Modeling hydrography and marine sedimentation in the Cariaco Basin since the Last Glacial Maximum

The Cariaco Basin has shallow connections with the Caribbean Sea, and these are further reduced at times of lower sea level, such as at the Last Glacial Maximum (LGM). A numerical model was developed to describe the oceanography and biogenic sedimentation in the Cariaco Basin and nearby Caribbean. The model is run with different sea levels in order to simulate the changing oceanography and the development of deep water anoxia in the Cariaco Basin since the LGM. In the main sequence of numerical experiments, the surface forcing is kept fixed at present?day values while the sea level is changed in order to separate the effects of sea level from the effects of climate. As the sea level rises, the main sedimentation zone moves first to the shallow broad northern sill and NE part of the Cariaco Basin and then, once sea level reaches approximately 60 m below present, moves south to the northern coast of mainland Venezuela. The model shows that there would be an overall increase in sedimentation in the basin as the sea level rises, even if there was no change in the surface forcing. However, the model also shows that sedimentation at particular points in the basin exhibits more complicated behavior, which needs to be taken into account when interpreting individual records. Preliminary numerical experiments examine the effects of changing surface forcing while keeping the sea level at LGM values, and the applicability of a mathematical hydraulic control model in this case is also considered

Deposition of cohesive sediment from turbulent plumes, gravity currents, and turbidity currents

Models for the deposition of cohesive sediment from turbulent plumes (or “buoyant jets”), gravity currents, and turbidity currents are provided in this paper. The cohesive sediment is made up of small particles that aggregate together to form larger flocs, which are in turn broken up by turbulent shear. The equilibrium mean floc size (and thus the equilibrium mean fall speed) is a function of the turbulent dissipation rate and the sediment concentration. The flows are modeled by using integral and box models, with dissipation related to bulk flow properties. For plumes it is shown that there is a well-defined equilibrium fall speed at the virtual origin and that the fall speed changes relatively slowly in the momentum-dominated part of the flow (within one jet length or so of the source). If the flocs are assumed to adjust instantaneously to their equilibrium size, an integral model for a turbulent plume carrying cohesive sediment can be described in terms of two parameters: the angle between the plume and the horizontal at the virtual origin and the (nondimensional) fall speed there. Next, a typical time scale for flocs to adjust to their equilibrium size is identified, and the model is extended to include an equation for the rate of change of the mean floc size along the plume. The time scale over which the mean floc size changes can be compared with a natural time scale for the plume (the time taken for a particle traveling at the mean plume speed to travel a jet length). Thus, in this nonequilibrium model, a further nondimensional parameter is identified, B, which is proportional to the ratio of a typical plume time scale to the typical floc size adjustment time scale. When B is large, the flocs adjust almost instantaneously to the equilibrium size, whereas when B is very small, the flocs remain close to their size at the source. However, whatever the value of B (which is in terms of typical time scales), the local adjustment time scale always tends to zero approaching an idealized source (virtual origin) so that the equilibrium model is always valid there. For plumes injected horizontally, the equilibrium floc size tends to reduce with distance from the source, with any reduction in turbulent shear more than compensated for by the reduction in sediment concentration. The equilibrium model is then applied to two-dimensional and axisymmetric gravity currents and turbidity currents. The gravity currents are assumed to be steady flows driven by a constant source of dense fluid with the sediment having a negligible effect on the fluid density. In contrast, the turbidity currents modeled are initiated by the release of a finite volume of fluid containing the sediment, with the sediment concentration providing the density difference from the ambient fluid. For these flows, the basic scales are identified, and the concentration and deposition distributions given

A Receptor's Tale: An Eon in the Life of a Trypanosome Receptor

African trypanosomes have complex life cycles comprising at least ten developmental forms, variously adapted to different niches in their tsetse fly vector and their mammalian hosts. Unlike many other protozoan pathogens, they are always extracellular and have evolved intricate surface coats that allow them to obtain nutrients while also protecting them from the immune defenses of either insects or mammals. The acquisition of macromolecular nutrients requires receptors that function within the context of these surface coats. The best understood of these is the haptoglobin-hemoglobin receptor (HpHbR) of $\textit{Trypanosoma brucei}$, which is used by the mammalian bloodstream form of the parasite, allowing heme acquisition. However, in some primates it also provides an uptake route for trypanolytic factor-1, a mediator of innate immunity against trypanosome infection. Recent studies have shown that during the evolution of African trypanosome species the receptor has diversified in function from a hemoglobin receptor predominantly expressed in the tsetse fly to a haptoglobin-hemoglobin receptor predominantly expressed in the mammalian bloodstream. Structural and functional studies of homologous receptors from different trypanosome species have allowed us to propose an evolutionary history for how one receptor has adapted to different roles in different trypanosome species. They also highlight the challenges that a receptor faces in operating on the complex trypanosome surface and show how these challenges can be met.This has been funded by the Medical Research Council (Grant reference MR/L008246/1) and the Wellcome Trust (reference: 101020/Z/13/Z)

Laboratory observations of enhanced entrainment in dense overflows in the presence of submarine canyons and ridges

Author Posting. © Elsevier B.V., 2008. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part I: Oceanographic Research Papers 55 (2008): 737-750, doi:10.1016/j.dsr.2008.02.007.The continental slopes in the oceans are often covered by small-scale topographic features such as submarine canyons and ridges. When dense plumes, flowing geostrophically along the slope, encounter such features they may be steered downslope inside and alongside the topography. A set of laboratory experiments was conducted at the rotating Coriolis platform to investigate the effect of small-scale topography on plume mixing. A dense water source was placed on top of a slope, and experiments were repeated with three topographies: a smooth slope, a slope with a ridge, and a slope with a canyon. Three flow regimes were studied: laminar, waves, and eddies. When a ridge or a canyon were present on the slope, the dense plume was steered downslope and instabilities developed along the ridge and canyon wall. This happened regardless of the flow characteristics on the smooth slope. Froude and Reynolds numbers were estimated, and were found to be higher for the topographically steered flow than for flow on smooth topography. The stratification in the collecting basin was monitored and the mixing inferred. The total mixing and the entrainment rate increased when a ridge or a canyon were present. The difference in mixing levels between the regimes was smaller when topography was present, indicating that it was the small-scale topography and not the large-scale characteristics of the flow that determined the properties of the product water.AW was funded by the Swedish Research Council and ED in part by Meltzer Stiftelsen, for which we are grateful. CC was supported by an NSF grant OCE-0085089. The work described in this publication was supported by the European Community's Sixth Framework Programme through the grant to the budget of the Integrated Infrastructure Initiative HYDRALAB III, Contract no. 022441 (RII3)

Evolutionary diversification of the trypanosome haptoglobin-haemoglobin receptor from an ancestral haemoglobin receptor.

The haptoglobin-haemoglobin receptor of the African trypanosome species, Trypanosoma brucei, is expressed when the parasite is in the bloodstream of the mammalian host, allowing it to acquire haem through the uptake of haptoglobin-haemoglobin complexes. Here we show that in Trypanosoma congolense this receptor is instead expressed in the epimastigote developmental stage that occurs in the tsetse fly, where it acts as a haemoglobin receptor. We also present the structure of the T. congolense receptor in complex with haemoglobin. This allows us to propose an evolutionary history for this receptor, charting the structural and cellular changes that took place as it adapted from a role in the insect to a new role in the mammalian host.Medical Research Counci

Structure and variability of the Denmark Strait Overflow: Model and observations

We report on a combined modeling and observational effort to understand the Denmark Strait Overflow (DSO). Four cruises over the course of 3 years mapped hydrographic properties and velocity fields with high spatial resolution. The observations reveal the mean path of the dense water, as well as the presence of strong barotropic flows, energetic variability, and strong bottom friction and entrainment. A regional sigma coordinate numerical model of interbasin exchange using realistic bottom topography and an overflow forced only by an upstream reservoir of dense fluid is compared with the observations and used to further investigate these processes. The model successfully reproduces the volume transport of dense water at the sill, as well as the 1000-m descent of the dense water in the first 200 km from the sill and the intense eddies generated at 1–3 day intervals. Hydraulic control of the mean flow is indicated by a region supercritical to long gravity waves in the dense layer located approximately 100 km downstream of the sill in both model and observations. In addition, despite the differences in surface forcing, both model and observations exhibit similar transitions from mostly barotropic flow at the sill to a bottom-trapped baroclinic flow downstream, indicating the dominant role of the overflow in determining the full water column dynamics

The upper-oceanic response to overflows : a mechanism for the Azores Current

Author Posting. © American Meteorological Society, 2008. This article is posted here by permission of American Meteorological Society for personal use, not for redistribution. The definitive version was published in Journal of Physical Oceanography 38 (2008): 880–895, doi:10.1175/2007JPO3750.1.The oceanic response to overflows is explored using a two-layer isopycnal model. Overflows enter the open ocean as dense gravity currents that flow along and down the continental slope. While descending the slope, overflows typically double their volume transport by entraining upper oceanic water. The upper oceanic layer must balance this loss of mass, and the resulting convergent flow produces significant vortex stretching. Overflows thus represent an intense and localized mass and vorticity forcing for the upper ocean. In this study, simulations show that the upper ocean responds to the overflow-induced forcing by establishing topographic β plumes that are aligned more or less along isobaths and that have a transport that is typically a few times larger than that of the overflows. For the topographic β plume driven by the Mediterranean overflow, the occurrence of eddies near Cape St. Vincent, Portugal, allows the topographic β plume to flow across isobaths. The modeled topographic β-plume circulation forms two transatlantic zonal jets that are analogous to the Azores Current and the Azores Countercurrent. In other cases (e.g., the Denmark Strait overflow), the same kind of circulation remains trapped along the western boundary and hence would not be readily detected.SK’s support during the time of his Ph.D. research in the MIT/WHOI Joint Program was provided by the National Science Foundation through Grant OCE04-24741. JP and JY have also received support from the Climate Process Team on Gravity Current Entrainment, NSF Grant OCE-0611530