Primary cilia are generated through the extension of the microtubule-based axoneme. Centrosomal protein 104 (CEP104) localizes to the tip of the elongating axoneme, and CEP104 mutations are linked to ...a ciliopathy, Joubert syndrome. Thus, CEP104 has been implicated in ciliogenesis. However, the mechanism by which CEP104 regulates ciliogenesis remains elusive. We report here that CEP104 is critical for cilium elongation but not for initiating ciliogenesis. We also demonstrated that the tumor-overexpressed gene (TOG) domain of CEP104 exhibits microtubule-polymerizing activity and that this activity is essential for the cilium-elongating activity of CEP104. Knockdown/rescue experiments showed that the N-terminal jelly-roll (JR) fold partially contributes to cilium-elongating activity of CEP104, but neither the zinc-finger region nor the SXIP motif is required for this activity. CEP104 binds to a centriole-capping protein, CP110, through the zinc-finger region and to a microtubule plus-end–binding protein, EB1, through the SXIP motif, indicating that the binding of CP110 and EB1 is dispensable for the cilium-elongating activity of CEP104. Moreover, CEP104 depletion does not affect CP110 removal from the mother centriole, which suggests that CEP104 functions after the removal of CP110. Last, we also showed that CEP104 is required for the ciliary entry of Smoothened and export of GPR161 upon Hedgehog signal activation and that the TOG domain plays a critical role in this activity. Our results define the roles of the individual domains of CEP104 in its functions in cilium elongation and Hedgehog signaling and should enhance our understanding of the mechanism underlying CEP104 mutation–associated ciliopathies.
Umeda, S., 2013. Scour process around monopiles during various phases of sea storms An understanding of scour processes during the passage of sea storms is particularly important for the design of ...structures and the development of effective scour protection works. This study investigates the scour process at a slender monopile during various phases of a storm to give a better understanding of scour and backfilling mechanisms. Laboratory experiments were carried out to simulate the scouring effect at a pile by a storm consisting of a succession of seven phases of irregular waves. Detailed examinations were conducted to explore variations in the scour depth and bed topography. It turns out that scour patterns resulting from irregular waves can be characterized using the Keulegan-Carpenter number and the Shields parameter (KC1/3, θ1/3), which require significant near-bottom velocities. The scour process during a heavy storm consists of four main phases: (1) no bed deformation, (2) accretion, (3) erosion, and (4) backfilling. The amount of scouring increases as the order of the phase increased during a storm. The scour during phase (2), accretion, is in the transient condition between clear-water scour and live-bed scour. The scour in phase (3), erosion, is distinguished by live-bed scour, horseshoe vortices, vortex shedding and cone-shaped scour holes with vortex ripples. The influence of backfilling, phase (4), as a storm decreases in intensity, has a significant effect on the scour depth around the perimeter of the pile. The scour depth at the end of the event is much lower than the maximum scour depth during the event. However, backfilling of the scour hole makes only a weak recovery in total sediment volume around the pile, because the backfilling is confined almost exclusively to the neighborhood of the pile.
Yuhi, M. and Umeda, S., 2018. Characteristics of systematic migrations of multiple sandbars and related cross-shore sediment transport at Chirihama and adjacent coasts, Japan. In: Shim, J.-S.; Chun, ...I., and Lim, H.S. (eds.), Proceedings from the International Coastal Symposium (ICS) 2018 (Busan, Republic of Korea). Journal of Coastal Research, Special Issue No. 85, pp. 231–235. Coconut Creek (Florida), ISSN 0749-0208. Characteristics of systematic migration of multiple bar system on the Chirihama and adjacent coasts, Japan, have been investigated based on a set of annual field surveys collected over 11 years. The morphological variations were first separated into time-averaged profiles and deviation components. An EOF analysis was conducted on the deviation components in order to extract the principal modes of periodic bar migration. The migration cycle consisting of generation, migration and degeneration were well reproduced by the combination of first and second modes. The cross-shore sediment transport and sediment volume variation related to bar migration were then examined. An integration of the equation for sediment volume conservation revealed that the principal modes of cross-shore sediment transport was characterized by the spatial integration of spatial eigen-functions and the temporal derivative of the temporal eigen-functions. Corresponding to the cyclic behaviors of sandbar system, the direction of sediment transport changed alternatively between seaward and landward directions. On short-term, cyclic exchange of sediment occurred between the bar migration zone and foreshore, but on long-term the principal modes of bar migration made little contribution to overall sediment volume variation.
This study discusses the coastal sediment budget for the Ishikawa coast using 12 years of observational datasets; it involves an understanding the local and regional sediment dynamics, the intensity ...of the transport processes in the region, and sediment supply from a local river. Although alongshore sediment transport and sediment budgets have been analyzed in previous studies, only a few conducted cross-shore sediment transport evaluations. The concentration of suspended sediments will be determined in this study, taking into account the influence of waves that are associated with the coastal current. The cross-shore sediment transport using sediment budget analysis indicated that the net alongshore sediment transport directions in the surf and offshore zones are opposite on the Ishikawa coast. The increase in the sediment budget of the surf zone can be attributed to the river sediment supply and longshore sediment transport inflow. Because of the significant outflow components of longshore and cross-shore sediment transports, the offshore zone budget showed a decreasing trend. A detailed sensitivity study was performed by varying the input parameters, in order to determine the possible ranges of net transport rates and sediment transport to the adjacent coasts. The results demonstrated the possibility of a clockwise residual sediment circulation. Our method can be used to analyze the alongshore sediment transport for other coasts and supplement future studies on coastal sedimentology and sediment budgets.
The hydraulic performance of onshore barriers in response to tsunami and a tsunami-driven shipping container was examined experimentally. For the barriers subjected to tsunami up to twice their ...designed height, experiments with various barrier permeability were conducted to assess the mitigation effect and the concurrent forces on the barrier. The perforated barrier with 30% porosity reduced the momentum flux of the inundation flow behind the barrier by 40–60% even when the water overflowed the barrier. Below the overflow limit, the barrier reduced the fluid force acting on it by 40% of the corresponding force on the impermeable barrier. The force on the perforated barrier was close to half the momentum flux of the incoming inundation. The low-permeability barrier buffered the impact of the drifting shipping container and reduced the impact force on the barrier. The total force induced by the inundation flow associated with the driftage was reduced with decreasing permeability of the barrier. The inverse relation between the impact forces acting on the high- and low-porosity barriers was in contrast to that of the fluid forces. The permeability of wall-type structures has an important influence on inundation mitigation and reduction of the fluid force and the impact force.
•Onshore permeable barriers mitigate tsunami up to twice their height effectively.•Fluid force on the barrier efficiently decreases with increasing barrier porosity.•Low-permeability barriers buffer the impact of tsunami-driven shipping container.•The effects of barrier permeability on the impact force and fluid force are opposite.•Total force caused by tsunami and the driftage varies with permeability and momentum.
Umeda, S.; Yuhi, M., and Karunarathana, H., 2018. Seasonal to Decadal Variability of Shoreline Position on a Multiple Sandbar Beach. In: Shim, J.-S.; Chun, I., and Lim, H.S. (eds.), Proceedings from ...the International Coastal Symposium (ICS) 2018 (Busan, Republic of Korea). Journal of Coastal Research, Special Issue No. 85, pp. 261–265. Coconut Creek (Florida), ISSN 0749-0208. Seasonal to decadal variability of shoreline position at a long multi-barred beach with gentle slopes was investigated using a dataset of biannual shoreline surveys of 23 years. An empirical orthogonal function (EOF) and spectral analysis on 15.2 km long stretch were conducted to describe characteristic patterns of shoreline variation at multiple scales in time and space. A relatively alongshore uniform shoreline migration toward offshore in summer and onshore in winter was dominant in the first EOF mode which secondarily exhibited a long-term trend of shoreline recession. Mid-term shoreline variations related to shoreline sand wave and longshore sandbars were represented by the combinations of the second to sixth EOF modes filtered through two bands of dominant frequency. The shoreline pattern reconstructed on a longer time scale represented a large scale shoreline undulation whose scale and migration speed were comparable to shoreline sand waves observed in various coasts. On the otherhand, the shoreline pattern reconstructed on a shorter time scale represented alongshore uniform shoreline migration toward onshore and offshore in about five-year cycles, which corresponded to the average cycle of net offshore sandbar migration observed at the site. The periodic shoreline recession-advance related to sandbar migration was estimated to be comparable to seasonal scale shoreline variation. A correlation analysis between seasonal scale shoreline variation and wave statistics exhibited that shoreline advance in summer increased with low wave heights. It was suggested that a moderate waves were responsible for seasonal scale shoreline advance in this coast.
Long-term variation in the morphological characteristics of rivers is complicated as a result of temporally and spatially variable natural processes and anthropogenic disturbances. Better ...understanding of their relationship is therefore important for river basin management. The present study conducted a detailed analysis of a long-term dataset consisting of a 58-year topographic survey and related data on human impact to clarify the long-term variation in the morphological characteristics of the lower Tedori River in Japan. An empirical model was established through the assessment of spatiotemporal variations in nonlinear rates of adjustment. The results indicated that sediment extraction and dam construction profoundly affected the morphological characteristics of the lower Tedori River and that the vertical adjustment of the river channel experienced five phases. Degradation occurred from 7 to 16 km upstream from the river mouth over all phases. Two aggradation phases following two degradation phases were observed from the river mouth to 2 km upstream. Aggradation and degradation phases appeared alternately from 2 to 7 km. The representative nonlinear rates of vertical adjustment in the second phase were the highest compared with those in the other phases in the entire reach. The correlation analysis revealed that the incision phase was mostly coupled with channel narrowing, while widening followed the deposition phase. It was deduced from aerial photo analysis and a comparison between slope and empirical critical slope that the pattern in the lower Tedori River was braided during the period 1950–2000.
Abstract An earthquake with a moment magnitude of 7.5 (Mw) struck the northern Noto Peninsula, Ishikawa Prefecture, Japan, at 16:10 local time on January 1, 2024. This earthquake triggered a tsunami ...that propagated along the coastline of Ishikawa, Toyama, and Niigata Prefectures facing the Sea of Japan and significantly damaged coastal communities and infrastructure. Approximately 70 researchers from 23 universities or other institutes throughout Japan formed a joint research group to conduct a post-tsunami survey along a 340 km stretch of the coast. Based on the watermarks and traces of the tsunami, the inundation and run-up heights were surveyed using total stations, automatic optical levels, laser range finders, and a real-time kinematic (RTK) Global Navigation Satellite System (GNSS). The tidal correction was adjusted using astronomical tidal tables. In total, 303 survey records have been compiled, generating the NP2024TS (Noto Peninsula 2024 Tsunami Survey) dataset. This dataset provides comprehensive information on the inundation and run-up heights of the tsunami, which is useful for understanding tsunami characteristics and validating numerical tsunami models.
We observed the growth of the Ga0.80In0.20N (2nm)/GaN (3nm) superlattice (SL) structure by in situ X-ray diffraction (XRD) monitoring. The satellite peaks from the −1st to the +1st order can be ...obtained from these in situ XRD spectrums. From the full width at half maximums (FWHMs) of the 0th and −1st satellite peaks as a function of the SL periods, we observed a clear trend in each FWHM. It was found that by analyzing this trend along with florescence microscopic and transmission electron microscopic analysis, an analysis of the In segregation and misfit dislocation are possible. Accordingly, if we employ in situ XRD under various growth conditions, the optimization of the growth conditions will become easier because it would be possible to determine the number of periods at which In segregation and misfit dislocation increases by only one growth procedure.
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