HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation.

The internal ribosome entry site (IRES) of the hepatitis C virus (HCV) drives noncanonical initiation of protein synthesis necessary for viral replication. Functional studies of the HCV IRES have focused on 80S ribosome formation but have not explored its role after the 80S ribosome is poised at the start codon. Here, we report that mutations of an IRES domain that docks in the 40S subunit's decoding groove cause only a local perturbation in IRES structure and result in conformational changes in the IRES-rabbit 40S subunit complex. Functionally, the mutations decrease IRES activity by inhibiting the first ribosomal translocation event, and modeling results suggest that this effect occurs through an interaction with a single ribosomal protein. The ability of the HCV IRES to manipulate the ribosome provides insight into how the ribosome's structure and function can be altered by bound RNAs, including those derived from cellular invaders

The formation and fate of internal waves in the South China Sea

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature 521 (2015): 65-69, doi:10.1038/nature14399.Internal gravity waves, the subsurface analogue of the familiar surface gravity waves that break on beaches, are ubiquitous in the ocean. Because of their strong vertical and horizontal currents, and the turbulent mixing caused by their breaking, they impact a panoply of ocean processes, such as the supply of nutrients for photosynthesis1, sediment and pollutant transport2 and acoustic transmission3; they also pose hazards for manmade structures in the ocean4. Generated primarily by the wind and the tides, internal waves can travel thousands of kilometres from their sources before breaking5, posing severe challenges for their observation and their inclusion in numerical climate models, which are sensitive to their effects6-7. Over a decade of studies8-11 have targeted the South China Sea, where the oceans’ most powerful internal waves are generated in the Luzon Strait and steepen dramatically as they propagate west. Confusion has persisted regarding their generation mechanism, variability and energy budget, however, due to the lack of in-situ data from the Luzon Strait, where extreme flow conditions make measurements challenging. Here we employ new observations and numerical models to (i) show that the waves begin as sinusoidal disturbances rather than from sharp hydraulic phenomena, (ii) reveal the existence of >200-m-high breaking internal waves in the generation region that give rise to turbulence levels >10,000 times that in the open ocean, (iii) determine that the Kuroshio western boundary current significantly refracts the internal wave field emanating from the Luzon Strait, and (iv) demonstrate a factor-of-two agreement between modelled and observed energy fluxes that enables the first observationally-supported energy budget of the region. Together, these findings give a cradle-to-grave picture of internal waves on a basin scale, which will support further improvements of their representation in numerical climate predictions.Our work was supported by the U.S. Office of Naval Research and the Taiwan National Science Council.2015-10-2

The formation and fate of internal waves in the South China Sea

Internal gravity waves, the subsurface analogue of the familiar surface gravity waves that break on beaches, are ubiquitous in the ocean. Because of their strong vertical and horizontal currents, and the turbulent mixing caused by their breaking, they affect a panoply of ocean processes, such as the supply of nutrients for photosynthesis¹, sediment and pollutant transport² and acoustic transmission³; they also pose hazards for man-made structures in the ocean⁴. Generated primarily by the wind and the tides, internal waves can travel thousands of kilometres from their sources before breaking⁵, making it challenging to observe them and to include them in numerical climate models, which are sensitive to their effects[superscript 6,7]. For over a decade, studies[superscript 8–11] have targeted the South China Sea, where the oceans’ most powerful known internal waves are generated in the Luzon Strait and steepen dramatically as they propagate west. Confusion has persisted regarding their mechanism of generation, variability and energy budget, however, owing to the lack of in situ data from the Luzon Strait, where extreme flow conditions make measurements difficult. Here we use new observations and numerical models to (1) show that the waves begin as sinusoidal disturbances rather than arising from sharp hydraulic phenomena, (2) reveal the existence of >200-metre-high breaking internal waves in the region of generation that give rise to turbulence levels >10,000 times that in the open ocean, (3) determine that the Kuroshio western boundary current noticeably refracts the internal wave field emanating from the Luzon Strait, and (4) demonstrate a factor-of-two agreement between modelled and observed energy fluxes, which allows us to produce an observationally supported energy budget of the region. Together, these findings give a cradle-to-grave picture of internal waves on a basin scale, which will support further improvements of their representation in numerical climate predictions

Numerical studies of flow over a sill: sensitivity of the non-hydrostatic effects to the grid size

A non-hydrostatic terrain-following model in cross sectional form is applied to study the processes in the lee of a sill in an idealized stratified fjord during super-critical tidal inflow. A sequence of numerical studies with horizontal grid sizes in the range from 100 to 1.5625 m are performed. All experiments are repeated using both hydrostatic and non-hydrostatic versions of the model, allowing a systematic study of possible non-hydrostatic pressure effects and also of the sensitivity of these effects to the horizontal grid size. The length scales and periods of the internal waves in the lee of the sill are gradually reduced and the amplitudes of these waves are increased as the grid size is reduced from 100 down to 12.5 m. With a further reduction in grid size, more short time and space scale motions become superimposed on the internal waves. Associated with the internal wave activity, there is a deeper separation point that is fairly robust to all parameters investigated. Another separation point nearer to the top of the sill appears in the numerical results from the high-resolution studies with the non-hydrostatic model. Associated with this shallower separation point, an overturning vortex appears in the same set of numerical solutions. This vortex grows in strength with reduced grid size in the non-hydrostatic experiments. The effects of the non-hydrostatic pressure on the velocity and temperature fields grow with reduced grid size. In the experiments with horizontal grid sizes equal to 100 or 50 m, the non-hydrostatic pressure effects are small. For smaller grid sizes, the time mean velocity and temperature fields are also clearly affected by the non-hydrostatic pressure adjustments