One-dimensional simulation of solute transfer in saturated-unsaturated porous media using the discontinuous finite elements method

A one-dimensional transport model for simulating water flow and solute transport in homogeneous-heterogeneous, saturated-unsaturated porous media is presented. The model is composed of a combination of accurate numerical algorithms for solving the nonlinear Richard's and advection-dispersion equations (ADE). The mixed form of Richard's equation is solved using a standard finite element method (FEM) with primary variable switching. The transport equation is solved using operator splitting, with the discontinuous finite element method (DFE) for discretization of the advective term. A slope limiting procedure for DFE avoids numerical instabilities but creates very limited numerical dispersion for high Peclet numbers. An implicit finite differences scheme (FD) is used for the dispersive term. The unsaturated flow and transport model (Wamos-T) is applied to a variety of rigorous problems including transient flow, heterogeneous medium and abrupt variations of velocity in magnitude and direction due to time-varying boundary conditions. It produces accurate and mass-conservative solutions for a very large range of grid Peclet numbers. The Wamos-T model is a good and robust alternative for the simulation of mass transport in unsaturated domain.     

Identification of sperm proteins as candidate biomarkers for the analysis of reproductive isolation in Mytilus: a case study for the enkurin locus

Sperm proteins of the marine sessile mussels of the Mytilus edulis species complex are models to investigate reproductive isolation and speciation. This study aimed at identifying sperm proteins and their corresponding genes. This was aided by the use of monoclonal antibodies that preferentially bind to yet unknown sperm molecules. By identifying their target molecules, this approach identified proteins with relevance to Mytilus sperm function. This procedure identified 16 proteins, for example, enkurin, laminin, porin and heat shock proteins. The potential use of these proteins as genetic markers to study reproductive isolation is exemplified by analysing the enkurin locus. Enkurin evolution is driven by purifying selection, the locus displays high levels of intraspecific variation and species-specific alleles group in distinct phylogenetic clusters. These findings characterize enkurin as informative candidate biomarker for analyses of clinal variation and differential introgression in hybrid zones, for example, to understand determinants of reproductive isolation in Baltic Mytilus populations.     

Speciation and long- and short-term molecular-level dynamics of soil organic sulfur studied by X-ray absorption near-edge structure spectroscopy

We investigated speciation, oxidative state changes, and long- and short-term molecular-level dynamics of organic S after 365 d of aerobic incubation with and without the addition of sugarcane residue using XANES spectroscopy. Soil samples were collected from the upper 15 cm of undisturbed grasslands since 1880, from undisturbed grasslands since 1931, and from cultivated fields since 1880 in the western United States. We found three distinct groups of organosulfur compounds in these grassland-derived soils: (i) strongly reduced (S to S) organic S that encompasses thiols, monosulfides, disulfides, polysulfides, and thiophenes; (ii) organic S in intermediate oxidation (S to S) states, which include sulfoxides and sulfonates; and (iii) strongly oxidized (S) organic S, which comprises ester-SO-S. The first two groups represent S directly linked to C and accounted for 80% of the total organic S detected by XANES from the undisturbed soils. Aerobic incubation without the addition of sugarcane residue led to a 21% decline in organanosulfur compounds directly linked to C and to up to an 82% increase inorganic S directly bonded to O. Among the C-bonded S compounds, low-valence thiols, sulfides, thiophenic S, and intermediate-valence sulfoxide S seem to be highly susceptible to microbial attack and may represent the most reactive components of organic S pool in these grassland soils. Sulfonate S exhibited a much lower short-term reactivity. The incorporation of sugarcane residue resulted in an increase in organosulfur compounds directly bonded to C at the early stage of incubation. However, similar to soils incubated without residue addition, the proportion of organic S directly linked to C continued to decline with increasing duration of aerobic incubation, whereas the proportion of organic S directly bonded to O showed a steady rise.     

RAPD-PCR investigations of systematic relationships among four species of eels (Teleostei: Anguillidae), particularly Anguilla anguilla and A. rostrata

 We examined the genetic identities of 49 individuals of four species of eels in the genus Anguilla Shaw, A. anguilla, A. japonica, A. reinhardti and A. rostrata, using the random(ly) amplified polymorphic DNA (RAPD)-PCR technique. We used 15 random decamer primers. Out of the 22 148 amplification products detected, 454 markers were evaluated using Nei's distance coefficient, two numerical methods (neighbor-joining, UPGMA), and phylogenetic analysis using parsimony (PAUP). Both numerical and parsimony methods were congruent and confirmed the specific status of all four examined Anguilla species. In all dendrograms, all individuals of each of the species clustered together within four closed groups with highly significant bootstrap values (between 97 and 100%). Additionally 1 to 18 species-specific monomorphic diagnostic fragments were detected in three of the species; none were detected in A. anguilla. Mean interspecific genetic distances ranged from 0.384 to 0.559, with the minimum between A. anguilla and A. rostrata and the maximum between A. anguilla and A. reinhardti. Individuals collected at one locality and belonging to a single species did not cluster together, and neither were any diagnostic monomorphic fragments found for individuals of single localities. This probably reflects a random dispersal of larvae in ocean currents before they reach coastal waters. Among all possible species pairs, only the two Atlantic species were consistently clustered in all dendrograms, with highly significant bootstrap values (100%). Additionally, we detected ten diagnostic markers for this pair of eel species. From RAPD data, we suggest a phylogram which was routed by the descending analysis method: A. reinhardti appears to have been the first species to diverge from a putative common ancestor of the four eel species. Later, A. japonica separated from the hypothetical ancestor of the Atlantic species, which then split recently into A. anguilla and A. rostrata. The close relationship of A. anguilla and A. rostrata is indicated by their low genetic distance (GD = 0.384) and a high degree of shared RAPD fragments (SF = 71.2%); this compares with the following means for all other species pairs: ( = 0.531,  = 44.2%). The prerequisites for using RAPD data for the reconstruction of phylogenies are discussed. Received: 2 September 1999 / Accepted: 8 May 2000     

Chemical structure and biological activities of lipid A's from various bacterial families

The endotoxic principle of lipopolysaccharides (LPS) is localized in their lipid A component. Biological effects of LPS on, for instance, body temperature, blood pressure, and blood picture, are also induced by free lipid A. In contrast to the great variability of the 0-specific chains, the chemical structure of lipid A is much more constant. It is common for Salmonella and similar for other genera of the Enterobacteriaceae. Recently, a number of lipid A's have been recognized that exhibited distinct structural features compared with Enterobacteriaceae. These lipid A's were found to be also distinct with regard to some of their biological properties.