References of "Soetaert, K"
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See detailImpact of anthropogenic disturbance on a mangrove forest assessed by a 1-D cellular automaton model using Lotka Volterra type competition.
Obade, P; Koedam, N; Soetaert, K et al

in International Journal of Design and Nature and Ecodynamics (2009), 3(4), 296-320

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See detailA mathematical modelling of bloom of the coccolithophore Emiliania huxleyi in a mesocosm experiment
Joassin, Pascal ULg; Delille, Bruno ULg; Soetaert, K. et al

in Biogeosciences Discussions (2008), 5

A dynamic model has been developed to represent biogeochemical variables and processes observed during a bloom of Emiliania huxleyi coccolithophore. This bloom was induced in a mesocosm experiment during ... [more ▼]

A dynamic model has been developed to represent biogeochemical variables and processes observed during a bloom of Emiliania huxleyi coccolithophore. This bloom was induced in a mesocosm experiment during which the ecosystem development was followed over a period of 23-days through changes in various biogeochemical parameters such as inorganic nutrients (nitrate, ammonium and phosphate), total alkalinity (TA), dissolved inorganic carbon (DIC), partial pressure of CO[SUB]2[/SUB] (pCO[SUB]2[/SUB]), dissolved oxygen (O[SUB]2[/SUB]), photosynthetic pigments, particulate organic carbon (POC), dissolved organic carbon (DOC), Transparent Exopolymer Particles (TEP), primary production, and calcification. This dynamic model is based on unbalanced algal growth and balanced bacterial growth. In order to adequately reproduce the observations, the model includes an explicit description of phosphorus cycling, calcification, TEP production and an enhanced mortality due to viral lysis. The model represented carbon, nitrogen and phosphorus fluxes observed in the mesocosms. Modelled profiles of algal biomass and final concentrations of DIC and nutrients are in agreement with the experimental observations. [less ▲]

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See detailApplication of a SEEK filter to a 1D biogeochemical model of the Ligurian Sea: Twin experiments and real in-situ data assimilation
Raick, Caroline ULg; Alvera Azcarate, Aïda ULg; Barth, Alexander ULg et al

in Journal of Marine Systems (2007), 65(1-4), 561-583

The Singular Evolutive Extended Kalman (SEEK) filter has been implemented to assimilate in-situ data in a 1D coupled physical-ecosystem model of the Ligurian Sea. The biogeochemical model describes the ... [more ▼]

The Singular Evolutive Extended Kalman (SEEK) filter has been implemented to assimilate in-situ data in a 1D coupled physical-ecosystem model of the Ligurian Sea. The biogeochemical model describes the partly decoupled nitrogen and carbon cycles of the pelagic food web. The GHER hydrodynamic model (1D version) is used to represent the physical forcings. The data assimilation scheme (SEEK filter) parameterizes the error statistics by means of a set of empirical orthogonal functions (EOFs). Twin experiments are first performed with the aim to choose the suitable experimental protocol (observation and estimation vectors, number of EOFs, frequency of the assimilation,...) and to assess the SEEK filter performances. This protocol is then applied to perform real data assimilation experiments using the DYFAMED data base. By assimilating phytoplankton observations, the method has allowed to improve not only the representation of the phytoplankton community, but also of other variables such as zooplankton and bacteria that evolve with model dynamics and that are not corrected by the data assimilation scheme. The validation of the assimilation method and the improvement of model results are studied by means of suitable error measurements. (c) 2006 Elsevier B.V. All rights reserved. [less ▲]

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See detailModelling the Ligurian Sea ecosystem by means of a 1D couled physical-biogeochemical model. Improvement of model results using sequential data assimilation
Raick, C.; Soetaert, K.; Grégoire, Marilaure ULg

in Geophysical Research Abstracts (2005), 7

A 1D coupled physical-biogeochemical model has been built to study the pelagic food web of the Ligurian Sea (NW Mediterranean Sea). The physical model is the turbulent closure model (version 1D) developed ... [more ▼]

A 1D coupled physical-biogeochemical model has been built to study the pelagic food web of the Ligurian Sea (NW Mediterranean Sea). The physical model is the turbulent closure model (version 1D) developed at the GHER (University of Liège, Belgium). The ecosystem model contains nineteen state variables describing the carbon and nitrogen cycles of the pelagic food web. Silicate is considered as a potential limiting nutrient of diatoms’ growth. The aggregation model described in Kriest and Evans (2000) is used to evaluate the sinking rate of particulate detritus. The model is forced at the air-sea interface by the METEO France meteorological data. The DYFAMED time series data of year 2000 are used to calibrate and validate the biological model (Raick et al., 2005). By combining the numerical model and the available observations, data assimilation techniques are useful to improve the state estimation of the ocean. A Singular Fixed Extended Kalman filter (Pham et al., 1998) has been implemented in this way. Twin experiments are first performed to choose the suitable experimental protocol, which is then applied to perform real data assimilation experiments using DYFAMED data (Raick et al., submitted). To be coupled in a 3D environment, the ecosystem model is too complex. Our ongoing work is to perform a simplification, by studying simplified structures in comparison with the original ecosystem model. The advantage of deriving a simplified model from the complex one, is that we would be able to identify the most important processes of the Ligurian Sea ecosystem. [less ▲]

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See detailApplication of a sequential data assimilation technique to improve the results of a 1D couled physical-biogeochemical model of the Ligurian Sea
Raick, C.; Soetaert, K.; Grégoire, Marilaure ULg

in VLIZ Young Scientists' Day, Brugge, Belgium 25th February 2005: book of abstracts (2005)

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See detailStudy of the biogeochemical processes in the Ligurian Sea using a 1D mathematical model
Raick, C.; Soetaert, K.; Grégoire, Marilaure ULg

Poster (2004, May)

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See detailEvidence For Specific And Non-Covalent Binding Of Lipids To Natural And Recombinant Mycobacterium Bovis Bcg Hsp60 Proteins, And To The Escherichia Coli Homologue Groel
De Bruyn, J.; Soetaert, K.; Buyssens, P. et al

in Microbiology-Sgm (2000), 146

Heat-shock proteins (Hsps) from various origins are known to share a conserved structure and are assumed to be key partners in the biogenesis of proteins. Fractionation of the mycobacterial Hsp60, a 65 ... [more ▼]

Heat-shock proteins (Hsps) from various origins are known to share a conserved structure and are assumed to be key partners in the biogenesis of proteins. Fractionation of the mycobacterial Hsp60, a 65 kDa protein also called Cpn60, from Mycobacterium bovis BCG zinc-deficient culture filtrate on phenyl-Sepharose followed by Western blotting revealed the existence of four Hsp60-1 and Hsp60-2 forms, based on their hydrophobicity behaviour. Hsp60-2 species were further purified by ion-exchange chromatography and partial amino acid sequences of cyanogen bromide (CNBr) peptides of purified Hsp60-2 species showed identity with the amino acid sequence deduced from the hsp60-2 gene, indicating that the various Hsp60-2 forms are encoded by the same gene. In addition, the mycobacterial Hsp60-2 was overexpressed in E. coli using the pRR3Hsp60-2 plasmid and analysed on phenyl-Sepharose. The elution pattern of the recombinant Hsp60-2, as well as that of Escherichia coli GroEL, was similar to that of the native Hsp60-2 from the culture filtrate of M. bovis BCG and entirely different from that of the mycobacterial antigen 85. Extraction of mycobacterial Hsp60-2 forms, recombinant BCG Hsp60-2 and E. coli GroEL with organic solvents releases various amounts of non-covalently bound lipids. The presence of lipids on Hsp60-2 was confirmed by labelling M. bovis BCG with radioactive palmitate. The radioactivity was specifically associated with Hsp60 in the aqueous phase and the 19 and 38 kDa lipoproteins in the Triton X-114 phase. Analysis of the lipids extracted from purified Hsp60-2, recombinant BCG Hsp60-2 and E. coli GroEL by TLC showed the same pattern for all the samples. Acid methanolysis of the lipids followed by GC analysis led to the identification of C(16:0), C(18:0) and C(18:1) as the major fatty acyl constituents, and of methylglycoside in these proteins. Altogether, these data demonstrate that lipids are non-covalently bound to Hsp60-2 and homologous proteins. [less ▲]

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See detailOverexpression, purification and characterization of Mycobacterium bovis BCG alcohol dehydrogenase.
Wilkin, J. M.; Soetaert, K.; Stelandre, M. et al

in European Journal of Biochemistry (1999), 262(2), 299-307

A previous study of the effect of zinc deprivation on Mycobacterium bovis BCG pointed out the potential importance of an alcohol dehydrogenase for maintaining the hydrophobic character of the cell ... [more ▼]

A previous study of the effect of zinc deprivation on Mycobacterium bovis BCG pointed out the potential importance of an alcohol dehydrogenase for maintaining the hydrophobic character of the cell envelope. In this report, the effect of the overexpression of the M. bovis BCG alcohol dehydrogenase (ADH) in Mycobacterium smegmatis and M. bovis BCG is described. The purification of the enzyme was performed to apparent homogeneity from overexpressing M. bovis BCG cells and its kinetic parameters were determined. The enzyme showed a strong preference for both aromatic and aliphatic aldehydes while the corresponding alcohols were processed 100-1000-fold less efficiently. The best kcat/Km values were found with benzaldehyde > 3-methoxybenzaldehyde > octanal > coniferaldehyde. A phylogenetic analysis clearly revealed that the M. bovis BCG ADH together with the ADHs from Bacillus subtilis and Helicobacter pylori formed a sister group of the class C medium-chain alcohol dehydrogenases, the plant cinnamyl alcohol dehydrogenases (CADs). Comparison of the kinetic properties of our ADH with some related class C enzymes indicated that the mycobacterial enzyme substrate profile resembled that of the CADs involved in plant defence rather than those implicated in lignification. A possible role for the M. bovis BCG ADH in the biosynthesis of the lipids composing the mycobacterial cell envelope is proposed. [less ▲]

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