Determining the Reaeration Coefficient and Hydrodynamic Properties of Rivers Using Inert Gas Tracers

Various contaminants which can be aerobically degraded find their way directly or indirectly into surface water bodies. The reaeration coefficient (K2) characterises the rate at which oxygen can transfer from the atmosphere across the air-water interface following oxygen depletion in a water body. Other mechanisms (like advection, dispersion and transient storage) determine how quickly the contaminants can spread in the water, affecting their spatial and temporal concentrations. Tracer methods involving injection of a gas into the water body have traditionally been used for direct (in-situ) measurement of K2 in a given reach. This paper shows how additional modelling of tracer test results can be used to quantify also hydrodynamic mechanisms (e.g. dispersion and storage exchange coefficients, etc.). Data from three tracer tests conducted in the River Lagan (Northern Ireland) using an inert gas (krypton, Kr) are re-analysed using two solute transport models (ADM, TSM) and an inverse-modelling framework (OTIS-P). Results for K2 are consistent with previously published values for this reach (K2(20)~10-40 d-1). The storage area constituted 30-60% of the main cross-section area and the storage exchange rate was between 2.5×10-3-3.2×10-3s-1. The additional hydrodynamic parameters obtained give insight into transport and dispersion mechanisms within the reach.

Determination of the molar extinction coefficient for the ferric reducing/antioxidant power assay

The FRAP reagent contains 2,4,6-tris(2-pyridyl)-s-triazine, which forms a blue-violet complex ion in the presence of ferrous ions. Although the FRAP (ferric reducing/antioxidant power) assay is popular and has been in use for many years, the correct molar extinction coefficient of this complex ion under FRAP assay conditions has never been published, casting doubt on the validity of previous calibrations. A previously reported value of 19.800 is an underestimate. We determined that the molar extinction coefficient was 21,140. The value of the molar extinction coefficient was also shown to depend on the type of assay and was found to be 22,230 under iron assay conditions, in good agreement with published data. Redox titration indicated that the ferrous sulfate heptahydrate calibrator recommended by Benzie and Strain, the FRAP assay inventors, is prone to efflorescence and, therefore, is unreliable. Ferrous ammonium sulfate hexahydrate in dilute sulfuric acid was a more stable alternative. Few authors publish their calibration data, and this makes comparative analyses impossible. A critical examination of the limited number of examples of calibration data in the published literature reveals only that Benzie and Strain obtained a satisfactory calibration using their method. (C) 2011 Elsevier Inc. All rights reserved.

The wbbD gene of E. coli strain VW187 (O7:K1) encodes a UDP-Gal:GlcNAc{alpha}-pyrophosphate-R {beta}1,3-galactosyltransferase involved in the biosynthesis of O7-specific lipopolysaccharide

In this work, we demonstrate that the wbbD gene of the O7 lipopolysaccharide (LPS) biosynthesis cluster in Escherichia coli strain VW187 (O7:K1) encodes a galactosyltransferase involved in the synthesis of the O7-polysaccharide repeating unit. The galactosyltransferase catalyzed the transfer of Gal from UDP-Gal to the GlcNAc residue of a GlcNAc-pyrophosphate-lipid acceptor. A mutant strain with a defective wbbD gene was unable to form O7 LPS and lacked this specific galactosyltransferase activity. The normal phenotype was restored by complementing the mutant with the cloned wbbD gene. To characterize the WbbD galactosyltransferase, we used a novel acceptor substrate containing GlcNAcalpha-pyrophosphate covalently bound to a hydrophobic phenoxyundecyl moiety (GlcNAc alpha-O-PO(3)-PO(3)-(CH(2))(11)-O-phenyl). The WbbD galactosyltransferase had optimal activity at pH 7 in the presence of 2.5 mM MnCl(2). Detergents in the assay did not increase glycosyl transfer. Digestion of enzyme product by highly purified bovine testicular beta-galactosidase demonstrated a beta-linkage. Cleavage of product by pyrophosphatase and phosphatase, followed by HPLC and NMR analyses, revealed a disaccharide with the structure Gal beta1-3GlcNAc. Our results conclusively demonstrate that WbbD is a UDP-Gal: GlcNAcalpha-pyrophosphate-R beta1,3-galactosyltransferase and suggest that the novel synthetic glycolipid acceptor may be generally applicable to characterize other bacterial glycosyltransferases.

A simple inhibition coefficient for quantifying potency of biocontrol agents against plant-pathogenic fungi

Microbial interactions depend on a range of biotic and environmental variables, and are both dynamic and unpredictable. For some purposes, and under defined conditions, it is nevertheless imperative to evaluate the inhibitory efficacy of microbes, such as those with potential as biocontrol agents. We selected six, phylogenetically diverse microbes to determine their ability to inhibit the ascomycete Fusarium
coeruleum, a soil-dwelling pathogen of potato tubers that causes the storage disease dry rot. Interaction assays, where colony development was quantified (for both fungal pathogen and potential control agents), were therefore carried out on solid media. The key parameters that contributed to, and were indicative of, inhibitory efficacy were identified as: fungal growth-rates (i) prior to contact with the biocontrol
agent and (ii) if/once contact with the biocontrol agent was established (i.e. in the zone of mixed
culture), and (iii) the ultimate distance traveled by the fungal mycelium. It was clear that there was no correlation between zones of fungal inhibition and the overall reduction in the extent of fungal colony development. An inhibition coefficient was devised which incorporated the potential contributions of distal inhibition of fungal growth-rate; prevention of mycelium development in the vicinity of the biocontrol
agent; and ability to inhibit plant-pathogen growth-rate in the zone of mixed culture (in a ratio of 2:2:1). The values derived were 84.2 for Bacillus subtilis (QST 713), 74.0 for Bacillus sp. (JC12GB42), 30.7 for Pichia anomala (J121), 19.3 for Pantoea agglomerans (JC12GB34), 13.9 for Pantoea sp. (S09:T:12), and
21.9 (indicating a promotion of fungal growth) for bacterial strain (JC12GB54). This inhibition coefficient, with a theoretical maximum of 100, was consistent with the extent of F. coeruleum-colony development (i.e. area, in cm2) and assays of these biocontrol agents carried out previously against Fusarium
spp., and other fungi. These findings are discussed in relation to the dynamics and inherent complexity of natural ecosystems, and the need to adapt models for use under specific sets of conditions.

Genome analysis of a simultaneously predatory and prey-independent, novel Bdellovibrio bacteriovorus from the River Tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria

BACKGROUND: Evolution equipped Bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. Bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of Bdellovibrio converted to prey-independent growth. A previous genomic analysis of B. bacteriovorus strain HD100 suggested that predatory consumption of prey DNA by lytic enzymes made Bdellovibrio less likely than other bacteria to acquire DNA by lateral gene transfer (LGT). However the Doolittle and Pan groups predicted, in silico, both ancient and recent lateral gene transfer into the B. bacteriovorus HD100 genome.

RESULTS: To test these predictions, we isolated a predatory bacterium from the River Tiber- a good potential source of LGT as it is rich in diverse bacteria and organic pollutants- by enrichment culturing with E. coli prey cells. The isolate was identified as B. bacteriovorus and named as strain Tiberius. Unusually, this Tiberius strain showed simultaneous prey-independent growth on organic nutrients and predatory growth on live prey. Despite the prey-independent growth, the homolog of bd0108 did not have typical prey-independent-type mutations. The dual growth mode may reflect the high carbon content of the river, and gives B. bacteriovorus Tiberius extended non-predatory contact with the other bacteria present. The HD100 and Tiberius genomes were extensively syntenic despite their different cultured-terrestrial/freshly-isolated aquatic histories; but there were significant differences in gene content indicative of genomic flux and LGT. Gene content comparisons support previously published in silico predictions for LGT in strain HD100 with substantial conservation of genes predicted to have ancient LGT origins but little conservation of AT-rich genes predicted to be recently acquired.

CONCLUSIONS: The natural niche and dual predatory, and prey-independent growth of the B. bacteriovorus Tiberius strain afforded it extensive non-predatory contact with other marine and freshwater bacteria from which LGT is evident in its genome. Thus despite their arsenal of DNA-lytic enzymes; Bdellovibrio are not always predatory in natural niches and their genomes are shaped by acquiring whole genes from other bacteria.

Combined Conduction-Convection-Radiation Heat Transfer of Slip Flow inside a Micro-channel Filled with a Cellular Porous Material

Combined conduction–convection–radiation heat transfer is investigated numerically in a micro-channel filled with a saturated cellular porous medium, with the channel walls held at a constant heat flux. Invoking the velocity slip and temperature jump, the thermal behaviour of the porous–fluid system are studied by considering hydrodynamically fully developed flow and applying the Darcy–Brinkman flow model. One energy equation model based on the local thermal equilibrium condition is adopted to evaluate the temperature field within the porous medium. Combined conduction and radiation heat transfer is treated as an effective conduction process with a temperature-dependent effective thermal conductivity. Results are reported in terms of the average Nusselt number and dimensionless temperature distribution, as a function of velocity slip coefficient, temperature jump coefficient, porous medium shape parameter and radiation parameters. Results show that increasing the radiation parameter (Tr)(Tr) and the temperature jump coefficient flattens the dimensionless temperature profile. The Nusselt numbers are more sensitive to the variation in the temperature jump coefficient rather than to the velocity slip coefficient. Such that for high porous medium shape parameter, the Nusselt number is found to be independent of velocity slip. Furthermore, it is found that as the temperature jump coefficient increases, the Nusselt number decrease. In addition, for high temperature jump coefficients, the Nusselt number is found to be insensitive to the radiation parameters and porous medium shape parameter. It is also concluded that compared with the conventional macro-channels, wherein using a porous material enhances the rate of heat transfer (up to about 40 % compared to the clear channel), insertion of a porous material inside a micro-channel in slip regime does not effectively enhance the rate of heat transfer that is about 2 %.