Differential Gene Expression Patterns of Male Sterile Lines of Alfalfa Hybrids at Bud Differentiation Stage and Heterosis

Alfalfa (Medicago sativa L.) is important legume forage that is widely cultivated in China and other countries. Alfalfa breeding can’t meet the need of production now, highlighted in yield and resistance of current alfalfa cultivars (He et al., 2000; Wei et al., 2007). Increasing heterozygosity of hybrids and thus the heterosis is a way to breed alfalfa cultivars with high yield and resistance (Hong et al., 2009). The objective of this study was to investigate the correlations of various differential gene expression patterns with forage yield in order to better understand the role the alfalfa male sterile lines may play in the heterosis of their progeny

Hydrodynamic and sediment transport modeling of New River Inlet (NC) under the interaction of tides and waves

Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 120 (2015): 4028–4047, doi:10.1002/2014JC010425.The interactions between waves, tidal currents, and bathymetry near New River Inlet, NC, USA are investigated to understand the effects on the resulting hydrodynamics and sediment transport. A quasi-3-D nearshore community model, NearCoM-TVD, is used in this integrated observational and modeling study. The model is validated with observations of waves and currents at 30 locations, including in a recently dredged navigation channel and a shallower channel, and on the ebb tidal delta, for a range of flow and offshore wave conditions during May 2012. In the channels, model skills for flow velocity and wave height are high. Near the ebb tidal delta, the model reproduces the observed rapid onshore (offshore) decay of wave heights (current velocities). Model results reveal that this sharp transition coincides with the location of the breaker zone over the ebb tidal delta, which is modulated by semidiurnal tides and by wave intensity. The modulation of wave heights is primarily owing to depth changes rather than direct wave-current interaction. The modeled tidally averaged residual flow patterns show that waves play an important role in generating vortices and landward-directed currents near the inlet entrance. Numerical experiments suggest that these flow patterns are associated with the channel-shoal bathymetry near the inlet, similar to the generation of rip currents. Consistent with other inlet studies, model results suggest that tidal currents drive sediment fluxes in the channels, but that sediment fluxes on the ebb tidal delta are driven primarily by waves.Funding was provided by the Office of Naval Research (N00014-13-1–0120 and N00014-14-1-0586) and the Office of the Assistant Secretary of Defense for Research and Engineering.2015-12-0

Tidal flow asymmetry owing to inertia and waves on an unstratified, shallow ebb shoal

Author Posting. © American Geophysical Union, 2018. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 123 (2018): 6779-6799, doi:10.1029/2017JC013625.Observations of water levels, waves, currents, and bathymetry collected for a month at an unstratified tidal inlet with a shallow (1 to 2 m deep) ebb shoal are used to evaluate the asymmetry in flows and dynamics owing to inertia and waves. Along‐channel currents ranged from −1.5 to 0.6 m/s (positive inland) inside the main (3 to 5 m deep) channel crossing the ebb shoal. Net discharge is negligible, and ebb dominance of the channel flows is owing to inflow and outflow asymmetries near the inlet mouth. Offshore wave heights ranged from 0.5 to 2.5 m. During moderate to large wave events (offshore significant wave heights >1.2 m), wave forcing enhanced onshore mass flux near the shoal edge and inside the inlet, leading to reduced ebb flow dominance. Momentum balances estimated with the water depths, currents, and waves simulated with a quasi 3‐D numerical model reproduce the momentum balances estimated from the observations reasonably well. Both observations and simulations suggest that ebb‐dominant bottom stresses are balanced by the ebb‐dominant pressure gradient and the tidally asymmetric inertia, which is a sink (source) of momentum on flood (ebb). Simulations with and without waves suggest that waves drive local and nonlocal changes in the water levels and flows. Specifically, breaking waves at the offshore edge of the ebb shoal induce setup and partially block the ebb jet (local effects), which leads to a more onshore‐directed mass flux, changes to the advection across the ebb shoal, and increased water levels inside the inlet mouth (nonlocal effects).WHOI Coastal Ocean Institute Student Research; Office of the Assistant Secretary of Defense for Research and Engineering; National Defense Science and Engineering; National Science Foundation; Office of Naval Research2019-03-2

On nonhydrostatic coastal model simulations of shear instabilities in a stratified shear flow at high Reynolds number

Author Posting. © American Geophysical Union, 2017. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 122 (2017): 3081–3105, doi:10.1002/2016JC012334.The nonhydrostatic surface and terrain-following coastal model NHWAVE is utilized to simulate a continually forced stratified shear flow in a straight channel, which is a generic problem to test the existing nonhydrostatic coastal models' capability in resolving shear instabilities in the field scale. The resolved shear instabilities in the shear layer has a Reynolds number of about 1.4 × 106, which is comparable to field observed value. Using the standard Smagorinsky closure with a grid size close to the Ozmidov length scale, simulation results show that the resolved energy cascade exceeds 1 order of magnitude and the evolution and turbulent mixing characteristics are predicted well. Two different approaches are used to estimate the turbulent dissipation rate, namely using the resolved turbulent energy spectrum and the parameterized subgrid turbulent dissipation rate, and the predicted results provide the upper and lower bounds that encompass the measured values. Model results show significantly higher turbulence in braids of shear instabilities, which is similar to field observations while both the subgrid turbulent dissipation rate and resolved vorticity field can be used as surrogates for measured high acoustic backscatter signals. Simulation results also reveal that the surface velocity divergence/convergence is an effective identifier for the front of the density current and the shear instabilities. To guide future numerical studies in more realistic domains, an evaluation on the effects of different grid resolutions and subgrid viscosity on the resolved flow field and subgrid dissipation rate are discussed.Office of Naval Research Grant Numbers: N00014-15-1-2612 , N00014-16-1-2948; National Science Foundation Grant Numbers: OCE-1334325 , OCE-1232928; Extreme Science and Engineering Discovery Environment (XSEDE) SuperMIC Grant Number: TG-OCE1000152017-10-1

Block-structured, equal-workload, multi-grid-nesting interface for the Boussinesq wave model FUNWAVE-TVD (Total Variation Diminishing)

We describe the development of a block-structured, equal-CPU-load (central processing unit), multi-grid-nesting interface for the Boussinesq wave model FUNWAVE-TVD (Fully Nonlinear Boussinesq Wave Model with Total Variation Diminishing Solver). The new model framework does not interfere with the core solver, and thus the core program, FUNWAVE-TVD, is still a standalone model used for a single grid. The nesting interface manages the time sequencing and two-way nesting processes between the parent grid and child grid with grid refinement in a hierarchical manner. Workload balance in the MPI-based (message passing interface) parallelization is handled by an equal-load scheme. A strategy of shared array allocation is applied for data management that allows for a large number of nested grids without creating additional memory allocations. Four model tests are conducted to verify the nesting algorithm with assessments of model accuracy and the robustness in the application in modeling transoceanic tsunamis and coastal effects

Did a submarine landslide contribute to the 2011 Tohoku tsunami?

Many studies have modeled the Tohoku tsunami of March 11, 2011 as being due entirely to slip on an earthquake fault, but the following discrepancies suggest that further research is warranted. (1) Published models of tsunami propagation and coastal impact underpredict the observed runup heights of up to 40 m measured along the coast of the Sanriku district in the northeast part of Honshu Island. (2) Published models cannot reproduce the timing and high-frequency content of tsunami waves recorded at three nearshore buoys off Sanriku, nor the timing and dispersion properties of the waveforms at offshore DART buoy #21418. (3) The rupture centroids obtained by tsunami inversions are biased about 60 km NNE of that obtained by the Global CMT Project. Based on an analysis of seismic and geodetic data, together with recorded tsunami waveforms, we propose that, while the primary source of the tsunami was the vertical displacement of the seafloor due to the earthquake, an additional tsunami source is also required. We infer the location of the proposed additional source based on an analysis of the travel times of higher-frequency tsunami waves observed at nearshore buoys. We further propose that the most likely additional tsunami source was a submarine mass failure (SMF—i.e., a submarine landslide). A comparison of pre- and post-tsunami bathymetric surveys reveals tens of meters of vertical seafloor movement at the proposed SMF location, and a slope stability analysis confirms that the horizontal acceleration from the earthquake was sufficient to trigger an SMF. Forward modeling of the tsunami generated by a combination of the earthquake and the SMF reproduces the recorded on-, near- and offshore tsunami observations well, particularly the high-frequency component of the tsunami waves off Sanriku, which were not well simulated by previous models. The conclusion that a significant part of the 2011 Tohoku tsunami was generated by an SMF source has important implications for estimates of tsunami hazard in the Tohoku region as well as in other tectonically similar regions

Runup of landslide-generated tsunamis controlled by paleogeography and sea-level change

Abstract: Pre-Holocene landslides and tsunami deposits are commonly observed on continental margins and oceanic islands. However, scarce evidence has thus far linked pre-historic submarine landslides to particular tsunami events. This work focuses on an 839 km3 submarine landslide that occurred in the South China Sea at 0.54 Ma. Bathymetric restorations show that the paleoshoreline at 0.54 Ma was 180–580 km to the south of its present-day location. In such a setting, the tsunami triggered by the landslide at 0.54 Ma was able to generate larger waves with shorter arrive times when compared to an equivalent landslide-generated tsunami under present-day conditions. This observation proves that tsunamis generated by submarine landslides during sea-level lowstands caused catastrophic damage to the South China Sea coast in the past, and so will do in future sea-level lowstands. This study stresses the importance of restoring paleoshorelines for detailed analysis of historic landslide-generated tsunamis

Tide-surge Interaction Intensified by the Taiwan Strait

The Taiwan Strait is a long and wide shelf-channel where the hydrodynamics is extremely complex, being characterized by strong tides, and where storm surges frequently occur during the typhoon season. Obvious oscillations due to tide-surge interaction were observed by tide gauges along the northern Fujian coast, the west bank of the Taiwan Strait, during Typhoon Dan (1999). Numerical experiments indicate that nonlinear bottom friction (described by the quadratic formula) is a major factor to predict these oscillations while the nonlinear advective terms and the shallow water effect have little contribution. It is found that the tide-surge interaction in the northern portion of the Taiwan Strait is intensified by the strait. Simulations based on simplified topographies with and without the island of Taiwan show that, in the presence of the island, the channel effect strengthens tidal currents and tends to align the major axes of tidal ellipses along the channel direction. Storm-induced currents are also strengthened by the channel. The pattern of strong tidal currents and storm induced currents along the channel direction enhances tide-surge interaction via the nonlinear bottom friction, resulting in the obvious oscillations along the northern Fujian coast.Science Foundation of Fujian Province [2009J01223]; National High-tech RD Program [2006AA09A302-6]; National Oceanographic Partnership Program [N00014-06-1-0945

miR-200 Enhances Mouse Breast Cancer Cell Colonization to Form Distant Metastases

BACKGROUND: The development of metastases involves the dissociation of cells from the primary tumor to penetrate the basement membrane, invade and then exit the vasculature to seed, and colonize distant tissues. The last step, establishment of macroscopic tumors at distant sites, is the least well understood. Four isogenic mouse breast cancer cell lines (67NR, 168FARN, 4TO7, and 4T1) that differ in their ability to metastasize when implanted into the mammary fat pad are used to model the steps of metastasis. Only 4T1 forms macroscopic lung and liver metastases. Because some miRNAs are dysregulated in cancer and affect cellular transformation, tumor formation, and metastasis, we examined whether changes in miRNA expression might explain the differences in metastasis of these cells. METHODOLOGY/PRINCIPAL FINDINGS: miRNA expression was analyzed by miRNA microarray and quantitative RT-PCR in isogenic mouse breast cancer cells with distinct metastatic capabilities. 4T1 cells that form macroscopic metastases had elevated expression of miR-200 family miRNAs compared to related cells that invade distant tissues, but are unable to colonize. Moreover, over-expressing miR-200 in 4TO7 cells enabled them to metastasize to lung and liver. These findings are surprising since the miR-200 family was previously shown to promote epithelial characteristics by inhibiting the transcriptional repressor Zeb2 and thereby enhancing E-cadherin expression. We confirmed these findings in these cells. The most metastatic 4T1 cells acquired epithelial properties (high expression of E-cadherin and cytokeratin-18) compared to the less metastatic cells. CONCLUSIONS/SIGNIFICANCE: Expression of miR-200, which promotes a mesenchymal to epithelial cell transition (MET) by inhibiting Zeb2 expression, unexpectedly enhances macroscopic metastases in mouse breast cancer cell lines. These results suggest that for some tumors, tumor colonization at metastatic sites might be enhanced by MET. Therefore the epithelial nature of a tumor does not predict metastatic outcome