Hydrological assessment and monitoring of wetlands

The physical and chemical characteristics which favour wetland plant communities, primarily high soil water levels and anaerobic soil chemistry, are related directly to the hydrology/hydrogeology of the wetland and often its surrounding catchment. Appreciation and successful management of a wetland therefore almost always requires an understanding of its hydrological functioning, including the influences on hydrological functioning which often lie beyond the designated boundary of the sit

The Cosmological Constant

This is a review of the physics and cosmology of the cosmological constant. Focusing on recent developments, I present a pedagogical overview of cosmology in the presence of a cosmological constant, observational constraints on its magnitude, and the physics of a small (and potentially nonzero) vacuum energy.Comment: 50 pages. Submitted to Living Reviews in Relativity (http://www.livingreviews.org/), December 199

The stellar halo of the Galaxy

Stellar halos may hold some of the best preserved fossils of the formation history of galaxies. They are a natural product of the merging processes that probably take place during the assembly of a galaxy, and hence may well be the most ubiquitous component of galaxies, independently of their Hubble type. This review focuses on our current understanding of the spatial structure, the kinematics and chemistry of halo stars in the Milky Way. In recent years, we have experienced a change in paradigm thanks to the discovery of large amounts of substructure, especially in the outer halo. I discuss the implications of the currently available observational constraints and fold them into several possible formation scenarios. Unraveling the formation of the Galactic halo will be possible in the near future through a combination of large wide field photometric and spectroscopic surveys, and especially in the era of Gaia.Comment: 46 pages, 16 figures. References updated and some minor changes. Full-resolution version available at http://www.astro.rug.nl/~ahelmi/stellar-halo-review.pd

PKQuest: a general physiologically based pharmacokinetic model. Introduction and application to propranolol

BACKGROUND: A "physiologically based pharmacokinetic" (PBPK) approach uses a realistic model of the animal to describe the pharmacokinetics. Previous PBPKs have been designed for specific solutes, required specification of a large number of parameters and have not been designed for general use. METHODS: This new PBPK program (PKQuest) includes a "Standardhuman" and "Standardrat" data set so that the user input is minimized. It has a simple user interface, graphical output and many new features: 1) An option that uses the measured plasma concentrations to solve for the time course of the gastrointestinal, intramuscular, intraperotineal or skin absorption and systemic availability of a drug – for a general non-linear system. 2) Capillary permeability limitation defined in terms of the permeability-surface area products. 4) Saturable plasma and tissue protein binding. 5) A lung model that includes perfusion-ventilation mismatch. 6) A general optimization routine using either a global (simulated annealing) or local (Powell) minimization applicable to all model parameters. RESULTS: PKQuest was applied to measurements of human propranolol pharmacokinetics and intestinal absorption. A meal has two effects: 1) increases portal blood flow by 50%; and 2) decreases liver metabolism by 20%. There is a significant delay in the oval propranolol absorption in fasting subjects that is absent in fed subjects. The oral absorption of the long acting form of propranolol continues for a period of more than 24 hours. CONCLUSIONS: PKQuest provides a new general purpose, easy to use, freely distributed and physiologically rigorous PBPK software routine

Predicting the F(ab)-mediated effect of monoclonal antibodies in vivo by combining cell-level kinetic and pharmacokinetic modelling

Cell-level kinetic models for therapeutically relevant processes increasingly benefit the early stages of drug development. Later stages of the drug development processes, however, rely on pharmacokinetic compartment models while cell-level dynamics are typically neglected. We here present a systematic approach to integrate cell-level kinetic models and pharmacokinetic compartment models. Incorporating target dynamics into pharmacokinetic models is especially useful for the development of therapeutic antibodies because their effect and pharmacokinetics are inherently interdependent. The approach is illustrated by analysing the F(ab)-mediated inhibitory effect of therapeutic antibodies targeting the epidermal growth factor receptor. We build a multi-level model for anti-EGFR antibodies by combining a systems biology model with in vitro determined parameters and a pharmacokinetic model based on in vivo pharmacokinetic data. Using this model, we investigated in silico the impact of biochemical properties of anti-EGFR antibodies on their F(ab)-mediated inhibitory effect. The multi-level model suggests that the F(ab)-mediated inhibitory effect saturates with increasing drug-receptor affinity, thereby limiting the impact of increasing antibody affinity on improving the effect. This indicates that observed differences in the therapeutic effects of high affinity antibodies in the market and in clinical development may result mainly from Fc-mediated indirect mechanisms such as antibody-dependent cell cytotoxicity

Amyloidogenic Regions and Interaction Surfaces Overlap in Globular Proteins Related to Conformational Diseases

Protein aggregation underlies a wide range of human disorders. The polypeptides involved in these pathologies might be intrinsically unstructured or display a defined 3D-structure. Little is known about how globular proteins aggregate into toxic assemblies under physiological conditions, where they display an initially folded conformation. Protein aggregation is, however, always initiated by the establishment of anomalous protein-protein interactions. Therefore, in the present work, we have explored the extent to which protein interaction surfaces and aggregation-prone regions overlap in globular proteins associated with conformational diseases. Computational analysis of the native complexes formed by these proteins shows that aggregation-prone regions do frequently overlap with protein interfaces. The spatial coincidence of interaction sites and aggregating regions suggests that the formation of functional complexes and the aggregation of their individual subunits might compete in the cell. Accordingly, single mutations affecting complex interface or stability usually result in the formation of toxic aggregates. It is suggested that the stabilization of existing interfaces in multimeric proteins or the formation of new complexes in monomeric polypeptides might become effective strategies to prevent disease-linked aggregation of globular proteins

Individual-based model of juvenile eel movement parametrized with computational fluid dynamics-derived flow fields informs improved fish pass design

European eel populations have declined markedly in recent decades, caused in part by in-stream barriers, such as weirs and pumping stations, which disrupt the upstream migration of juvenile eels, or elvers, into rivers. Eel passes, narrow sloping channels lined with substrata that enable elvers to ascend, are one way to mitigate against these barriers. Currently, studded eel tiles are a popular substrate. This study is the first to evaluate the flow fields within studded eel tiles and to model the swimming performance of elvers using cellular automata (CA) and individual- (or agent-) based models. Velocities and flow depths predicted by a computational fluid dynamics model of studded eel tiles are first validated against published values for a single installation angle–discharge combination. The validated model is then used to compute three-dimensional flow fields for eel passes at five different installation angles and three inflow discharges. CA and individual-based models are employed to assess upstream passage efficiency for a range of elver sizes. The individual-based model approximates measured passage efficiencies better than the CA model. Passage efficiency is greatest for shallow slopes, low discharges and large elvers. Results are synthesized into an easy-to-understand graphic to help practitioners improve eel pass designs

Surface-induced aggregation of type I procollagen.

International audienceWe have examined the state of aggregation of type I procollagen in the concentration range 5 to 800 micrograms/ml. Electron microscopy typically indicates a high proportion of aggregated material (greater than 50%), when a range of preparative techniques are used. Aggregates of in-register molecules (segment-long-spacing-like aggregates) are frequently observed, often with units of in-register molecules connected via the C-terminal propeptides. In contrast, studies using gel-filtration chromatography and density-gradient ultracentrifugation demonstrate only limited aggregation in solution (less than 5%) even at 800 micrograms/ml. The aggregated material is mainly dimeric and probably not segment-long-spacing-like. We conclude that aggregation of procollagen is strongly favoured by adsorption to a surface when samples are prepared for electron microscopy. The possible relevance of these observations to the fate of procollagen secreted by cells in vivo is discussed.We have examined the state of aggregation of type I procollagen in the concentration range 5 to 800 micrograms/ml. Electron microscopy typically indicates a high proportion of aggregated material (greater than 50%), when a range of preparative techniques are used. Aggregates of in-register molecules (segment-long-spacing-like aggregates) are frequently observed, often with units of in-register molecules connected via the C-terminal propeptides. In contrast, studies using gel-filtration chromatography and density-gradient ultracentrifugation demonstrate only limited aggregation in solution (less than 5%) even at 800 micrograms/ml. The aggregated material is mainly dimeric and probably not segment-long-spacing-like. We conclude that aggregation of procollagen is strongly favoured by adsorption to a surface when samples are prepared for electron microscopy. The possible relevance of these observations to the fate of procollagen secreted by cells in vivo is discussed

The CUB domains of procollagen C-proteinase enhancer control collagen assembly solely by their effect on procollagen C-proteinase/bone morphogenetic protein-1.

International audienceProcollagen C-proteinase enhancer (PCPE) is a 55 kDa glycoprotein that increases the activity of procollagen C-proteinase (PCP)/bone morphogenetic protein-1 (BMP-1) during C-terminal processing of fibrillar collagen precursors. Here we show that the 36 kDa, active fragment of PCPE enhances the activity of both the short (mouse) and long (chick) forms of PCP/BMP-1. The activity of PCPE is not associated with the formation of sedimentable procollagen aggregates. In addition, PCPE (36 kDa) has no effect in vitro on N-terminal procollagen processing by highly purified procollagen N-proteinase. Finally, when the amount of PCP is adjusted so that the rate of C-terminal processing remains constant, PCPE (36 kDa) has no effect on the assembly of collagen or pN-collagen in vitro following C-terminal processing of the corresponding precursors.Procollagen C-proteinase enhancer (PCPE) is a 55 kDa glycoprotein that increases the activity of procollagen C-proteinase (PCP)/bone morphogenetic protein-1 (BMP-1) during C-terminal processing of fibrillar collagen precursors. Here we show that the 36 kDa, active fragment of PCPE enhances the activity of both the short (mouse) and long (chick) forms of PCP/BMP-1. The activity of PCPE is not associated with the formation of sedimentable procollagen aggregates. In addition, PCPE (36 kDa) has no effect in vitro on N-terminal procollagen processing by highly purified procollagen N-proteinase. Finally, when the amount of PCP is adjusted so that the rate of C-terminal processing remains constant, PCPE (36 kDa) has no effect on the assembly of collagen or pN-collagen in vitro following C-terminal processing of the corresponding precursors