Functional characterization of Rhizobium leguminosarum bv. viciae DmeRF, a cation diffusion facilitator system involved in nickel and cobalt resistance

In prokaryotes, nickel is an essential element participating in the structure of enzymes involved in multiple cellular processes. Nickel transport is a challenge for microorganisms since, although essential, high levels of this metal inside the cell are toxic. For this reason, bacteria have developed high-affinity nickel transporters as well as nickel-specific detoxification systems. Ultramafic soils, and soils contaminated with heavy metals are excellent sources of nickel resistant bacteria. Molecular analysis of strains isolated in the habitats has revealed novel genetic systems involved in adaptation to such hostile conditions.

Identification and analysis of a nickel-inducible cation diffusion facilitator-NiCoT combined system in Rhizobium leguminosarum bv. viciae

Nickel, like other transition metals, can be toxic to cells even at moderate concentration (low microM range) by displacing essential metals from their native binding sites or by generating reactive oxygen species that cause oxidative DNA damage. For this reason, cells have evolved mechanisms to deal with excess nickel. Efflux systems include members of the Resistance-Nodulation-cell Division (RND) protein family, P-type ATPases, cation diffusion facilitators (CDF) and other resistance factors. Nickel-specific exporters have been characterized in Cupravidus metallidurans, Helicobacter pylori, Achromobacter xylosoxidans, Serratia marcenses and Escherichia coli.

(Table 1) Stable nitrogen isotopes of ammonium in interstitial waters from ODP Site 164-997

Ammonium (NH4+) concentration profiles in piston-core sediments of the Carolina Rise and Blake Ridge generally have linear concentration profiles within the sulfate reduction zone (Borowski, 1998). Deep Sea Drilling Project (DSDP) Site 533, located on the Blake Ridge, also displayed a linear ammonium concentration profile through the sulfate reduction zone and the profile linearity continues into the upper methanogenic zone to a depth of ~200 meters below seafloor (mbsf), where the first methane gas hydrates probably occur (Jenden and Gieskes, 1983, doi:10.2973/dsdp.proc.76.114.1983; Kvenvolden and Barnard, 1983, doi:10.2973/dsdp.proc.76.106.1983). Sediments from the Ocean Drilling Program (ODP) Leg 164 deep holes (Sites 994, 995, and 997) also exhibit linear ammonium profiles above the top of the gas hydrate zone (~200 mbsf) (Paull, Matsumoto, Wallace, et al., 1996, doi:10.2973/odp.proc.ir.164.1996). We hypothesized that a possible cause of linear ammonium profiles was diffusion of ammonium from a concentrated ammonium source at depth. We further reasoned that if this ammonium were produced by microbial fermentation reactions at depth, that a comparison of the nitrogen isotopic composition of sedimentary organic nitrogen and the nitrogen with pore-water ammonium would test this hypothesis. Convergence with depth of d15N values of the nitrogen source (sedimentary organic matter) and the nitrogen product (dissolved NH4+) would strongly suggest that ammonium was produced within a particular depth zone by microbial fermentation reactions. Here, we report d15N values of pore-water ammonium from selected interstitial water (IW) samples from Site 997, sampled during ODP Leg 164.

Detailed analysis of a conservative difference approximation for the time fractional diffusion equation

Diffusion equations that use time fractional derivatives are attractive because they describe a wealth of problems involving non-Markovian Random walks. The time fractional diffusion equation (TFDE) is obtained from the standard diffusion equation by replacing the first-order time derivative with a fractional derivative of order α ∈ (0, 1). Developing numerical methods for solving fractional partial differential equations is a new research field and the theoretical analysis of the numerical methods associated with them is not fully developed. In this paper an explicit conservative difference approximation (ECDA) for TFDE is proposed. We give a detailed analysis for this ECDA and generate discrete models of random walk suitable for simulating random variables whose spatial probability density evolves in time according to this fractional diffusion equation. The stability and convergence of the ECDA for TFDE in a bounded domain are discussed. Finally, some numerical examples are presented to show the application of the present technique.

A second order control-volume finite-element least-squares strategy for simulating diffusion in strongly anisotropic media

An unstructured mesh �nite volume discretisation method for simulating di�usion in anisotropic media in two-dimensional space is discussed. This technique is considered as an extension of the fully implicit hybrid control-volume �nite-element method and it retains the local continuity of the ux at the control volume faces. A least squares function recon- struction technique together with a new ux decomposition strategy is used to obtain an accurate ux approximation at the control volume face, ensuring that the overall accuracy of the spatial discretisation maintains second order. This paper highlights that the new technique coincides with the traditional shape function technique when the correction term is neglected and that it signi�cantly increases the accuracy of the previous linear scheme on coarse meshes when applied to media that exhibit very strong to extreme anisotropy ratios. It is concluded that the method can be used on both regular and irregular meshes, and appears independent of the mesh quality.

Implicit difference approximation for the time fractional diffusion equation

In this paper, we consider a time fractional diffusion equation on a finite domain. The equation is obtained from the standard diffusion equation by replacing the first-order time derivative by a fractional derivative (of order $0<\alpha<1$ ). We propose a computationally effective implicit difference approximation to solve the time fractional diffusion equation. Stability and convergence of the method are discussed. We prove that the implicit difference approximation (IDA) is unconditionally stable, and the IDA is convergent with $O(\tau+h^2)$, where $\tau$ and $h$ are time and space steps, respectively. Some numerical examples are presented to show the application of the present technique.