Importance of the Two Dissimilatory (Nar) Nitrate Reductases in the Growth and Nitrate Reduction of the Methylotrophic Marine Bacterium Methylophaga nitratireducenticrescens JAM1

Methylophaga nitratireducenticrescens JAM1 is the only reported Methylophaga species capable of growing under anaerobic conditions with nitrate as electron acceptor. Its genome encodes a truncated denitrification pathway, which includes two nitrate reductases, Nar1 and Nar2; two nitric oxide reductases, Nor1 and Nor2; and one nitrous oxide reductase, Nos; but no nitrite reductase (NirK or NirS). The transcriptome of strain JAM1 cultivated with nitrate and methanol under anaerobic conditions showed the genes for these enzymes were all expressed. We investigated the importance of Nar1 and Nar2 by knocking out narG1, narG2 or both genes. Measurement of the specific growth rate and the specific nitrate reduction rate of the knockout mutants JAM1ΔnarG1 (Nar1) and JAM1ΔnarG2 (Nar2) clearly demonstrated that both Nar systems contributed to the growth of strain JAM1 under anaerobic conditions, but at different levels. The JAM1ΔnarG1 mutant exhibited an important decrease in the nitrate reduction rate that consequently impaired its growth under anaerobic conditions. In JAM1ΔnarG2, the mutation induced a 20-h lag period before nitrate reduction occurred at specific rate similar to that of strain JAM1. The disruption of narG1 did not affect the expression of narG2. However, the expression of the Nar1 system was highly downregulated in the presence of oxygen with the JAM1ΔnarG2 mutant. These results indicated Nar1 is the major nitrate reductase in strain JAM1 but Nar2 appears to regulate the expression of Nar1

Contribution à l'étude des carbonates, des borates, des silicates et des arséniates

Québec Université Laval, Bibliothèque 201

Réussite scolaire, symptômes anxieux et dépressifs rapport de recherche /

"La présente recherche a été subventionnée par le Ministère de l'éducation, du loisir et du sport dans le cadre du Programme d'aide à la recherche sur l'enseignement et l'apprentissage (PAREA)"Titre de l'écran-titre (visionné le 19 février 2008).Également disponible en format papier.Bibliogr

An Efficient, Semi-implicit Pressure-based Scheme Employing a High-resolution Finitie Element Method for Simulating Transient and Steady, Inviscid and Viscous, Compressible Flows on Unstructured Grids

A new semi-implicit pressure-based Computational Fluid Dynamics (CFD) scheme for simulating a wide range of transient and steady, inviscid and viscous compressible flow on unstructured finite elements is presented here. This new CFD scheme, termed the PCICEFEM (Pressure-Corrected ICE-Finite Element Method) scheme, is composed of three computational phases, an explicit predictor, an elliptic pressure Poisson solution, and a semiimplicit pressure-correction of the flow variables. The PCICE-FEM scheme is capable of second-order temporal accuracy by incorporating a combination of a time-weighted form of the two-step Taylor-Galerkin Finite Element Method scheme as an explicit predictor for the balance of momentum equations and the finite element form of a time-weighted trapezoid rule method for the semi-implicit form of the governing hydrodynamic equations. Second-order spatial accuracy is accomplished by linear unstructured finite element discretization. The PCICE-FEM scheme employs Flux-Corrected Transport as a high-resolution filter for shock capturing. The scheme is capable of simulating flows from the nearly incompressible to the high supersonic flow regimes. The PCICE-FEM scheme represents an advancement in mass-momentum coupled, pressurebased schemes. The governing hydrodynamic equations for this scheme are the conservative form of the balance of momentum equations (Navier-Stokes), mass conservation equation, and total energy equation. An operator splitting process is performed along explicit and implicit operators of the semi-implicit governing equations to render the PCICE-FEM scheme in the class of predictor-corrector schemes. The complete set of semi-implicit governing equations in the PCICE-FEM scheme are cast in this form, an explicit predictor phase and a semi-implicit pressure-correction phase with the elliptic pressure Poisson solution coupling the predictor-corrector phases. The result of this predictor-corrector formulation is that the pressure Poisson equation in the PCICE-FEM scheme is provided with sufficient internal energy information to avoid iteration. The ability of the PCICE-FEM scheme to accurately and efficiently simulate a wide variety of inviscid and viscous compressible flows is demonstrated here

EXAMINATION OF THE PCICE METHOD IN THE NEARLY INCOMPRESSIBLE, AS WELL AS STRICTLY INCOMPRESSIBLE, LIMITS

The conservative-form, pressure-based PCICE numerical method (Martineau and Berry, 2004) (Berry, 2006), recently developed for computing transient fluid flows of all speeds from very low to very high (with strong shocks), is simplified and generalized. Though the method automatically treats a continuous transition of compressibility, three distinct, limiting compressibility regimes are formally defined for purposes of discussion and comparison with traditional methods – the strictly incompressible limit, the nearly incompressible limit, and the f ully compressible limit. The PCICE method’s behavior is examined in each limiting regime. In the strictly incompressible limit the PCICE algorithm reduces to the traditional MAC-type method with velocity divergence driving the pressure Poisson equation. In the nearly incompressible limit the PCICE algorithm is found to reduce to a generalization of traditional incompressible methods, i.e. to one in which not only the velocity divergence effect, but also the density gradient effect is included as a driving function in the pressure Poisson equation. This nearly incompressible regime has received little attention, and it appears that in the past, strictly incompressible methods may have been conveniently applied to flows in this regime at the expense of ignoring a potentially important coupling mechanism. This could be significant in many important flows; for example, in natural convection flows resulting from high heat flux. In the f ully compressible limit or regime, the algorithm is found to reduce to an expression equivalent to density-based methods for high-speed flow

RELAP-7 Level 2 Milestone Report: Demonstration of a Steady State Single Phase PWR Simulation with RELAP-7

The document contains the simulation results of a steady state model PWR problem with the RELAP-7 code. The RELAP-7 code is the next generation nuclear reactor system safety analysis code being developed at Idaho National Laboratory (INL). The code is based on INL's modern scientific software development framework - MOOSE (Multi-Physics Object-Oriented Simulation Environment). This report summarizes the initial results of simulating a model steady-state single phase PWR problem using the current version of the RELAP-7 code. The major purpose of this demonstration simulation is to show that RELAP-7 code can be rapidly developed to simulate single-phase reactor problems. RELAP-7 is a new project started on October 1st, 2011. It will become the main reactor systems simulation toolkit for RISMC (Risk Informed Safety Margin Characterization) and the next generation tool in the RELAP reactor safety/systems analysis application series (the replacement for RELAP5). The key to the success of RELAP-7 is the simultaneous advancement of physical models, numerical methods, and software design while maintaining a solid user perspective. Physical models include both PDEs (Partial Differential Equations) and ODEs (Ordinary Differential Equations) and experimental based closure models. RELAP-7 will eventually utilize well posed governing equations for multiphase flow, which can be strictly verified. Closure models used in RELAP5 and newly developed models will be reviewed and selected to reflect the progress made during the past three decades. RELAP-7 uses modern numerical methods, which allow implicit time integration, higher order schemes in both time and space, and strongly coupled multi-physics simulations. RELAP-7 is written with object oriented programming language C++. Its development follows modern software design paradigms. The code is easy to read, develop, maintain, and couple with other codes. Most importantly, the modern software design allows the RELAP-7 code to evolve with time. RELAP-7 is a MOOSE-based application. MOOSE (Multiphysics Object-Oriented Simulation Environment) is a framework for solving computational engineering problems in a well-planned, managed, and coordinated way. By leveraging millions of lines of open source software packages, such as PETSC (a nonlinear solver developed at Argonne National Laboratory) and LibMesh (a Finite Element Analysis package developed at University of Texas), MOOSE significantly reduces the expense and time required to develop new applications. Numerical integration methods and mesh management for parallel computation are provided by MOOSE. Therefore RELAP-7 code developers only need to focus on physics and user experiences. By using the MOOSE development environment, RELAP-7 code is developed by following the same modern software design paradigms used for other MOOSE development efforts. There are currently over 20 different MOOSE based applications ranging from 3-D transient neutron transport, detailed 3-D transient fuel performance analysis, to long-term material aging. Multi-physics and multiple dimensional analyses capabilities can be obtained by coupling RELAP-7 and other MOOSE based applications and by leveraging with capabilities developed by other DOE programs. This allows restricting the focus of RELAP-7 to systems analysis-type simulations and gives priority to retain and significantly extend RELAP5's capabilities

Étude d'une bactérie dénitrifiante du Biodôme de Montréal

Le nitrate est une molécule soluble qui diffuse rapidement dans les eaux de surfaces et les eaux souterraines, contaminant ainsi l’eau potable. Le nitrate contribue à l’eutrophisation des lacs et des rivières et devient toxique pour les animaux à partir de certaines concentrations. Methylophaga nitratireducticrescens JAM1 est une bactérie méthylotrophe isolée à partir d'un système de dénitrification d'eau de mer supplémenté en méthanol au Biodôme de Montréal. Cette bactérie compose à elle seule plus de 50% du biofilm dénitrifiant retrouvé dans le système de dénitrification. Contrairement aux autres espèces de Methylophaga, la souche JAM1 possède la particularité de croitre dans des conditions dénitrifiantes en présence de nitrate et de méthanol. La croissance de JAM1 dans les conditions dénitrifiantes, réduisant le nitrate en nitrite, est corrélée avec la présence de deux gènes codant pour des nitrate reductase narG. Le génome de JAM1 a été séquencé et consiste en un chromosome de 3,137,192 bp. Le séquençage du génome de JAM1 a confirmé la présence de deux opérons nar mais aussi de deux opérons nor (nitric oxide reductase) et d'un opéron nos (nitrous oxide reductase). De plus, une sequence nirK codant pour une nitrite reductase tronquée de 82 acides aminés a été trouvée, ce qui pourrait expliquer que la souche JAM1 est seulement capable de réduire le nitrate en nitrite. Notre travail consiste à étudier les gènes de dénitrification de la souche JAM1. Les deux gènes narG sont exprimés aussi bien en conditions aérobies que dénitrifiantes. Par ailleurs, les autres gènes liés à la dénitrification sont également exprimés, incluant le nirK tronqué. Des mesures d'expression ont montré que les gènes narG étaient exprimés différemment en fonction des conditions de cultures. Un mutant knockout de narG1 a montré de grosses différences de croissance et de taux de réduction du nitrate par rapport à la souche sauvage. Des différences d'expression du gène narG2 entre le mutant narG1 et la souche sauvage ont également été démontrées. La construction du mutant knockout narG2 est en cours et permettra de révéler l'importance de ce gène pour la croissance de la bactérie et la réduction du nitrate