49 research outputs found
Restriction of retroviral replication by APOBEC3G/F and TRIM5α
No full textPathogenic viral infections have exerted selection pressure on their hosts to evolve cellular antiviral inhibitors referred to as restriction factors. Examples of such molecules are APOBEC3G, APOBEC3F and TRIM5 alpha. APOBEC3G and APOBEC3F are cytidine deaminases that are able to strongly inhibit retroviral replication by at least two mechanisms. They are counteracted by the lentiviral Vif protein. TRIM5a binds to sensitive, incoming retroviruses via its C-terminal PRY/SPRY domain and rapidly recruits them to the proteasome before significant viral DNA synthesis can occur. Both of these proteins robustly block retroviral replication in a species-specific way. It remains an open but important question as to whether innate restriction factors such as these can be harnessed to inhibit HIV-1 replication in humans
On the absence of wind bow-shocks around OB-runaway stars: Probing the physical conditions of the interstellar medium
No full textHigh-resolution IRAS maps are used to search for the
presence of stellar-wind bow-shocks around high-mass X-ray binaries
(HMXBs). Their high space velocities, recently confirmed with Hipparcos observations, combined with their strong stellar winds
should result in the formation of wind bow-shocks. Except for the
already known bow-shock around Vela X-1 (Kaper et al. [CITE]),
we do not find convincing evidence for a bow-shock around any of the
other HMXBs. Also in the case of (supposedly single) OB-runaway stars,
only a minority appears to be associated with a bow-shock (Van Buren
et al. [CITE]). We investigate why wind bow-shocks are
not detected for the majority of these OB-runaway systems: is this due
to the IRAS sensitivity, the system's space velocity, the stellar-wind
properties, or the height above the galactic plane? It turns out that
none of these suggested causes can explain the low detection rate
(~40%). We propose that the conditions of the interstellar
medium mainly determine whether a wind bow-shock is formed or not. In
hot, tenuous media (like inside galactic superbubbles) the sound speed
is high (~100 km s-1), such that many runaways move at subsonic
velocity through a low-density medium, thus preventing the formation
of an observable bow-shock. Superbubbles are expected (and observed)
around OB associations, where the OB-runaway stars were once
born. Turning the argument around, we use the absence (or presence) of
wind bow-shocks around OB runaways to probe the physical conditions of
the interstellar medium in the solar neighbourhood
Sediment transport over sills at longitudinal training dams with unaligned main flow
No full textLongitudinal training dams (LTDs) are constructed in the River Waal in the Netherlands. They are aligned parallel to the river shore and divide the river into a main and side channel. The existing groynes are removed yielding more discharge capacity at high flows. The side channel creates possibly a sheltered environment for species compared to the traditional groyne field (Collas, 2014). Although the lay-out of the LTDs has been extensively studied using numerical models (e.g. Huthoff et al., 2011), the morphodynamic response is yet unclear and depends strongly on the dimensions (length and height) of the openings. The inlet and openings (see Fig. 1) are sill-type structures which can be changed relatively easy. These sills are designed in such a way that they serve as a barrier for water and bed load sediment. To make long-term morphological predictions, it is necessary to understand the bed load transport processes over these sills. Suspended sediment transport is not considered in this study. We developed an analytical model to predict sediment transport paths on a slope, using a correction on the well-known critical Shields parameter. </p
The effect of hydraulic roughness on design water levels in river models
No full textAccurate estimates of design water levels are essential, because they determine the required dimensions of the flood defences. Hydrodynamic models are used for the prediction of flood water levels to support flood safety and are often applied in a deterministic way. However, the modelling of river processes involves numerous uncertainties. Literature has shown that the hydraulic roughness is one of the main sources of uncertainty in hydrodynamic computations. Knowledge of the type and magnitude of uncertainties is crucial for a meaningful interpretation of the model outcomes and their usefulness in decision making. We show that the uncertainty of a complex model factor, such as the hydraulic roughness, can be quantified explicitly. The hydraulic roughness has been unravelled in separate components, which have been quantified separately and then combined and propagated through the model. Expert opinions revealed that the uncertainty due to bed form roughness in the main channel and vegetation roughness in the floodplains were shown to be the major contributors. Quantifica-tion of these sources and propagation through the WAQUA model using Monte Carlo analyses showed that this resulted in a 95% confidence interval around the Design Water Levels (DWL) of 68 cm for the river Waal. This uncertainty range consisted of the uncertainty due to bed forms with an uncertainty of 49 cm on the DWL, and an uncertainty of 34 cm due to vegetation roughness uncertainty. The main source of uncertainty was shown to be the variability of the roughness values depending on the various possible roughness models
Effects of a river intervention on water levels in a bifurcating river system
No full textIn bifurcating river systems, river interventions affect the water levels in all of the downstream branches. An accurate impact quantification is therefore import ant. However, the hydraulic models used to estimate these impacts are inherently uncer tain. This study assesses the impact of a dike set-back and its uncertainty in a bifurcating river system using a 1D network model. The results show that the presence of the river bifurcation strongly decreases the maximum water level reduction and the uncertainty of it. Generally, the uncertainty of the impact scales with the impact itself. However, in a bifurcating river system, the hydraulic roughness parameters that cause the uncertainty in the impact, also have an own influence on the discharge distribution. These interactions all affect the uncertainty of the impact in a bifurcating river system. The knowledge on these interactions can aid in the decision process for the future design of interventions near bifurcations
Hydrodynamic modelling with unstructured grid using D-Flow-FM: case study Afferden-Deest
No full textAccurate predictions of water levels play an important role in the management of flood safety. Nowadays, it has become common practice to use multi-dimensional numerical hydrodynamic models for such purposes. Currently, two model types are the standard tools in the Netherlands, namely WAQUA/TRIWAQ (Rijkswaterstaat, 2012) and Delft3D (Deltares, 2014). WAQUA and Delft3D are both based on a structured curvilinear grid, which can follow large-scale topographical changes and uses similar grid resolution throughout the entire computational domain. Drawbacks of the structured curvilinear grid approach are that elevation jumps in the river's topography may lead to unrealistic staircase representations in the model, and the inner bends of meandering rivers gridlines may become focussed to unnecessarily small grid cells (Kernkamp et al., 2011). To improve on these issues, Deltares is developing the unstructured-grid-based hydrodynamic model Flexible Mesh (also referred to as “D-Flow-FM”). The unstructured grid approach enables the user to use a spatially variable grid resolution. By combining curvilinear grid cells with triangular grid cells, the modeller can increase grid resolution on the locations where, because of local topographical variations, it is most desired. In this study, modelling results of Flexible Mesh and WAQUA are presented for a selected river reach near Afferden-Deest and benefits of local grid refinements in Flexible Mesh are demonstrated
