Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Mayflies in Ecotoxicity Testing: Methodological Needs and Knowledge Gaps
    Sibley, Paul ; Lagadic, Laurent ; McCoole, Matt ; Norberg-King, Teresa ; Roessink, Ivo ; Soucek, David ; Watson-Leung, Trudy ; Wirtz, Jeff - \ 2020
    Integrated Environmental Assessment and Management 16 (2020)2. - ISSN 1551-3793 - p. 292 - 293.
    Herpes simplex virus 1 can enter dynamin 1 and 2 double- knockout fibroblasts
    Möckel, Maureen ; Rahn, Elena ; La Cruz, Nydia De; Wirtz, Lisa ; Lent, Jan W.M. Van; Pijlman, Gorben P. ; Knebel-Mörsdorf, Dagmar - \ 2019
    Journal of Virology 93 (2019)16. - ISSN 0022-538X
    Dynamin - Dynamin DKO - Dynasore - Endocytosis - HSV-1 - Low temperature - Murine embryonic fibroblasts - Semliki Forest virus - Virus entry

    Dynamin GTPases, best known for their role in membrane fission of endocytic vesicles, provide a target for viruses to be exploited during endocytic uptake. Recently, we found that entry of herpes simplex virus 1 (HSV-1) into skin cells depends on dynamin, although our results supported that viral internalization occurs via both direct fusion with the plasma membrane and via endocytic pathways. To further explore the role of dynamin for efficient HSV-1 entry, we utilized conditional dynamin 1 and dynamin 2 double-knockout (DKO) fibroblasts as an experimental tool. Strikingly, HSV-1 entered control and DKO fibroblasts with comparable efficiencies. For comparison, we infected DKO cells with Semliki Forest virus, which is known to adopt clathrin-mediated endocytosis as its internalization pathway, and observed efficient virus entry. These results support the notion that the DKO cells provide alternative pathways for viral uptake. Treatment of cells with the dynamin inhibitor dynasore confirmed that HSV-1 entry depended on dynamin in the control fibroblasts. As expected, dynasore did not interfere with viral entry into DKO cells. Electron microscopy of HSV-1-infected cells suggests viral entry after fusion with the plasma membrane and by endocytosis in both dynaminexpressing and dynamin-deficient cells. Infection at low temperatures where endocytosis is blocked still resulted in HSV-1 entry, although at a reduced level, which suggests that nonendocytic pathways contribute to successful entry. Overall, our results strengthen the impact of dynamin for HSV-1 entry, as only cells that adapt to the lack of dynamin allow dynamin-independent entry. IMPORTANCE The human pathogen herpes simplex virus 1 (HSV-1) can adapt to a variety of cellular pathways to enter cells. In general, HSV-1 is internalized by fusion of its envelope with the plasma membrane or by endocytic pathways, which reflects the high adaptation to differences in its target cells. The challenges are to distinguish whether multiple or only one of these internalization pathways leads to successful entry and, furthermore, to identify the mode of viral uptake. In this study, we focused on dynamin, which promotes endocytic vesicle fission, and explored how the presence and absence of dynamin can influence viral entry. Our results support the idea that HSV-1 entry into mouse embryonic fibroblasts depends on dynamin; however, depletion of dynamin still allows efficient viral entry, suggesting that alternative pathways present upon dynamin depletion can accomplish viral internalization.

    The minimum detectable difference (MDD) and the interpretation of treatmentr related effects of pesticides in experimental ecosystems
    Brock, T.C.M. ; Hammers-Wirtz, M. ; Hommen, U. ; Preuss, T.G. ; Ratte, H.T. ; Roessink, I. ; Strauss, T. ; Brink, P.J. van den - \ 2015
    Environmental Science and Pollution Research 22 (2015)2. - ISSN 0944-1344 - p. 1160 - 1174.
    zero dose control - risk-assessment - insecticide - mesocosms - models - replicability - microcosms - responses - recovery - systems
    In the European registration procedure for pesticides, microcosm and mesocosm studies are the highest aquatic experimental tier to assess their environmental effects. Evaluations of microcosm/mesocosm studies rely heavily on no observed effect concentrations (NOECs) calculated for different population-level endpoints. Ideally, a power analysis should be reported for the concentration–response relationships underlying these NOECs, as well as for measurement endpoints for which significant effects cannot be demonstrated. An indication of this statistical power can be provided a posteriori by calculated minimum detectable differences (MDDs). The MDD defines the difference between the means of a treatment and the control that must exist to detect a statistically significant effect. The aim of this paper is to expand on the Aquatic Guidance Document recently published by the European Food Safety Authority (EFSA) and to propose a procedure to report and evaluate NOECs and related MDDs in a harmonised way. In addition, decision schemes are provided on how MDDs can be used to assess the reliability of microcosm/mesocosm studies and for the derivation of effect classes used to derive regulatory acceptable concentrations. Furthermore, examples are presented to show how MDDs can be reduced by optimising experimental design and sampling techniques.
    Applicability of Different Hydraulic Parameters to Describe Soil Detachment in Eroding Rills
    Wirtz, S. ; Seeger, K.M. ; Zell, A. ; Wagner, C. ; Wagner, J.F. ; Ries, J.B. - \ 2013
    PLoS ONE 8 (2013)5. - ISSN 1932-6203
    gravel-bed streams - sediment transport capacity - concentrated flow - bedload transport - molecular dimensions - aggregate transport - size distribution - erosion process - load transport - natural rivers
    This study presents the comparison of experimental results with assumptions used in numerical models. The aim of the field experiments is to test the linear relationship between different hydraulic parameters and soil detachment. For example correlations between shear stress, unit length shear force, stream power, unit stream power and effective stream power and the detachment rate does not reveal a single parameter which consistently displays the best correlation. More importantly, the best fit does not only vary from one experiment to another, but even between distinct measurement points. Different processes in rill erosion are responsible for the changing correlations. However, not all these procedures are considered in soil erosion models. Hence, hydraulic parameters alone are not sufficient to predict detachment rates. They predict the fluvial incising in the rill's bottom, but the main sediment sources are not considered sufficiently in its equations. The results of this study show that there is still a lack of understanding of the physical processes underlying soil erosion. Exerted forces, soil stability and its expression, the abstraction of the detachment and transport processes in shallow flowing water remain still subject of unclear description and dependence.
    Field experiments for understanding and quantification of rill erosion processes
    Wirtz, S. ; Seeger, K.M. ; Ries, J.B. - \ 2012
    Catena 91 (2012)April. - ISSN 0341-8162 - p. 21 - 34.
    concentrated flow erosion - ephemeral gully erosion - soil-erosion - sediment transport - interrill erosion - rainfall simulation - water erosion - slope length - shallow flow - detachment
    Despite many efforts over the last decades to understand rill erosion processes, they remain unclear. This paper presents the results of rill experiments accomplished in Andalusia in September 2008 using a novel experimental set up. 72 L of water are introduced with an intensity of 9 L min(-1) into a rill. Rill cross sections, slope values, flow velocities and sediment concentrations were measured and these values were used to calculate sediment detachment and transport. Each experiment was repeated once within 15 min. With this new experimental setup it is possible to calculate several hydraulic parameters like hydraulic radius, wetted perimeter, flow cross section, transport rate and transport capacity which are usually estimated from coarse flow and rill parameters. In rill experiments, four different natural rills were flooded with the same experimental setup. Several processes like transport of loose material, erosion, bank failure and knickpoint retreat and the runoff effectiveness showed different and variable intensities. The sediment concentrations ranged between 5.2 and 438 g L-1. most cases, detachment rates are close to the transport capacity and, in some cases, the transport capacity is even exceeded. This can be explained by the occurrence of different erosion processes within a rill (e.g. detachment, bank failure, and headcut retreat) which are not all explained by the given equations. The results suggest that the existing soil erosion equations based on shear forces exerted by the flowing water are not able to describe rill erosion processes satisfactory. Too many different processes with a high spatial and temporal variability are responsible for rill development. (C) 2010 Elsevier B.V. All rights reserved.
    Investigation of the spatial distribution of runoff generation and soil erosion processes by means of experimental methods and field mapping
    Butzen, V. ; Seeger, K.M. ; Wirtz, S. ; Ries, J.B. - \ 2011
    Experimental validation of some basic assumptions used in physically based soil
    Wirtz, S. ; Seeger, K.M. ; Wagner, J.F. ; Ries, J.B. - \ 2011
    Hydrology and Earth System Sciences Discussions 2011 (2011)8. - ISSN 1812-2108 - p. 1247 - 1286.
    In spring 2009, four rill experiments were accomplished on a fallow land. Most external factors as well as discharge quantity (9 L min-1) were held constant or at least in the same range. Following most process based soil erosion models, detachment or runoff values should therefore be similar, but the experimental results show clear differences in sediment concentration, runoff and other measured and calculated values. This fact underlines the problems of process based models: concerning rill erosion, different processes take part and the process described by the models is only responsible for a part of the eroded material.
    Method ensemble for quantification of soil erosion processes in the field
    Wirtz, S. ; Iserloh, T. ; Butzen, V. ; Wengel, R. ; Marzen, M. ; Seeger, K.M. ; Rock, G. ; Remke, A. ; Fister, W. ; Ries, J.B. - \ 2010
    Geophysical Research Abstracts 2010 (2010). - ISSN 1029-7006 - p. EGU2010 - 4013.
    Rill erosion dynamics investigated by rill experiments in different rills in Andalusia
    Wirtz, S. ; Seeger, K.M. ; Remke, A. ; Wengel, R. ; Ries, J.B. - \ 2010
    In: Geophysical Research Abstracts 12. - - p. EGU2010 - 3897.
    Hydraulic parameters in eroding rills and their influence on detachment processes
    Wirtz, S. ; Seeger, K.M. ; Zell, A. ; Wagner, C. ; Wengel, R. ; Ries, J.B. - \ 2010
    In: Geophysical Research Abstracts 12. - Vienna, Austria : - p. EGU2010 - 3902.
    Investigation of the spatial distribution of runoff generation and soil erosion processes by means of experimental methods
    Butzen, V. ; Huemann, M. ; Mueller, C. ; Casper, M.C. ; Hansen, R. ; Seeger, K.M. ; Wirtz, S. ; Iserloh, T. ; Ries, J.B. - \ 2010
    In: Geophysical Research Abstracts 12. - Vienna, Austria : - p. EGU2010 - 3420.
    The rill experiment as a method to approach a quantification of rill erosion process activity
    Wirtz, S. ; Seeger, K.M. ; Ries, J.B. - \ 2010
    Zeitschrift für Geomorphologie 54 (2010)1. - ISSN 0372-8854 - p. 47 - 64.
    concentrated flow erosion - ephemeral gully erosion - sediment transport - resistance - areas - mine - soil
    Within this paper a standardized method to quantify sediment transport and runoff in natural rills is described. In order to achieve this, several rill experiments (RE) were accomplished in March 2007 in the Arnás catchment in the Spanish Pyrenees. Both, anthropogenically initiated and naturally developed rills were flushed with a total water quantity of 72 l in 8 minutes (equivalent to 9 l min-1). For the characterisation of the rill, slope is measured and micromorphological features like scours are registered. The experiments are characterised by the flow velocities along the whole flushed rill, sediment concentrations at different points and different times during the experiment. Runoff is measured after 25 m continuously. With this data, a set of characteristic variables is generated, which reflects the infiltration and flow behaviour along the rill. By means of rainfall simulations within the rills catchments, their contributing runoff was estimated also. The tested rills were developed on average slopes oscillating between 7.6° and 11.3°, the steepest slope reached 16°. The sediment concentrations reached average values between 0.69 and 2.21 g l-1, the maximum values ranged between 1.59 and 6.31 g l-1. Comparing the sediment concentrations measured in the rills to the sediment concentrations in the runoff of the river Arnás, it can be stated that the concentrations in the rills are usually higher. Though, the runoff was to low to cause erosion. Accordingly, the runoff amount that can be produced within the rills catchments was found to be about 10-25 times higher. By means of the developed rill experiments, for which easy to handle devices were built and are described in detail, it becomes possible to assess the effectivity of individual rills in a catchment and to evaluate their hydraulic functioning as well as their geomorphodynamic activity
    Influence of flowing water's turbulence to soil erosion
    Wirtz, S. ; Zell, A. ; Wagner, C. ; Seeger, K.M. ; Ries, J.B. - \ 2009
    Geophysical Research Abstracts 2009 (2009)11. - ISSN 1029-7006 - p. 8838 - 8838.
    Experimental investigations of rill erosion dynamics in Andalusia
    Wirtz, S. ; Seeger, K.M. ; Ries, J.B. - \ 2009
    Development and validation of an individual based Daphnia magna population model: The influence of crowding on population dynamics
    Preuss, T.G. ; Hammers-Wirtz, M. ; Hommen, U. ; Rubach, M.N. ; Ratte, H.T. - \ 2009
    Ecological Modelling 220 (2009)3. - ISSN 0304-3800 - p. 310 - 329.
    food concentration - toxicity tests - offspring size - feeding rate - reproduction - growth - zooplankton - density - pulex - consequences
    An individual-based model was developed to predict the population dynamics of Daphnia magna at laboratory conditions from individual life-history traits observed in experiments with different feeding conditions. Within the model, each daphnid passes its individual life cycle including feeding on algae, aging, growing, developing and – when maturity is reached – reproducing. The modelled life cycle is driven by the amount of ingested algae and the density of the Daphnia population. At low algae densities the population dynamics is mainly driven by food supply, when the densities of algae are high, the limiting factor is “crowding” (a density-dependent mechanism due to chemical substances released by the organisms or physical contact, but independent of food competition). The model was calibrated using data from life cycle tests at flow-through conditions with different levels of algae concentrations. In addition to the average life cycle parameters for different food levels, the variability between the individuals was considered by stochastic assignment of values from the observed distributions in the experiments to each individual property. The model was tested on the individual and the population level. Individual growth and reproduction were tested based on the results of life cycle tests conducted under semi-batch conditions; the population level was considered by testing at different food levels under flow-trough and static conditions, including extinction at starvation conditions. The model was not only able to predict the total abundance of the population over time, but also predicted the size structure in good accordance with the observations. The population dynamics emerge directly from the life cycle of the individual daphnids. It depends on the available food and–this had not been considered in other Daphnia models–on crowding effects due to high Daphnia abundances
    A ß-glucosidase/xylosidase from the phytopathogenic oomycete, Phytophthora infestans
    Brunner, F. ; Wirtz, W. ; Rose, J.K.C. ; Darvill, A.G. ; Govers, F. ; Scheel, D. ; Nürnberger, T. - \ 2002
    Phytochemistry 59 (2002). - ISSN 0031-9422 - p. 689 - 696.
    High affinity binding of very long chain fatty acyl-CoA esters to the peroxisomal non-specific lipid transfer protein(sterolcarrier protein-2)
    Dansen, T.B. ; Westerman, J. ; Wouters, F.S. ; Wanders, R.J.A. ; Hoek, A. van; Gadella, T.W.J. ; Wirtz, K.W.A. - \ 1999
    Biochemical Journal 339 (1999)1. - ISSN 0264-6021 - p. 193 - 199.
    Tissue-specific distribution of a peroxisomal 46-kDa protein related to the 58kDa protein (Sterol Carrier Protein X; Sterol Carrier Protein 2/3-Oxoacyl-CoA Thiolase)
    Ossendorp, B.C. ; Voorhout, W.F. ; Amerongen, A. van; Brunink, F. ; Batenburg, J.J. ; Wirtz, K.W.A. - \ 1996
    Archives of Biochemistry and Biophysics 334 (1996). - ISSN 0003-9861 - p. 251 - 260.
    Quantitative analysis of lipid-lipid and lipid-protein interactions in membranes by use of pyrene-labeled phosphoinositides.
    Pap, E.H.W. ; Hanicak, A. ; Hoek, A. van; Wirtz, K.W.A. ; Visser, A.J.W.G. - \ 1995
    Biochemistry 34 (1995). - ISSN 0006-2960 - p. 9118 - 9125.
    Fluorescopic evaluation of protein-lipid relations in cellular signalling
    Pap, E.H.W. - \ 1994
    Agricultural University. Promotor(en): C. Veeger; K.W.A. Wirtz; A.J.W.G. Visser. - S.l. : Pap - ISBN 9789054853190 - 154
    eiwitten - celmembranen - lipiden - cholesterol - fluorescentie - spectroscopie - analyse - luminescentie - proteins - cell membranes - lipids - cholesterol - fluorescence - spectroscopy - analysis - luminescence
    Introduction

    Cellular communication is partly mediated through the modulation of protein activity, structure and dynamics by lipids. In contrast to the biochemical aspects of lipid signalling, relatively little is known about the physical properties of the "signal" lipids (lipids involved in cellular signalling) in membranes and their interaction with membrane proteins. Knowledge about these properties contributes to the understanding of the molecular mechanism of intracellular communication. The main objective of this thesis is to evaluate organisational and motional aspects of protein-lipid systems that play a role in this signalling. Fluorescence spectroscopy was employed to distinguish between interacting elements of the protein-lipid binding equilibrium from the non-interacting ones and to reveal their motional properties and characteristics in organisation. The first chapter of this thesis summarises the functional relevance and fundamental mechanisms of protein-lipid interactions and introduces some fluorescopic tools which can be applied in these investigations. In the remaining chapters the biophysical properties of the phosphoinositides phosphatidylinositol (PI), phosphatidylinositol- 4-phosphate (PIP) and phosphatidylinositol-4, 5-biphosphate (PIP 2 ) and diacylglycerol (DG) and their relation to protein kinase C (PKC) and Band 3 (an abundant anion exchanging protein in erythrocyte membranes) form a central theme. Three types of binding are evaluated: 1) peripheral membrane binding of proteins, 2) lipids replacing other lipids at the protein surface and 3) lipids which bind to vacant cofactor sites at the protein. By combining complementary fluorescopic techniques, and by refinement of fluorescence data analysis, new aspects of protein-lipid relations have been elucidated which are summarised below. As a model study and introduction for the protein-lipid studies described in this thesis, Chapter 2 considers the association of lysozyme with acidic vesicles. From the experiments it could be concluded that the protein conformation and dynamics of lysozyme are effected when the protein interacts with acidic membranes. Apart from the general interest in protein-lipid interactions, this study demonstrates that a fractional analysis of time-resolved fluorescence and fluorescence anisotropy decay curves can provide accurate binding curves of protein molecules to lipid interfaces.

    The interaction of PKC with PS and phosphoinositides and DG
    Various aspects of the application of fluorescence anisotropy in the evaluation of lipid motion are introduced in Chapter 3. In that Chapter the motional characteristics of three 1, 6- diphenyl-1, 3, 5-hexatriene (DPH) labelled phosphatidylcholines are compared.

    Based on the results of this study the effect of PKC on the reorientational properties of fluorescent analogues of DG and PC have been evaluated using a constrained model of analysis (Chapter 4). It appeared that in membranes DPH-DG experiences a larger motional freedom than DPH-PC, which indicates that DG induces a lipid packing irregularity. Defects in membrane organisation lead to a partial exposure of hydrophobic regions of phospholipids to aqueous environment and thereby increase the ground state energy of bilayers (Jain & Zakim, 1987). Therefore the activation energy associated with insertion of PKC into the hydrophobic membrane core could be reduced by DG. Three complementary observations provide evidence that PKC is able to interact with PS containing membranes in the absence of calcium:
    1) The isotropic rotation of PS containing micelles slows down upon addition of PKC (Chapter 4).
    2) Micelles and vesicles containing pyrene labelled lipids quench the tryptophan fluorescence of PKC (Chapter 5).
    3) PKC significantly reduces the collision frequency of pyrene labelled PS (Chapter 5).

    Addition of calcium results in the binding of PKC to DG (Chapter 6). For this DG-PKC interaction the presence of PS is a prerequisite (Chapters 4, 5, 6). The precise mechanism of this calcium dependence of DG binding remains unclear. Calcium enhances the binding of PKC to PS. As a result of this enhanced PS binding the probability of finding a DG molecule close to PKC may increase since PKC molecules retain longer at the membrane surface. Alternatively, calcium may induce changes in PKC that result in exposure of a shielded lipid cofactor site for DG. As a consequence of the interaction with PKC, the lateral and rotational diffusion and orientational freedom (Chapters 4 and 5) of labelled DG are reduced. The interaction with DG is highly specific, since the motional properties of labelled PC, PS and PI analogues are only moderately effected by PKC (Chapters 4 and 5) and these lipids are not able to quench PKC fluorescence at low concentrations (Chapter 6). However, labelled phosphoinositides PIP and PIP 2 partly mimic the properties of DG. They bind with high affinity to PKC and the acyl chain dynamics of (dipyr)PIP and (dipyr)DG are equally effected by PKC (Chapters 5 and 6). In addition, like is known for DG, only a very limited number of phosphoinositides bind to one PKC molecule (Chapter 6). Double labelling experiments and replacement studies suggest that PIP and DG can bind simultaneously to PKC while PIP 2 and DG cannot (Chapters 5 and 6). In addition, it appeared that only PIP 2 and DG effectively activate PKC. Combined, these results indicate a cofactor role of PIP 2 for PKC.

    Although the role of PIP 2 in the activation of PKC has to be established in vivo , its properties do fit excellently to a messenger function. Radioactive labelling studies with H-inositol and P-phosphate revealed that the turnover of PIP 2 is extremely rapid and in resting cells its level is low (reviewed by Hokin, 1985). The major part of PIP 2 present at resting conditions, may even be not available for PKC activation. Several studies have shown that the inositol lipids are heterogeneously distributed in the different cellular membranes and that only a small fraction of the total inositol lipid content is available for enzymes like phospholipase C (see for a review Downes & Michell, 1985). Like most other signalling lipids the PIP 2 concentration increases transiently to high levels within seconds after hormone stimulation of cells (Hansen et al., 1986). The dual role of PIP 2 as a DG-precursor and as a direct PKC-activator opens new avenues for the differentiation of signals via the various PKC families. The cell responses that induce the PLC catalysed hydrolysis of phosphoinositides always result in the co-appearance of DG and calcium. Several PKC-isoforms, however, do no need calcium for their activity. Other lipid cofactors like PIP 2 may function as cofactors for these calcium independent protein kinases. For the calcium dependent protein kinases an inositol triphosphate (IP 3 ) mediated calcium release would imply the production of DG.


    When calcium is provided via calcium channels in the plasma membrane or via sphingosine phosphate signalling (Dessai et al., 1992), no DG is released and other lipid activators like PIP 2 can take over the cofactor role. In this DG-independent activation, the temporal availability of calcium in the cytosol is the main switch for PKC activity. In this respect, it would be interesting to know if there are situations in the cell in which the PIP-kinase and (phosphoinositide-specific) phospholipase C activities are uncoupled. In that case the levels of PIP 2 can be regulated independently from those of DG, which would make the double role of PIP 2 in the regulation of PKC activity even more attractive (Figure 1).

    Heterogeneous distribution of phosphoinositides in membranes
    In Chapter 7, the interaction of the phosphoinositides with human erythrocyte Band 3 protein was characterised using resonance energy transfer. The efficiency of quenching of the fluorescence from tryptophan residues in the protein by pyrene lipids in the membrane decreased in the order pyrPIP 2 , pyrPIP, pyrPI and pyrPC indicating different spatial distributions of these lipids with respect to Band 3. Global analysis of the quenched tryptophan fluorescence decays yielded indices for the spatial distributions of the different lipids. It appeared that the charged lipids PIP 2 and PIP spend longer time in the vicinity of Band 3 than PI and PC. In investigations complementary to these protein fluorescence observations, the monomer/excimer fluorescence of pyrene labelled phosphoinositides in DOPC membranes was evaluated in the absence and presence of Band 3 protein (Chapter 8). In combination with theoretical refinements of the model for lipid migration, these experiments revealed estimates for the lateral dynamics and lipid-lipid repulsion in membranes. In addition, the relative binding constants and the minimum number of Band 3 sites possessing affinity for the phosphoinositides could be roughly estimated. Consistent with intuitive expectations the lipid-lipid repulsion appeared highly dependent on the amount of negative charge of the lipid headgroups. Combining these experiments indicates that lipid-lipid repulsion and the Band 3-lipid interactions induce a non- random distribution of the Phosphoinositides. This non-random distribution will probably effect the accessibility of the inositol lipids for phospholipase C and for other phosphoinositide dependent proteins like PKC and may result in the functional heterogeneity of the phosphoinositides (Downes & Michell, 1985).

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