Interactive Coupling of TELEMAC with the Open Source Water Quality Model 143 DELWAQ

Water Qualit

Participatory plant breeding: a way to arrive at better-adapted onion varieties

The search for varieties that are better adapted to organic farming is a current topic in the organic sector. Breeding programmes specific for organic agriculture should solve this problem. Collaborating with organic farmers in such programmes, particularly in the selection process, can potentially result in varieties better adapted to their needs. Here, we assume that organic farmers' perceptive of plant health is broader than that of conventional breeders. Two organic onion farmers and one conventional onion breeder were monitored in their selection activities in 2004 and 2005 in order to verify whether and in which way this broader view on plant health contributes to improvement of organic varieties. They made selections by positive mass selection in three segregating populations under organic conditions. The monitoring showed that the organic farmers selected in the field for earliness and downy mildew and after storage for bulb characteristics. The conventional breeder selected only after storage. Farmers and breeder applied identical selection directions for bulb traits as a round shape, better hardness and skin firmness. This resulted in smaller bulbs in the breeders’ populations, while the bulbs in the farmer populations were bigger than in the original population. In 2006 and 2007 the new onion populations will be compared with each other and the original populations to determine the selection response

Tactic Response of Shewanella oneidensis MR-1 toward Insoluble Electron Acceptors

Exoelectrogenic bacteria are defined by their ability to respire on extracellular and insoluble electron acceptors and have applications in bioremediation and microbial electrochemical systems (MESs), while playing important roles in biogeochemical cycling. Shewanella oneidensis MR-1, which has become a model organism for the study of extracellular respiration, is known to display taxis toward insoluble electron acceptors, including electrodes. Multiple mechanisms have been proposed for MR-1’s tactic behavior, and, here, we report on the role of electrochemical potential by video microscopy cell tracking experiments in three-electrode electrochemical cells. MR-1 trajectories were determined using a particle tracking algorithm and validated with Shannon’s entropy method. Tactic response by MR-1 in the electrochemical cell was observed to depend on the applied potential, as indicated by the average velocity and density of motile (>4 µm/s) MR-1 close to the electrode (<50 µm). Tactic behavior was observed at oxidative potentials, with a strong switch between the potentials −0.15 to −0.25 V versus the standard hydrogen electrode (SHE), which coincides with the reduction potential of flavins. The average velocity and density of motile MR-1 close to the electrode increased when riboflavin was added (2 µM), but were completely absent in a ΔmtrC/ΔomcA mutant of MR-1. Besides flavin’s function as an electron mediator to support anaerobic respiration on insoluble electron acceptors, we propose that riboflavin is excreted by MR-1 to sense redox gradients in its environment, aiding taxis toward insoluble electron acceptors, including electrodes in MESs

Shewanella oneidensis MR-1 electron acceptor taxis and the perception of electrodes poised at oxidative potentials

Shewanella oneidensis MR-1 is a facultative anaerobe, capable of respiring on an extraordinarily large and diverse array of both intra- and extracellular terminal electron acceptors, including insoluble metal oxides and electrodes. The ability to perform extracellular electron transfer has sparked great interest over the last three decades and MR-1 has become both a model organism for fundamental research into extracellular electron transfer and a candidate microbe for microbial electrochemical systems, including microbial fuel cells. A pre-requisite for colonisation and biofilm formation on electrodes is the migration of bacteria towards the electrode. Here, we review current understanding in the steps involved in MR-1 migration towards insoluble electron acceptors and electrodes. The main experimental techniques used to evaluate taxis are summarised and different mechanisms proposed for MR-1 taxis are contrasted, in particular chemotaxis versus energy taxis

Molecular diagnostics of gliomas: state of the art

Modern neuropathology serves a key function in the multidisciplinary management of brain tumor patients. Owing to the recent advancements in molecular neurooncology, the neuropathological assessment of brain tumors is no longer restricted to provide information on a tumor’s histological type and malignancy grade, but may be complemented by a growing number of molecular tests for clinically relevant tissue-based biomarkers. This article provides an overview and critical appraisal of the types of genetic and epigenetic aberrations that have gained significance in the molecular diagnostics of gliomas, namely deletions of chromosome arms 1p and 19q, promoter hypermethylation of the O6-methylguanine-methyl-transferase (MGMT) gene, and the mutation status of the IDH1 and IDH2 genes. In addition, the frequent oncogenic aberration of BRAF in pilocytic astrocytomas may serve as a novel diagnostic marker and therapeutic target. Finally, this review will summarize recent mechanistic insights into the molecular alterations underlying treatment resistance in malignant gliomas and outline the potential of genome-wide profiling approaches for increasing our repertoire of clinically useful glioma markers

A functional description of CymA, an electron-transfer hub supporting anaerobic respiratory flexibility in Shewanella

CymA (tetrahaem cytochrome c) is a member of the NapC/NirT family of quinol dehydrogenases. Essential for the anaerobic respiratory flexibility of shewanellae, CymA transfers electrons from menaquinol to various dedicated systems for the reduction of terminal electron acceptors including fumarate and insoluble minerals of Fe(III). Spectroscopic characterization of CymA from Shewanella oneidensis strain MR-1 identifies three low-spin His/His co-ordinated c-haems and a single high-spin c-haem with His/H2O co-ordination lying adjacent to the quinol-binding site. At pH 7, binding of the menaquinol analogue, 2-heptyl-4-hydroxyquinoline-N-oxide, does not alter the mid-point potentials of the high-spin (approximately −240 mV) and low-spin (approximately −110, −190 and −265 mV) haems that appear biased to transfer electrons from the high- to low-spin centres following quinol oxidation. CymA is reduced with menadiol (Em=−80 mV) in the presence of NADH (Em=−320 mV) and an NADH–menadione (2-methyl-1,4-naphthoquinone) oxidoreductase, but not by menadiol alone. In cytoplasmic membranes reduction of CymA may then require the thermodynamic driving force from NADH, formate or H2 oxidation as the redox poise of the menaquinol pool in isolation is insufficient. Spectroscopic studies suggest that CymA requires a non-haem co-factor for quinol oxidation and that the reduced enzyme forms a 1:1 complex with its redox partner Fcc3 (flavocytochrome c3 fumarate reductase). The implications for CymA supporting the respiratory flexibility of shewanellae are discussed.</jats:p

Concentrating Membrane Proteins Using Asymmetric Traps and AC Electric Fields

Membrane proteins are key components of the plasma membrane and are responsible for control of chemical ionic gradients, metabolite and nutrient transfer, and signal transduction between the interior of cells and the external environment. Of the genes in the human genome, 30% code for membrane proteins (Krogh et al. J. Mol. Biol.2001, 305, 567). Furthermore, many FDA-approved drugs target such proteins (Overington et al. Nat. Rev. Drug Discovery2006, 5, 993). However, the structure-function relationships of these are notably sparse because of difficulties in their purification and handling outside of their membranous environment. Methods that permit the manipulation of membrane components while they are still in the membrane would find widespread application in separation, purification, and eventual structure-function determination of these species (Poo et al. Nature1977, 265, 602). Here we show that asymmetrically patterned supported lipid bilayers in combination with AC electric fields can lead to efficient manipulation of charged components. We demonstrate the concentration and trapping of such components through the use of a “nested trap” and show that this method is capable of yielding an approximately 30-fold increase in the average protein concentration. Upon removal of the field, the material remains trapped for several hours as a result of topographically restricted diffusion. Our results indicate that this method can be used for concentrating and trapping charged membrane components while they are still within their membranous environment. We anticipate that our approach could find widespread application in the manipulation and study of membrane proteins