A cDNA microarray technique applied for analysis of global gene expression profiles in tributyltin-exposed ascidians

To analyze global gene expressions, we constructed a cDNA microarray from a basal chordate, the ascidian Ciona intestinalis. Ciona is a cosmopolitan species and a genomic analysis of Ciona revealed that ascidians had approximately 15,500 protein-coding genes. Our "Ciona intestinalis cDNA chip version 1 (Ci cDNA chip ver. 1)" has arrayed 13,400 unique Ciona cDNAs. To establish a detection system for gene expression profiles in wild ascidians using a cDNA microarray, we analyzed gene expressions in the whole body of Ciona adults after exposure to 100 nM tributyltin (TBT) for 24 h. In our preliminary array data using Ci cDNA chip ver. 1, we found more than 200 genes that showed strong differential expressions. These genes encoded proteins that were concerned with stress response, detoxification, oxidoreduction reaction, biosynthesis, and catabolism. This, the first large cDNA microarray of this animal, should facilitate analyses of global gene expressions following exposure to TBT.     

Scaling model experiments on propagation of electromagnetic waves using salt solution to simulate the Earth's crust: Loma Prieta and Kobe earthquakes

Propagation of electromagnetic (EM) waves from an earthquake focus in the conductive Earth has been investigated using 1/1,000,000 scaling models taking earth-ionosphere and ocean-Moho plane parallel-plate waveguides into account. Microwaves at a frequency, ω_m, a million times higher than that of seismic EM signal (SEMS), ω, were generated at the model focus. They are propagated in a salt solution modeling the earth's crust and reflected by ocean, fault planes, ionosphere and Moho plane all made by aluminum. Distribution of EM power was mapped by scanning a detector antenna over the model Earth's surface. The skin depth, δ, calculated by the exact skin depth equation, 1/δ=ω(μ/2)^1/2 [(1+(1/ωρ)²)^1/2 −1]^1/2 where dielectric constant, and permeability, μ are the same but resistivity, ρ, 10⁻⁶ times smaller than that of Earth, gave 10⁻⁶ times small skin depth validating the model scaling index. Images for evanescent and wave-ripple standing waves disturbed by normal, strike-slip and dip-slip conductive fault planes have been obtained using an aluminum plate. The co-circular contour map above the epicenter due to evanescence was pushed to the north east direction from the epicenter by the presence of ocean for the Loma Prieta earthquake, while to north direction for the Kobe earthquake. The intensity of EM ULF emissions for the Loma Prieta earthquake is discussed quantitatively.     

Construction and Visualization of a Three Dimensional Geologic Model Using GRASS GIS

The present work aims at introducing a basic theory, implementing methodology and algorithms for 3‐D modeling, and visualizing a geologic model using the Open Source Free GIS GRASS environment. A 3‐D geologic model is constructed from the boundary surfaces of geologic units and the logical model of geologic structure. The algorithms for construction and visualization of the proposed model are based on the geologic function g . The geologic function g assigns a unique geologic unit to every point in the objective 3‐D space. The boundary surface that divides the objective space into two subspaces is estimated using data from field survey. The logical model showing the hierarchical relationship between these boundary surfaces and geologic units can be automatically generated based on the stratigraphic sequence and knowledge of geologic structures. Based on these algorithms, a 3‐D geologic model can be constructed virtually in the GRASS GIS. Applying this model, various geologic surfaces and section models can be visualized in the GRASS GIS environment. “Nviz” was used for dynamic visualization of geologic cross‐sections and generation of animated image sequences. Further, the described algorithms and methods are applied and an online 3‐D geologic modeling system is developed.     

Tropical synoptic-scale wave disturbances over the western Pacific simulated by a global cloud-system resolving model

Lower-tropospheric tropical synoptic-scale disturbances (TSDs) are associated with severe weather systems in the Asian Monsoon region. Therefore, exact prediction of the development and behavior of TSDs using atmospheric general circulation models is expected to improve weather forecasting for this region. Recent state-of-the art global cloud-system resolving modeling approaches using a Nonhydrostatic Icosahedral Atmospheric Model (NICAM) may improve representation of TSDs. This study evaluates TSDs over the western Pacific in output from an Atmospheric Model Intercomparison Project (AMIP)-like control experiment using NICAM. Data analysis compared the simulated and observed fields. NICAM successfully simulates the average activity, three-dimensional structures, and characteristics of the TSDs during the Northern summer. The variance statistics and spectral analysis showed that the average activity of the simulated TSDs over the western Pacific during Northern summer broadly captures that of observations. The composite analysis revealed that the structures of the simulated TSDs resemble the observed TSDs to a large degree. The simulated TSDs exhibited a typical southeast- to northwest-oriented wave-train pattern that propagates northwestward from near the equator around 150 ^° E toward the southern coast of China. However, the location of the simulated wave train and wave activity center was displaced northward by approximately a few degrees of latitude from that in the observation. This displacement can be attributed to the structure and strength of the background basic flow in the simulated fields. Better representation of the background basic states is required for more successful simulation of TSDs.     

Reservoir rainfall‐runoff geomorphological model. II: analysis,calibration and validation

The model presented in the complementary document entitled, Reservoir rainfall‐runoff geomorphological model I: parameter application and analysis is analysed, calibrated and validated in this paper. The accuracy of simulated hydrographs is analysed by means of the efficiency defined by Nash and Sutcliffe. The sensitivity of the influence of five parameters on the behaviour of the model developed is analysed. Two different calibration and validation processes of Reservoir rainfall‐runoff geomorphological model are performed in Aixola watershed. Twelve events have been selected for calibrations and 25 for validations. With the first calibration and validation process, the model parameters are set by assigning the medians' values of the distributions obtained by means of the optimum results. The second process is performed by calibrating the most determinant parameter in the adjustment, which is the one that indicates the proportion of infiltrated water that is retained and does not flow; this is done with an empirical formulation depending on the event characteristics. Subsequently, the obtained results are validated. This last process has achieved very good adjustments in both calibrated and validated events. Copyright © 2012 John Wiley & Sons, Ltd.     

Rockfall hazard in the Daisekkei Valley, the northern Japanese Alps, on 11 August 2005

This paper describes a rockfall event in the Daisekkei Valley of Mount Shirouma-dake (2,932 m), the northern Japanese Alps. The rockfall occurred on a steep cliff comprising well-jointed felsites and produced debris of ≥8,000 m³. Most debris was deposited on an elongated snowpatch located immediately beneath the cliff, and it caused casualties among people who were trekking along a trail on the snowpatch. Additionally, a large rock block slipped 1 km on the snowpatch. The rockfall could have been due to the differential retreat of the rockwall, which contains areas of high- and low-density joints. Seasonal and diurnal freeze–thaw activities and snow avalanches and wash appear to be important factors responsible for the retreat. Although some rock blocks that can collapse further remain on the rockwall, the position of the mountain trail in the Daisekkei Valley is fixed. Fundamental reform of tourism systems for climbers, including education on natural hazards, is required.     

The formation of large mudwaves by turbidity currents on the levees of the Toyama deep-sea channel, Japan Sea

The development of mudwaves on the levees of the modern Toyama deep‐sea channel has been studied using gravity core samples combined with 3·5‐kHz echosounder data and airgun seismic reflection profiles. The mudwaves have developed on the overbank flanks of a clockwise bend of the channel in the Yamato Basin, Japan Sea, and the mudwave field covers an area of 4000 km². Mudwave lengths range from 0·2 to 3·6 km and heights vary from 2 to 44 m, and the pattern of mudwave aggradation indicates an upslope migration direction. Sediment cores show that the mudwaves consist of an alternation of fine‐grained turbidites and hemipelagites whereas contourites are absent. Core samples demonstrate that the sedimentation rate ranged from 10 to 14 cm ka^?1 on the lee sides to 17–40 cm ka^?1 on the stoss sides. A layer‐by‐layer correlation of the deposits across the mudwaves shows that the individual turbidite beds are up to 20 times thicker on the stoss side than on the lee side, whereas hemipelagite thicknesses are uniform. This differential accretion of turbidites is thought to have resulted in the pattern of upcurrent climbing mudwave crests, which supports the notion that the mudwaves have been formed by spillover turbidity currents. The mudwaves are interpreted to have been instigated by pre‐existing large sand dunes that are up to 30 m thick and were created by high‐velocity (10°ms^?1), thick (c. 500 m) turbidity currents spilling over the channel banks at the time of the maximum uplift of the Northern Japan Alps during the latest Pliocene to Early Pleistocene. Draping of the dunes by the subsequent, lower‐velocity (10^?1ms^?1), mud‐laden turbidity currents is thought to have resulted in the formation of the accretionary mudwaves and the pattern of upflow climbing. The dune stoss slopes are argued to have acted as obstacles to the flow, causing localized loss of flow strength and leading to differential draping by the muddy turbidites, with greater accretion occurring on the stoss side than on the lee slope. The two overbank flanks of the clockwise channel bend show some interesting differences in mudwave development. The mudwaves have a mean height of 9·8 m on the outer‐bank levee and 6·2 m on the inner bank. The turbidites accreted on the stoss sides of the mudwaves are 4–6 times thicker on the outer‐bank levee than their counterparts on the inner‐bank levee. These differences are attributed to the greater flow volume (thickness) and sediment flux of the outer‐bank spillover flow due to the more intense stripping of the turbidity currents at the outer bank of the channel bend. Differential development of mudwave fields may therefore be a useful indicator in the reconstruction of deep‐sea channels and their flow hydraulics.