Dynamics of the Indonesian seas circulation. Part II – The role of pressure head

The aim of this paper is to analyze the role of the pressure head, i.e., the difference of total pressure forces acting on the Indonesian seas waters from the western Pacific and the eastern Indian Ocean, in driving the Indonesian Throughflow (ITF) and in determining the total transport of the ITF. These questions have been discussed in the literature but no consensus has been reached. A regional model of the Indonesian seas circulation has been developed that properly resolves all major topographic features in the region. The results of model runs have been used to calculate all components of the overall momentum balance. The estimates disclose that the dynamical balance is primarily between the volume integrated Coriolis acceleration, pressure gradient and the area integral of local wind stress. It is shown that consideration of components of momentum balance in the direction of the outflow through the Indian Ocean port leads to the formulation of a diagnostic relation between total inflow transports due to the Mindanao and New Guinea Coastal Currents and the external pressure head, internal pressure head, bottom form stress, and area integrated wind stress. Based on this relation, it is concluded that the external pressure head is not the major driving force of the ITF, which is why there is no unique relation between the total transport of the ITF and the external pressure head. However, Wyrtki's suggestion to monitor the variability of the total transport of the ITF by measurement of the sea-surface-height difference between the western Pacific and the eastern Indian Ocean is validated.

Dynamics of the Indonesian seas circulation. Part I – The influence of bottom topography on temperature and salinity distributions

The influence of bottom topography on the distribution of temperature and salinity in the Indonesian seas region has been studied with a high-resolution model based on the Princeton Ocean Model. One of the distinctive properties of the model is an adequate reproduction of all major topographic features in the region by the model bottom relief. The three major routes of flow of Pacific water through the region have been identified. The western route follows the flow of North Pacific Water through the Sulawesi Sea, Makassar Strait, Flores Sea, and Banda Sea. This is the main branch of the Indonesian Throughflow. The eastern routes follow the flow of South Pacific water through the eastern Indonesian seas. This water enters the region either through the Halmahera Sea or by flowing to the north around Halmahera Island into the Morotai Basin and then into the Maluku Sea. A deep southward flow of South Pacific Water fills the Seram Sea below 1200 m through the Lifamatola Passage. As it enters the Seram Sea, this overflow turns eastward at depths greater than 2000 m, then upwells in the eastern part of the Seram Sea before returning westward at ~1500-2000 m. The flow continues westward across the Seram Sea, spreading to greater depths before entering the Banda Sea at the Buru-Mangole passage. It is this water that shapes the temperature and salinity of the deep Banda Sea. Topographic elevations break the Indonesian seas region down into separate basins. The difference in the distributions of potential temperature, ?, and salinity, S, in adjacent basins is primarily due to specific properties of advection of ? and S across a topographic rise. By and large, the topographic rise blocks deep flow between basins whereas water shallower than the depth of the rise is free to flow between basins. To understand this process, the structure of simulated fields of temperature and salinity has been analyzed. To identify a range of advected ? or S, special sections over the sills with isotherms or isohalines and isotachs of normal velocity have been considered. Following this approach the impact of various topographic rises on the distribution of ? and S has been identified. There are no substantial structural changes of potential temperature and salinity distributions between seasons, though values of some parameters of temperature and salinity distributions, e.g., magnitudes of maxima and minima, can change. It is shown that the main structure of the observed distributions of temperature and salinity is satisfactorily reproduced by the model throughout the entire domain.

Towards a better understanding of the nature and contribution of the interflow to catchment dynamics.

A detailed understanding of flow and contaminant transfer along each of the key hydrological pathways within a catchment is critical for designing and implementing cost effective Programmes of Measures under the Water
Framework Directive.
The Contaminant Movement along Pathways Project (’The Pathways Project’) is an Irish, EPA STRIVE funded, large multi-disciplinary project which is focussed on understanding and modelling flow and attenuation along each of these pathways for the purposes of developing a catchment management tool. The tool will be used by EPA and RBD catchment managers to assess and manage the impacts of diffuse contamination on stream aquatic ecology. Four main contaminants of interest — nitrogen, phosphorus, sediment and pathogens — are being
investigated in four instrumented test catchments. In addition to the usual hydrological and water chemistry/quality parameters typically captured in catchment studies, field measurements at the test catchments include ecological
sampling, sediment dynamics, soil moisture dynamics, and groundwater levels and chemistry/quality, both during and between significant rainfall events. Spatial and temporal sampling of waters directly from the pathways of
interest is also being carried out.
Sixty-five percent of Ireland is underlain by poorly productive aquifers. In these hydrogeological settings, the main pathways delivering flow to streams are overland flow, interflow and shallow bedrock flow. Little is
known about the interflow pathway and its relative importance in delivery of flow and contaminants to the streams. Interflow can occur in both the topsoil and subsoil, and may include unsaturated matrix flow, bypass or macropore
flow, saturated flow in locally perched water tables and artificial field drainage.
Results to date from the test catchment experiments show that artificial field drains play an important role in the delivery of interflow to these streams, during and between rainfall events when antecedent conditions are
favourable. Hydrochemical mixing models, using silica and SAC254 (the absorbance of UV light at a wavelength of 254 nm which is a proxy for dissolved organic matter) as tracers, show that drain flow is an important end
member contributing to the stream and that proportionally, its contribution is relatively high.
Results from the study also demonstrate that waters originating from one pathway often mix with the waters from another, and are subsequently delivered to the stream at rates, and with chemical/quality characteristics,
that are not typical of either pathway. For example, pre-event shallow groundwater not far from the catchment divide comes up to the surface as rejected recharge during rainfall events and is rapidly delivered to the stream
via overland flow and/or artificial land drainage, bringing with it higher nitrate than would often be expected from a quickflow pathway contribution. This is contrary to the assumption often made in catchment studies that the
deeper hydrological pathways have slower response times in stream hydrographs during a rainfall event, and it emphasizes that it is critical to have a strong three-dimensional conceptual model as the basis for the interpretation
of catchment data.

Palaeoenvironmental changes since the Last Glacial Maximum: Patterns, timing and dynamics throughout South America

The vast diversity of present vegetation and environments that occur throughout South America (12°N to 56°S) is the result of diverse processes that have been operating and interacting at different spatial and temporal scales. Global factors, such as the concentration of CO2 in the atmosphere, may have been significant for high altitude vegetation during times of lower abundance, while lower sea levels of glacial stages potentially opened areas of continental shelf for colonisation during a substantial portion of the Quaternary. Latitudinal variation in orbital forcing has operated on a regional scale. The pace of climate change in the tropics is dominated by precessional oscillations of c. 20 kyr, while the high latitudes of the south are dominated by obliquity oscillations of c. 40 kyr. In particular, seasonal insolation changes forced by precessional oscillations must have had important consequences for the distribution limits of species, with potentially different effects depending on the latitude. The availability of taxa, altitude and human impact, among other events, have locally influenced the environments. Disentangling the different forcing factors of environmental change that operate on different timescales, and understanding the underlying mechanisms leads to considerable challenges for palaeoecologists. The papers in this Special Issue present a selection of palaeoecological studies throughout South America on vegetation changes and other aspects of the environment, providing a window on the possible complexity of the nature of transitions and timings that are potentially available.

The molecular dynamics of Trypanosoma brucei UDP-galactose 4'-epimerase:a drug target for African sleeping sickness

During the past century, several epidemics of human African trypanosomiasis, a deadly disease caused by the protist Trypanosoma brucei, have afflicted sub-Saharan Africa. Over 10 000 new victims are reported each year, with hundreds of thousands more at risk. As current drug treatments are either highly toxic or ineffective, novel trypanocides are urgently needed. The T. brucei galactose synthesis pathway is one potential therapeutic target. Although galactose is essential for T. brucei survival, the parasite lacks the transporters required to intake galactose from the environment. UDP-galactose 4'-epimerase (TbGalE) is responsible for the epimerization of UDP-glucose to UDP-galactose and is therefore of great interest to medicinal chemists. Using molecular dynamics simulations, we investigate the atomistic motions of TbGalE in both the apo and holo states. The sampled conformations and protein dynamics depend not only on the presence of a UDP-sugar ligand, but also on the chirality of the UDP-sugar C4 atom. This dependence provides important insights into TbGalE function and may help guide future computer-aided drug discovery efforts targeting this protein.

Plume characteristics and dynamics of UV and IR laser-desorbed oligonucleotides

Laser desorption of dye-tagged oligonucleotides was studied using laser-induced fluorescence imaging. Desorption with ultra violet (UV) and infra-red (IR) lasers resulted in forward directed plumes of molecules. In the case of UV desorption, the initial shot desorbed approximately seven-fold more material than subsequent shots. In contrast, the initial shot in IR desorption resulted in the ejection of less material compared to subsequent shots and these plumes had a component directed along the path of the laser. Thermal equilibrium of the molecules in the plume was achieved after approximately 25 µs with a spread in molecular temperature which was described by a modified Maxwell-Boltzmann equation.

Conformational Dynamics of the Human Propeller Telomeric DNA Quadruplex on a Microsecond Time Scale

The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. While G-quartet stems have been well characterised, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 µs. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A:A base pair, triad, pentad and hexad. The results present a threshold in quadruplex simulations, with regards to understanding the flexible nature of the sugar-phosphate backbone in formation of unusual architecture within the topology. Furthermore, this study stresses the importance of simulation time in sampling conformational space for this topology.