Selection of plants for roles in phytoremediation: the importance of glucosylation

Over-expression and transposon mutagenesis in root cultures of Arabidopsis thaliana demonstrated the importance of the family 1 glycosyltransferase UGT72B1 in catalysing the N-glucosylation of the persistent pollutant 3,4-dichloroaniline (DCA). In phytotoxicity studies with DCA in seedlings, over-expression of UGT72B1 enhanced sensitivity, whereas the knockouts were more resistant than the controls. In contrast, manipulating the expression of UGT72B1 had no effect on the O-glucosylation, or toxicity, of chlorophenols. When N-glucosylation was disrupted in plants, radioactivity derived from [14C]-DCA became covalently bound into high molecular weight insoluble material, principally associated with the lignin fraction. This suggested that insolubilization into stable cell wall components represented a more effective mechanism of DCA detoxification than the formation of N-glycosidic conjugates. A screen of plants used in remediation, identified low levels of N-glucosyltransferase activity in switchgrass and high activities in reed canary grass. When incubated with [14C]-DCA, reed canary grass plants accumulated soluble N-glycosides of DCA, whereas switchgrass formed insoluble residues. Consistent with the results obtained in studies with Arabidopsis, phytotoxicity trials with DCA demonstrated that switchgrass was more tolerant than reed canary grass. Our studies provide a new biochemical basis for selecting plants for useful remediating traits towards specific classes of pollutants

Crohn's disease: in vitro and ex vivo innate epithelial responses to bacterial stimulation.

Evidence in the literature suggests that Crohn's disease involves an abnormal, innate immune response to the "commensal microbiota". It is hypothesised that when symbiosis between the residential microbiota and the epithelial cells of the gastrointestinal tract is broken, secretion of potent inflammatory mediators initiates a chronic adaptive immune response, which leads to the pathology seen in Crohn's disease. The aims of the studentship were to a) characterise and compare the innate mucosal signals generated in vitro in response to the presence of "commensal", "probiotic" and "pathogenic bacteria" and b) to establish the typical ex vivo mucosal response in order to ascertain if the immunological responses to bacterial stimuli in Crohn's disease is abnormal. On investigation of a range of bacterial species it was found that bacterial "properties" that influence host responses are not necessarily linked to pathogenicity and bacteria did not segregate into good (commensal / probiotic) and bad (pathogenic) bacteria. Bacterial phenotype was assessed by electron microscopy and both pathogenic and non pathogenic bacteria expressed external structures associated with virulence. Virulence gene deletion mutants of pathogenic bacterial strains were used to determine what bacterial epitopes drove the in vitro responses. Epithelial responses to the whole organism were found to be complex, with a range of responses to soluble and/or external microbial structures. In addition, bacterial supernatants had minimal effect, implying that bacterial contact was an essential part of the process. Evidence was found to suggest that the host recognises the bacterium by combinations of microbial products and may also require co-stimulatory signals to confirm "danger" before responding. The influence of the maturity of the epithelium was studied using Caco-2 cells and immature primary crypt cells (HIEC). Evidence was found to support a hypothesis that the abnormal response in Crohn's disease could originate from the inappropriate stimulus of immature epithelial cells. In vitro organ culture was used to assess the mucosal response to bacterial stimulus ex vivo. Regional and bacterial specific differences were observed in biopsies from Crohn's disease, and evidence was found to support the hypothesis of abnormal innate immune responses to bacterial stimuli

Enhancing photocatalytic degradation of the cyanotoxin microcystin-LR with the addition of sulfate-radical generating oxidants.

This study investigated the coupling of sulfate radical generating oxidants, (persulfate, PS and peroxymonosulfate, PMS) with TiO2 photocatalysis for the degradation of microcystin-LR (MC-LR). Treatment efficiency was evaluated by estimating the electrical energy per order (EEO). Oxidant addition at 10 mg/L reduced the energy requirements of the treatment by 60% and 12% for PMS and PS, respectively compared with conventional photocatalysis. Quenching studies indicated that both sulfate and hydroxyl radicals contributed towards the degradation of MC-LR for both oxidants, while Electron Paramagnetic Resonance (EPR) studies confirmed that the oxidants prolonged that lifetime of both radicals (concentration maxima shifted from 10 to 20min), allowing for bulk diffusion and enhancing cyanotoxin removal. Structural identification of transformation products (TPs) formed during all treatments, indicated that early stage degradation of MC-LR occurred mainly on the aromatic ring and conjugated carbon double bonds of the ADDA amino acid. In addition, simultaneous hydroxyl substitution of the aromatic ring and the conjugated double carbon bonds of ADDA (m/z= 1027.5) are reported for the first time. Oxidant addition also increased the rates of formation/degradation of TPs and affected the overall toxicity of the treated samples. The detoxification and degradation order of the treatments was UVA/TiO2/PMS > UVA/TiO2/PS>> UVA/TiO2

The Importance of Time Congruity in the Organisation.

In 1991 Kaufman, Lane, and Lindquist proposed that time congruity in terms of an individual's time preferences and the time use methods of an organisation would lead to satisfactory performance and enhancement of quality of work and general life. The research reported here presents a study which uses commensurate person and job measures of time personality in an organisational setting to assess the effects of time congruity on one aspect of work life, job-related affective well-being. Results show that time personality and time congruity were found to have direct effects on well-being and the influence of time congruity was found to be mediated through time personality, thus contributing to the person–job (P–J) fit literature which suggests that direct effects are often more important than indirect effects. The study also provides some practical examples of ways to address some of the previously cited methodological issues in P–J fit research

Arches and contact forces in a granular pile

Assemblies of granular particles mechanically stable under their own weight contain arches. These are structural units identified as sets of mutually stable grains. It is generally assumed that these arches shield the weight above them and should bear most of the stress in the system. We test such hypothesis by studying the stress born by in-arch and out-of-arch grains. We show that, indeed, particles in arches withstand larger stresses. In particular, the isotropic stress tends to be larger for in-arch-grains whereas the anisotropic component is marginally distinguishable between the two types of particles. The contact force distributions demonstrate that an exponential tail (compatible with the maximization of entropy under no extra constraints) is followed only by the out-of-arch contacts. In-arch contacts seem to be compatible with a Gaussian distribution consistent with a recently introduced approach that takes into account constraints imposed by the local force balance on grains.Comment: 7 pages, 7 figures, major revisio

Square Patterns and Quasi-patterns in Weakly Damped Faraday Waves

Pattern formation in parametric surface waves is studied in the limit of weak viscous dissipation. A set of quasi-potential equations (QPEs) is introduced that admits a closed representation in terms of surface variables alone. A multiscale expansion of the QPEs reveals the importance of triad resonant interactions, and the saturating effect of the driving force leading to a gradient amplitude equation. Minimization of the associated Lyapunov function yields standing wave patterns of square symmetry for capillary waves, and hexagonal patterns and a sequence of quasi-patterns for mixed capillary-gravity waves. Numerical integration of the QPEs reveals a quasi-pattern of eight-fold symmetry in the range of parameters predicted by the multiscale expansion.Comment: RevTeX, 11 pages, 8 figure

Forage selection preferences of experienced cows and naïve heifers grazing native tallgrass range during winter

Beef Cattle Research, 2011 is known as Cattlemen’s Day, 2011Estimating the nutritive value of a grazing animal’s diet is a significant challenge. Description of the botanical composition of a grazed diet is vital in that regard. Microhistological analysis of fecal material has been used for estimating the botanical composition of wild and domestic ungulate diets since first described by Baumgartner and Martin in 1939. Little research has been conducted on the diet selection preferences of multiparous beef cows compared to primiparous beef cows. We hypothesized that foraging strategies change as cows age. To that end, our objective was to characterize differences in diet selection between experienced multiparous and naïve primiparous beef cows grazing dormant, native tallgrass pastures during winter

From manual curation to visualization of gene families and networks across Solanaceae plant species

High-quality manual annotation methods and practices need to be scaled to the increased rate of genomic data production. Curation based on gene families and gene networks is one approach that can significantly increase both curation efficiency and quality. The Sol Genomics Network (SGN; http://solgenomics.net) is a comparative genomics platform, with genetic, genomic and phenotypic information of the Solanaceae family and its closely related species that incorporates a community-based gene and phenotype curation system. In this article, we describe a manual curation system for gene families aimed at facilitating curation, querying and visualization of gene interaction patterns underlying complex biological processes, including an interface for efficiently capturing information from experiments with large data sets reported in the literature. Well-annotated multigene families are useful for further exploration of genome organization and gene evolution across species. As an example, we illustrate the system with the multigene transcription factor families, WRKY and Small Auxin Up-regulated RNA (SAUR), which both play important roles in responding to abiotic stresses in plants

Simulating spin systems on IANUS, an FPGA-based computer

We describe the hardwired implementation of algorithms for Monte Carlo simulations of a large class of spin models. We have implemented these algorithms as VHDL codes and we have mapped them onto a dedicated processor based on a large FPGA device. The measured performance on one such processor is comparable to O(100) carefully programmed high-end PCs: it turns out to be even better for some selected spin models. We describe here codes that we are currently executing on the IANUS massively parallel FPGA-based system.Comment: 19 pages, 8 figures; submitted to Computer Physics Communication