A 3-dimensional primary production model (BLOOM/GEM) and its applications to the (southern) North Sea (coupled physical–chemical–ecological model)

Los, F.J.; Villars, M.T.; Tol, M.W.M. van der

doi:10.1016/j.jmarsys.2008.01.002

Cited by 76 publications

(52 citation statements)

References 43 publications

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“…For example, the phytoplankton group Phaeocystis was replaced by Ulva in the Venice Lagoon and Veerse Meer case studies, microphytobenthos was added in the Veerse Meer case study and pH-dependent phosphorus adsorption was included in the Sea of Marmara and Veerse Meer case studies. For a more detailed description of the calibration and validation procedure for GEM & BLOOM applications, see Los et al (2008). A recent sensitivity analysis of GEM (Salacinska, 2008) using the Moris method (Saltelli et al, 2004), revealed that the Dutch coastal zone application of the GEM model is particularly sensitive to Chl:C ratios and light-related parameters (excl.…”

Section: Discussionmentioning

confidence: 99%

“…BLOOM allows for simultaneous co-existence of different phenotypes and/or species groups, representing a continuous variable stoichiometry restricted only by the limits set for the individual types. Notice that the stoichiometry of the types is fixed, but the relative proportion varies (see Los et al (2008) for a more detailed description of BLOOM). BLOOM was originally developed as a steady-state model that is now being applied in a dynamic setting.…”

Section: Phytoplankton Processesmentioning

confidence: 99%

“…variable time steps (see Los et al, 2008 for further details). BLOOM assumes that fast-growing (less efficient) phytoplankton species dominate in a situation where resources (light, nutrients) are abundant, while slowgrowing but efficient phytoplankton species gain dominance when resources become limited.…”

Section: Phytoplankton Processesmentioning

confidence: 99%

“…Over the years, GEM was applied to the North Sea system in a range of studies, including simulations to evaluate the impact of a proposed land reclamation scheme (Nolte et al, 2005), and as a screening tool for the Water Framework Directive (WFD) to demonstrate the potential impacts of reductions in nutrient loads (Blauw & Los, 2004;Los & Wijsman, 2007). Most recently, BLOOM/GEM applications to the southern North Sea were subjected to a detailed three-dimensional model validation (Los et al, 2008). Here, we present the results of a trend analysis of chlorophyll-a concentrations in the North Sea over a 24-year period (1975-1998) predicted by the GEM model and compared with field observations (DONAR database, monthly means measured over the same 24-year period) at six monitoring stations ( Fig.…”

Section: Case 2-north Seamentioning

confidence: 99%

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GEM: a generic ecological model for estuaries and coastal waters

Blauw

Los

Bokhorst³

et al. 2008

Hydrobiologia

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The set-up, application and validation of a generic ecological model (GEM) for estuaries and coastal waters is presented. This model is a comprehensive ecological model of the bottom of the foodweb, consisting of a set of modules, representing specific water quality processes and primary production that can be combined with any transport model to create a dedicated model for a specific ecosystem. GEM links different physical, chemical and ecological model components into one generic and flexible modelling tool that allows for variable sized, curvilinear grids to accomodate both the requirements for local accuracy while maintaining a relatively short model run-time. The GEM model describes the behaviour of nutrients, organic matter and primary producers in estuaries and coastal waters, incorporating dynamic process modules for dissolved oxygen, nutrients and phytoplankton. GEM integrates the best aspects of existing Dutch estuarine models that were mostly dedicated to only one type of ecosystem, geographic area or subset of processes. Particular strengths of GEM include its generic applicability and the integration and interaction of biological, chemical and physical processes into one predictive tool. The model offers flexibility in choosing which processes to include, and the ability to integrate results from different processes modelled simultaneously with different temporal resolutions. The generic applicability of the model is illustrated using a number of representative examples from case studies in which the GEM model was successfully applied. Validation of these examples was carried out using the 'cost function' to compare model results with field observations. The validation results demonstrated consistent accuracy of the GEM model for various key parameters in both spatial dimensions (horizontally and vertically) as well as temporal dimensions (seasonally and across years) for a variety of water systems without the need for major reparameterisation.

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Section: Discussionmentioning

confidence: 99%

Section: Phytoplankton Processesmentioning

confidence: 99%

Section: Phytoplankton Processesmentioning

confidence: 99%

Section: Case 2-north Seamentioning

confidence: 99%

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GEM: a generic ecological model for estuaries and coastal waters

Blauw

Los

Bokhorst³

et al. 2008

Hydrobiologia

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“…In addition, understanding the behaviour of SPM is important with respect to the effects of dredging activities, especially for the maintenance and protection of the coast, on coastal ecosystems. Understanding the current structure and mixing is important for the biotic environment as SPM influences the light penetration which has an effect on the primary growth of algae (phytoplankton) (Los et al 2008). It is therefore of great importance to gain a better understanding of the processes influencing the currents along the Dutch coast.…”

Section: Introductionmentioning

confidence: 99%

Simultaneous measurements of tidal straining and advection at two parallel transects far downstream in the Rhine ROFI

Rijnsburger

Hout

Tongeren³

et al. 2016

Ocean Dynamics

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This study identifies and unravels the processes that lead to stratification and destratification in the far field of a Region of Freshwater Influence (ROFI). We present measurements that are novel for two reasons: (1) measurements were carried out with two vessels that sailed simultaneously over two cross-shore transects; (2) the measurements were carried out in the far field of the Rhine ROFI, 80 km downstream from the river mouth. This unique four dimensional dataset allows the application of the 3D potential energy anomaly equation for one of the first times on field data. With this equation, the relative importance of the depth mean advection, straining and nonlinear processes over one tidal cycle is assessed. The data shows that the Rhine ROFI extends 80 km downstream and periodic stratification is observed. The analysis not only shows the Van Oord, Rotterdam, The Netherlands important role of cross-shore tidal straining but also the significance of along-shore straining and depth mean advection. In addition, the nonlinear terms seem to be small. The presence of all the terms influences the timing of maximum stratification. The analysis also shows that the importance of each term varies in the cross-shore direction. One of the most interesting findings is that the data are not inline with several hypotheses on the functioning of straining and advection in ROFIs. This highlights the dynamic behaviour of the Rhine ROFI, which is valuable for understanding the distribution of fine sediments, contaminants and the protection of coasts.

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Steric Effects in RNA Interference: Probing the Influence of Nucleobase Size and Shape

Somoza

Silverman

Miller

et al. 2008

Chemistry A European J

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Nonpolar nucleosides with varying size and shape have been used to study the hydrogen-bonding stabilization and steric effects on RNA interference. The uracil and adenine residues of siRNA guide strands have been replaced by nonpolar isosteres of uracil and adenine and by steric variants. RNAi experiments targeting Renilla luciferase mRNA have shown close correlation between siRNA thermal stability and gene suppression. Interestingly, siRNA modified at position 7 on the guide strand does not follow this correlation, having substantial RNAi activity despite low thermal stability. Sequence-selectivity studies were carried out at this position with mutated target mRNAs and nucleobase analogues with varied size (2,4-difluoro- and 2,4-dichlorobenzene) and different shape (2,3-dichlorobenzene, 4-methylbenzimidazole). The results point out the importance of nucleobase shape and steric effects in RNA interference.

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A 3-dimensional primary production model (BLOOM/GEM) and its applications to the (southern) North Sea (coupled physical–chemical–ecological model)

Cited by 76 publications

References 43 publications

GEM: a generic ecological model for estuaries and coastal waters

GEM: a generic ecological model for estuaries and coastal waters

Simultaneous measurements of tidal straining and advection at two parallel transects far downstream in the Rhine ROFI

Steric Effects in RNA Interference: Probing the Influence of Nucleobase Size and Shape

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