- ATP-Binding Cassette Transporters genetics, ATP-Binding Cassette Transporters metabolism, Amino Acids, Cyclic analysis, Amino Acids, Cyclic pharmacology, Cell Death drug effects, Ethylenes analysis, Fatty Acids analysis, Mutation, Organophosphorus Compounds pharmacology, Oryza genetics, Oryza physiology, Plant Growth Regulators analysis, Plant Growth Regulators biosynthesis, Plant Proteins genetics, Plant Proteins metabolism, Plant Roots drug effects, Plant Roots genetics, Plant Roots physiology, Ethylenes biosynthesis, Fatty Acids metabolism, Oryza drug effects, Plant Growth Regulators pharmacology
- Abstract
In rice (Oryza sativa) roots, lysigenous aerenchyma, which is created by programmed cell death and lysis of cortical cells, is constitutively formed under aerobic conditions, and its formation is further induced under oxygen-deficient conditions. Ethylene is involved in the induction of aerenchyma formation. reduced culm number1 (rcn1) is a rice mutant in which the gene encoding the ATP-binding cassette transporter RCN1/OsABCG5 is defective. Here, we report that the induction of aerenchyma formation was reduced in roots of rcn1 grown in stagnant deoxygenated nutrient solution (i.e. under stagnant conditions, which mimic oxygen-deficient conditions in waterlogged soils). 1-Aminocyclopropane-1-carboxylic acid synthase (ACS) is a key enzyme in ethylene biosynthesis. Stagnant conditions hardly induced the expression of ACS1 in rcn1 roots, resulting in low ethylene production in the roots. Accumulation of saturated very-long-chain fatty acids (VLCFAs) of 24, 26, and 28 carbons was reduced in rcn1 roots. Exogenously supplied VLCFA (26 carbons) increased the expression level of ACS1 and induced aerenchyma formation in rcn1 roots. Moreover, in rice lines in which the gene encoding a fatty acid elongase, CUT1-LIKE (CUT1L; a homolog of the gene encoding Arabidopsis CUT1, which is required for cuticular wax production), was silenced, both ACS1 expression and aerenchyma formation were reduced. Interestingly, the expression of ACS1, CUT1L, and RCN1/OsABCG5 was induced predominantly in the outer part of roots under stagnant conditions. These results suggest that, in rice under oxygen-deficient conditions, VLCFAs increase ethylene production by promoting 1-aminocyclopropane-1-carboxylic acid biosynthesis in the outer part of roots, which, in turn, induces aerenchyma formation in the root cortex., (© 2015 American Society of Plant Biologists. All Rights Reserved.)
- Published
- 2015
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41. RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice (Oryza sativa).
- Author
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Shiono K, Ando M, Nishiuchi S, Takahashi H, Watanabe K, Nakamura M, Matsuo Y, Yasuno N, Yamanouchi U, Fujimoto M, Takanashi H, Ranathunge K, Franke RB, Shitan N, Nishizawa NK, Takamure I, Yano M, Tsutsumi N, Schreiber L, Yazaki K, Nakazono M, and Kato K
- Subjects
- ATP-Binding Cassette Transporters genetics, Biological Transport, Cell Membrane metabolism, Cell Wall metabolism, Gene Expression Regulation, Plant, Genes, Reporter, Lignin metabolism, Lipids chemistry, Mutation, Oryza cytology, Oryza physiology, Plant Epidermis cytology, Plant Epidermis genetics, Plant Epidermis physiology, Plant Proteins genetics, Plant Proteins metabolism, Plant Roots cytology, Plant Roots genetics, Plant Roots physiology, Promoter Regions, Genetic genetics, Recombinant Fusion Proteins, ATP-Binding Cassette Transporters metabolism, Oryza genetics, Water physiology
- Abstract
Suberin is a complex polymer composed of aliphatic and phenolic compounds. It is a constituent of apoplastic plant interfaces. In many plant species, including rice (Oryza sativa), the hypodermis in the outer part of roots forms a suberized cell wall (the Casparian strip and/or suberin lamellae), which inhibits the flow of water and ions and protects against pathogens. To date, there is no genetic evidence that suberin forms an apoplastic transport barrier in the hypodermis. We discovered that a rice reduced culm number1 (rcn1) mutant could not develop roots longer than 100 mm in waterlogged soil. The mutated gene encoded an ATP-binding cassette (ABC) transporter named RCN1/OsABCG5. RCN1/OsABCG5 gene expression in the wild type was increased in most hypodermal and some endodermal roots cells under stagnant deoxygenated conditions. A GFP-RCN1/OsABCG5 fusion protein localized at the plasma membrane of the wild type. Under stagnant deoxygenated conditions, well suberized hypodermis developed in wild types but not in rcn1 mutants. Under stagnant deoxygenated conditions, apoplastic tracers (periodic acid and berberine) were blocked at the hypodermis in the wild type but not in rcn1, indicating that the apoplastic barrier in the mutant was impaired. The amount of the major aliphatic suberin monomers originating from C(28) and C(30) fatty acids or ω-OH fatty acids was much lower in rcn1 than in the wild type. These findings suggest that RCN1/OsABCG5 has a role in the suberization of the hypodermis of rice roots, which contributes to formation of the apoplastic barrier., (© 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.)
- Published
- 2014
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42. Microarray analysis of laser-microdissected tissues indicates the biosynthesis of suberin in the outer part of roots during formation of a barrier to radial oxygen loss in rice (Oryza sativa).
- Author
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Shiono K, Yamauchi T, Yamazaki S, Mohanty B, Malik AI, Nagamura Y, Nishizawa NK, Tsutsumi N, Colmer TD, and Nakazono M
- Subjects
- Cell Wall metabolism, Microdissection, Oligonucleotide Array Sequence Analysis, Oryza cytology, Oryza genetics, Plant Roots cytology, Plant Roots metabolism, Lignin metabolism, Lipids biosynthesis, Oryza metabolism, Oxygen metabolism
- Abstract
Internal aeration is crucial for root growth in waterlogged soil. A barrier to radial oxygen loss (ROL) can enhance long-distance oxygen transport via the aerenchyma to the root tip; a higher oxygen concentration at the apex enables root growth into anoxic soil. The ROL barrier is formed within the outer part of roots (OPR). Suberin and/or lignin deposited in cell walls are thought to contribute to the barrier, but it is unclear which compound is the main constituent. This study describes gene expression profiles during ROL barrier formation in rice roots to determine the relative responses of suberin and/or lignin biosyntheses for the barrier. OPR tissues were isolated by laser microdissection and their transcripts were analysed by microarray. A total of 128 genes were significantly up- or downregulated in the OPR during the barrier formation. Genes associated with suberin biosynthesis were strongly upregulated, whereas genes associated with lignin biosynthesis were not. By an ab initio analysis of the promoters of the upregulated genes, the putative cis-elements that could be associated with transcription factors, WRKY, AP2/ERF, NAC, bZIP, MYB, CBT/DREB, and MADS, were elucidated. They were particularly associated with the expression of transcription factor genes containing WRKY, AP2, and MYB domains. A semiquantitative reverse-transcription PCR analysis of genes associated with suberin biosynthesis (WRKY, CYP, and GPAT) confirmed that they were highly expressed during ROL barrier formation. Overall, these results suggest that suberin is a major constituent of the ROL barrier in roots of rice., (© The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)
- Published
- 2014
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43. Identification of genes expressed in maize root cortical cells during lysigenous aerenchyma formation using laser microdissection and microarray analyses.
- Author
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Rajhi I, Yamauchi T, Takahashi H, Nishiuchi S, Shiono K, Watanabe R, Mliki A, Nagamura Y, Tsutsumi N, Nishizawa NK, and Nakazono M
- Subjects
- Calcium Signaling genetics, Cell Wall genetics, Down-Regulation genetics, Free Radical Scavengers metabolism, Gene Expression Profiling, Genes, Plant genetics, Multigene Family, Organ Specificity genetics, Paraffin Embedding, Plant Proteins genetics, Plant Proteins metabolism, Plant Roots anatomy & histology, Plant Roots enzymology, Reactive Oxygen Species metabolism, Reproducibility of Results, Reverse Transcriptase Polymerase Chain Reaction, Up-Regulation genetics, Zea mays anatomy & histology, Zea mays cytology, Zea mays enzymology, Gene Expression Regulation, Plant, Lasers, Microdissection, Oligonucleotide Array Sequence Analysis, Plant Roots cytology, Plant Roots genetics, Zea mays genetics
- Abstract
• To adapt to waterlogging in soil, some gramineous plants, such as maize (Zea mays), form lysigenous aerenchyma in the root cortex. Ethylene, which is accumulated during waterlogging, promotes aerenchyma formation. However, the molecular mechanism of aerenchyma formation is not understood. • The aim of this study was to identify aerenchyma formation-associated genes expressed in maize roots as a basis for understanding the molecular mechanism of aerenchyma formation. Maize plants were grown under waterlogged conditions, with or without pretreatment with an ethylene perception inhibitor 1-methylcyclopropene (1-MCP), or under aerobic conditions. Cortical cells were isolated by laser microdissection and their mRNA levels were examined with a microarray. • The microarray analysis revealed 575 genes in the cortical cells, whose expression was either up-regulated or down-regulated under waterlogged conditions and whose induction or repression was suppressed by pretreatment with 1-MCP. • The differentially expressed genes included genes related to the generation or scavenging of reactive oxygen species, Ca(2+) signaling, and cell wall loosening and degradation. The results of this study should lead to a better understanding of the mechanism of root lysigenous aerenchyma formation., (© 2010 The Authors. New Phytologist © 2010 New Phytologist Trust.)
- Published
- 2011
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44. Contrasting dynamics of radial O2-loss barrier induction and aerenchyma formation in rice roots of two lengths.
- Author
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Shiono K, Ogawa S, Yamazaki S, Isoda H, Fujimura T, Nakazono M, and Colmer TD
- Subjects
- Lignin metabolism, Lipids, Oryza anatomy & histology, Plant Roots anatomy & histology, Plant Roots metabolism, Oryza metabolism, Oxygen metabolism
- Abstract
Background and Aims: Many wetland species form aerenchyma and a barrier to radial O(2) loss (ROL) in roots. These features enhance internal O(2) diffusion to the root apex. Barrier formation in rice is induced by growth in stagnant solution, but knowledge of the dynamics of barrier induction and early anatomical changes was lacking., Methods: ROL barrier induction in short and long roots of rice (Oryza sativa L. 'Nipponbare') was assessed using cylindrical root-sleeving O(2) electrodes and methylene blue indicator dye for O(2) leakage. Aerenchyma formation was also monitored in root cross-sections. Microstructure of hypodermal/exodermal layers was observed by transmission electron microscopy (TEM)., Key Results: In stagnant medium, barrier to ROL formation commenced in long adventitious roots within a few hours and the barrier was well formed within 24 h. By contrast, barrier formation took longer than 48 h in short roots. The timing of enhancement of aerenchyma formation was the same in short and long roots. Comparison of ROL data and subsequent methylene blue staining determined the apparent ROL threshold for the dye method, and the dye method confirmed that barrier induction was faster for long roots than for short roots. Barrier formation might be related to deposition of new electron-dense materials in the cell walls at the peripheral side of the exodermis. Histochemical staining indicated suberin depositions were enhanced prior to increases in lignin., Conclusions: As root length affected formation of the barrier to ROL, but not aerenchyma, these two acclimations are differentially regulated in roots of rice. Moreover, ROL barrier induction occurred before histochemically detectable changes in putative suberin and lignin deposits could be seen, whereas TEM showed deposition of new electron-dense materials in exodermal cell walls, so structural changes required for barrier functioning appear to be more subtle than previously described.
- Published
- 2011
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45. Comprehensive network analysis of anther-expressed genes in rice by the combination of 33 laser microdissection and 143 spatiotemporal microarrays.
- Author
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Aya K, Suzuki G, Suwabe K, Hobo T, Takahashi H, Shiono K, Yano K, Tsutsumi N, Nakazono M, Nagamura Y, Matsuoka M, and Watanabe M
- Subjects
- Gene Expression Profiling, Genes, Plant, Meiosis genetics, Microdissection methods, Oligonucleotide Array Sequence Analysis, Pollen genetics, Flowers genetics, Gene Expression Regulation, Plant, Gene Regulatory Networks, Oryza genetics
- Abstract
Co-expression networks systematically constructed from large-scale transcriptome data reflect the interactions and functions of genes with similar expression patterns and are a powerful tool for the comprehensive understanding of biological events and mining of novel genes. In Arabidopsis (a model dicot plant), high-resolution co-expression networks have been constructed from very large microarray datasets and these are publicly available as online information resources. However, the available transcriptome data of rice (a model monocot plant) have been limited so far, making it difficult for rice researchers to achieve reliable co-expression analysis. In this study, we performed co-expression network analysis by using combined 44 K agilent microarray datasets of rice, which consisted of 33 laser microdissection (LM)-microarray datasets of anthers, and 143 spatiotemporal transcriptome datasets deposited in RicexPro. The entire data of the rice co-expression network, which was generated from the 176 microarray datasets by the Pearson correlation coefficient (PCC) method with the mutual rank (MR)-based cut-off, contained 24,258 genes and 60,441 genes pairs. Using these datasets, we constructed high-resolution co-expression subnetworks of two specific biological events in the anther, "meiosis" and "pollen wall synthesis". The meiosis network contained many known or putative meiotic genes, including genes related to meiosis initiation and recombination. In the pollen wall synthesis network, several candidate genes involved in the sporopollenin biosynthesis pathway were efficiently identified. Hence, these two subnetworks are important demonstrations of the efficiency of co-expression network analysis in rice. Our co-expression analysis included the separated transcriptomes of pollen and tapetum cells in the anther, which are able to provide precise information on transcriptional regulation during male gametophyte development in rice. The co-expression network data presented here is a useful resource for rice researchers to elucidate important and complex biological events.
- Published
- 2011
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46. Separated transcriptomes of male gametophyte and tapetum in rice: validity of a laser microdissection (LM) microarray.
- Author
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Suwabe K, Suzuki G, Takahashi H, Shiono K, Endo M, Yano K, Fujita M, Masuko H, Saito H, Fujioka T, Kaneko F, Kazama T, Mizuta Y, Kawagishi-Kobayashi M, Tsutsumi N, Kurata N, Nakazono M, and Watanabe M
- Subjects
- Cluster Analysis, Gametogenesis genetics, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genes, Plant, Genome, Plant, Lasers, Microdissection methods, Oryza growth & development, Pollen growth & development, RNA, Plant genetics, Gene Expression Profiling methods, Oligonucleotide Array Sequence Analysis methods, Oryza genetics, Pollen genetics
- Abstract
In flowering plants, the male gametophyte, the pollen, develops in the anther. Complex patterns of gene expression in both the gametophytic and sporophytic tissues of the anther regulate this process. The gene expression profiles of the microspore/pollen and the sporophytic tapetum are of particular interest. In this study, a microarray technique combined with laser microdissection (44K LM-microarray) was developed and used to characterize separately the transcriptomes of the microspore/pollen and tapetum in rice. Expression profiles of 11 known tapetum specific-genes were consistent with previous reports. Based on their spatial and temporal expression patterns, 140 genes which had been previously defined as anther specific were further classified as male gametophyte specific (71 genes, 51%), tapetum-specific (seven genes, 5%) or expressed in both male gametophyte and tapetum (62 genes, 44%). These results indicate that the 44K LM-microarray is a reliable tool to analyze the gene expression profiles of two important cell types in the anther, the microspore/pollen and tapetum.
- Published
- 2008
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47. Switching from premixed human insulin to premixed insulin lispro: a prospective study comparing the effects on glucose control and quality of life.
- Author
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Yamada S, Watanabe M, Kitaoka A, Shiono K, Atsuda K, Tsukamoto Y, Kawana Y, and Irie J
- Subjects
- Aged, Blood Glucose metabolism, Chemistry, Pharmaceutical, Diabetes Mellitus, Type 2 blood, Diabetes Mellitus, Type 2 drug therapy, Humans, Insulin chemistry, Insulin pharmacology, Insulin Lispro, Middle Aged, Prospective Studies, Blood Glucose drug effects, Insulin analogs & derivatives, Insulin therapeutic use, Quality of Life
- Abstract
Aim: To evaluate the clinical effects of switching from premixed human insulin to a premixed rapid-acting insulin analogue in type 2 diabetic patients., Research Design and Methods: Thirty patients, who were treated with a twice-daily injection of premixed human insulin, were enrolled and randomized to (i) 50/50 premixed insulin lispro twice-daily at the same daily dose as premixed human insulin (analogue mix group), or (ii) continued premixed human insulin (control group). The doses of insulin were adjusted every month by registered diabetologists to achieve adequate blood glucose levels. At the beginning of the study, and again 4 months later, HbA1c and blood glucose levels were measured, and the amount of insulin required and BMI were recorded in both groups. Insulin therapy-related quality of life (ITR-QOL) and the diabetes treatment satisfaction questionnaire (DTSQ) were also assessed in the analogue mix group at the beginning of the study and again 4 months later., Results: Although HbA1c levels did not change significantly over the duration of the study in the control group (7.33 +/- 0.58 vs 7.29 +/- 0.65%), HbA1c did improve significantly in the analogue mix group (7.59 +/- 0.44 vs 7.24 +/- 0.49%; p<0.05). The dose of insulin required in the analogue mix group did not change significantly (0.37 +/- 0.11 vs 0.38 +/- 0.14 U/kg/day), but increased in the control group from 0.34 +/- 0.15 to 0.37 +/- 0.16 U/kg/day (p<0.05). The switch to the premixed insulin analogue did not affect ITR-QOL and DTSQ scores., Conclusions: This study showed that switching from premixed human insulin to 50/50 premixed insulin lispro improved blood glucose control without compromising QOL. This finding suggests that a premixed rapid-acting insulin analogue is more effective than human insulin for Japanese type 2 diabetic patients.
- Published
- 2007
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48. Effects of beta-adrenergic blocking drugs in hypertensive rats.
- Author
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Sukamoto T, Shiono K, Watanabe TX, and Sokabe H
- Subjects
- Acebutolol pharmacology, Adrenergic beta-Antagonists toxicity, Animals, Cerebrovascular Disorders etiology, Hypertension etiology, Hypertension metabolism, Kidney metabolism, Male, Practolol pharmacology, Propranolol pharmacology, Rats, Renin metabolism, Adrenergic beta-Antagonists pharmacology, Hypertension drug therapy
- Abstract
Antihypertensive effects of three beta-adrenergic blocking drugs, acebutolol, propranolol, and practolol were studied for 11 weeks. Spontaneously (SHR); one-clip, two-kidney (CLIP); and deoxycorticosterone and salt (DOC) hypertensive rats were used. The drugs were given orally, 100 mg/kg per day, 5 days per week before development of hypertension. Propranolol inhibited blood pressure (BP) increase significantly in SHR. Acebutolol and practolol also lowered BP in SHR. Three drugs did not affect BP in CLIP, but an apparent inhibition was seen when the results were analyzed including the cases of which BP stayed below 150 mmHg. Either of three drugs did not show antihypertensive effects in DOC. Acebutolol rather increased BP more rapidly. Practolol also increased BP slightly more rapidly. Cerebral stroke was seen in DOC. The incidences of the stroke in the groups given the solvent, acebutolol, propranolol, and practolol were 3/6, 4/7, 2/6, and 3/6, respectively. Acebutolol seemed to cause stroke earlier with the more rapid BP elevation. Acebutolol, propranolol, and practolol decreased incidence of the vascular disease in CLIP. Propranolol also decreased it in DOC. Plasma renin activity was suppressed by these drugs in SHR and CLIP. The mechanisms of antihypertensive effects of beta-adrenergic blocking drugs are unknown. The present study denies those due to inhibition of cardiac function, or renin release from the kidney. A better experimental model is necessary to study this. The possibility that acebutolol and other beta-blockers might accelerate BP elevation and incidence of stroke must be reexamined.
- Published
- 1980
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49. Ultrastructures of G cells and the mechanism of gastrin release before and after selective vagotomy with pyloroplasty.
- Author
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Miyagami H, Watanabe Y, Sawada Y, Kato K, and Shiono KF
- Subjects
- Adult, Duodenal Ulcer blood, Duodenal Ulcer pathology, Duodenal Ulcer surgery, Humans, Middle Aged, Pyloric Antrum metabolism, Pyloric Antrum surgery, Pylorus metabolism, Pylorus surgery, Chromaffin System ultrastructure, Enterochromaffin Cells ultrastructure, Gastrins metabolism, Pylorus ultrastructure, Vagotomy
- Published
- 1977
- Full Text
- View/download PDF
50. Role of the kidney in the development and maintenance of hypertension caused by renal segmental infarction in the rat.
- Author
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Kawabe K, Shiono K, Mizogami S, and Sokabe H
- Subjects
- Animals, Disease Models, Animal, Infarction, Kidney Transplantation, Male, Rats, Rats, Inbred Strains, Renin physiology, Transplantation, Homologous, Hypertension, Renal physiopathology, Kidney physiopathology, Renal Artery Obstruction physiopathology
- Abstract
Utilizing the microsurgical method of transplantation in the rat, the role of the kidney in an experimental renal hypertension due to segmental renal infarction was studied. When the infarcted kidney was transplanted into the bilaterally nephrectomized recipient, hypertension developed so long as the donor kidney was transplanted within 2 weeks after infarction. With transplantation of the normal kidney into the hypertensive rat 8 weeks after infarction, BP remained high unless the infarcted kidney was removed. PRA after transplantation, or KRA of the transplanted kidneys were not correlated to the blood pressure levels. It was suggested that the infarcted kidney has the pressor mechanism, lasting for 2 weeks or more after infarction. The infarcted kidney also has the maintenance mechanism, establishing 8 weeks after infarction.
- Published
- 1976
- Full Text
- View/download PDF
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