Regulation of membrane transport by rab GTPases

Membrane flow through the cell is a highly dynamic process in which intracellular compartments communicate via tubulo-vesicular structures shuttling cargo molecules to their destinations. Transport carriers are formed at a donor compartment and navigate through the cytoplasm to the target organelle, on which they subsequently dock and fuse. Many of these events are regulated by the cooperative action of monomeric rab GTPases and their effector proteins. Research in recent years resulted in the identification of many rab effectors, providing first glimpses how the GTPase switch of individual rab proteins is utilized in discrete transport steps.     

Beta-catenin and TCF mediate cell positioning in the intestinal epithelium by controlling the expression of EphB/ephrinB

In the small intestine, the progeny of stem cells migrate in precise patterns. Absorptive, enteroendocrine, and goblet cells migrate toward the villus while Paneth cells occupy the bottom of the crypts. We show here that beta-catenin and TCF inversely control the expression of the EphB2/EphB3 receptors and their ligand ephrin-B1 in colorectal cancer and along the crypt-villus axis. Disruption of EphB2 and EphB3 genes reveals that their gene products restrict cell intermingling and allocate cell populations within the intestinal epithelium. In EphB2/EphB3 null mice, the proliferative and differentiated populations intermingle. In adult EphB3(-/-) mice, Paneth cells do not follow their downward migratory path, but scatter along crypt and villus. We conclude that in the intestinal epithelium beta-catenin and TCF couple proliferation and differentiation to the sorting of cell populations through the EphB/ephrin-B system.     

Zinc ions and cation diffusion facilitator proteins regulate Ras-mediated signaling

C. elegans cdf-1 was identified in a genetic screen for regulators of Ras-mediated signaling. CDF-1 is a cation diffusion facilitator protein that is structurally and functionally similar to vertebrate ZnT-1. These proteins have an evolutionarily conserved function as positive regulators of the Ras pathway, and the Ras pathway has an evolutionarily conserved ability to respond to CDF proteins. CDF proteins regulate Ras-mediated signaling by promoting Zn(2+) efflux and reducing the concentration of cytosolic Zn(2+), and cytosolic Zn(2+) negatively regulates Ras-mediated signaling. Physiological concentrations of Zn(2+) cause a significant inhibition of Ras-mediated signaling. These findings suggest that Zn(2+) negatively regulates a conserved element of the signaling pathway and that Zn(2+) regulation is important for maintaining the inactive state of the Ras pathway.     

8-Epixanthatin, a light-induced growth inhibitor, mediates the phototropic curvature in sunflower (Helianthus annuus) hypocotyls

The distribution of the endogenous auxin-inhibiting substance, 8-epixanthatin, was determined in the lighted and shaded sides of phototropically-stimulated, de-etiolated sunflower ( Helianthus annuus L. cv. Taiyo) hypocotyls. From 40 min after the onset of phototropic stimulation, the growth rate at the lighted side was inhibited, whereas that at the shaded side showed no change. In the lighted side, 8-epixanthatin increased by 20 min after the onset of unilateral illumination and, after 40 min, reached a 3-fold larger concentration than that in the shaded side. Unilateral application of 8-epixanthatin suppressed the growth of etiolated hypocotyls at the applied side only, causing the hypocotyls to bend at the site of application. It is concluded that phototropic curvature in sunflower hypocotyls is caused by a lateral gradient of the auxin-inhibiting substance 8-epixanthatin.     

Differential effects of ammonium and nitrate on three heathland species

Arnica montana and Cirsium dissectum, typical of species-rich heathlands and acidic grasslands, have declined rapidly in The Netherlands in recent years. Field surveys suggest that the decline is caused by soil acidification as a result of enhanced atmospheric N and S deposition. Therefore, the survival, growth and development of these species were studied in a water culture experiment, using nutrient solutions which differed both in mineral nitrogen form and in ammonium concentration. For comparison, the performance of a third, acid tolerant species, Calluna vulgaris, was studied. The results showed that both Arnica and Cirsium performed better using nitrate than when using ammonium as a sole nitrogen source, whereas ammonium toxicity became apparent when ammonium concentrations were raised above 100 µM. Ammonium toxicity was expressed by an increase in mortality of Arnica plants with increasing ammonium concentrations and by a reduction of biomass in Arnica and Cirsium. Furthermore, cation concentrations in both roots and shoots decreased when ammonium was supplied as a nitrogen source. In contrast, Calluna showed optimal development when using ammonium as a sole nitrogen source. In this species, only root biomass was negatively affected by high ammonium concentrations. The ecological implications of these preferences are discussed in relation to soil acidification.     

Improvement of adventitious shoot formation from carnation leaf explants

Adventitious shoot formation from leaf explants of carnation (Dianthus caryophyllus L.) was investigated. The two leaves from one node of in vitro-grown plants showed different shoot-forming potential, depending on the order in which the leaves were removed from the stem. The leaf removed second formed more shoots and also had a large amount of adhering stem tissue. Explants with equal amounts of adhering stem tissue were obtained by making two incisions through the fused leaf bases, prior to their removal, resulting in an improved shoot formation. The procedure developed for leaf explants from in vitro-grown plants was also applied to leaf explants from greenhousegrown plants. Shoot formation from leaf explants taken from greenhouse-grown plants was further improved by cutting the leaf explant longitudinally into two parts.Abbreviations BA benzyladenine - NAA -naphthaleneacetic acid     

Protein synthesis of binucleate and trinucleate pollen and its relationship to tube emergence and growth

Under humid conditions, both bi- and trinucleate pollen species incorporate, on the average, very low amounts of leucine, e.g., 0.4 pmol min^-1mg pollen^-1. During germination in vitro, however, the two types of pollens greatly differ in their capacity for protein synthesis.Binucleate pollen species such as Typha, which are characterized by slow respiration in humid air and prolonged lag periods during germination in vitro, contain large amounts of monoribosomes at dehiscence. Polyribosomes are formed soon after the pollen is wetted in the germination medium, and a considerable incorporation of leucine is initiated after 10–15 min. More rapidly respiring, binucleate pollen showing a short lag period, such as Tradescantia, may already contain many polysomes at dehiscence and incorporate leucine within 2 min of germination. However, rapidly respiring, trinucleate Compositae pollen contains very limited amounts of ribosomal material and never attains any substantial level of incorporation. Cycloheximide completely inhibits both protein synthesis and tube emergence and growth in the slowly respiring, binucleate pollen species. The more rapidly respiring types are less dependent on protein synthesis, while germination of the phylogenetically advanced, trinucleate Compositae pollen proceeds completely independently. It is concluded that the level of phylogenetic advancement of the male gametophyte is characterized by its overall state of metabolic development at dehiscence rather than by the number of its generative cells.Abbreviations BSA bovine serum albumin - CHI cycloheximide - EGTA ethyleneglycol-bis(-aminoethyl ether) N,N-tetraacetic acid - RH relative humidity - TCA trichloroacetic acid     

A Computational Model for the Analysis of Lipoprotein Distributions in the Mouse: Translating FPLC Profiles to Lipoprotein Metabolism

Disturbances of lipoprotein metabolism are recognized as indicators of cardiometabolic disease risk. Lipoprotein size and composition, measured in a lipoprotein profile, are considered to be disease risk markers. However, the measured profile is a collective result of complex metabolic interactions, which complicates the identification of changes in metabolism. In this study we aim to develop a method which quantitatively relates murine lipoprotein size, composition and concentration to the molecular mechanisms underlying lipoprotein metabolism. We introduce a computational framework which incorporates a novel kinetic model of murine lipoprotein metabolism. The model is applied to compute a distribution of plasma lipoproteins, which is then related to experimental lipoprotein profiles through the generation of an in silico lipoprotein profile. The model was first applied to profiles obtained from wild-type C57Bl/6J mice. The results provided insight into the interplay of lipoprotein production, remodelling and catabolism. Moreover, the concentration and metabolism of unmeasured lipoprotein components could be determined. The model was validated through the prediction of lipoprotein profiles of several transgenic mouse models commonly used in cardiovascular research. Finally, the framework was employed for longitudinal analysis of the profiles of C57Bl/6J mice following a pharmaceutical intervention with a liver X receptor (LXR) agonist. The multifaceted regulatory response to the administration of the compound is incompletely understood. The results explain the characteristic changes of the observed lipoprotein profile in terms of the underlying metabolic perturbation and resultant modifications of lipid fluxes in the body. The Murine Lipoprotein Profiler (MuLiP) presented here is thus a valuable tool to assess the metabolic origin of altered murine lipoprotein profiles and can be applied in preclinical research performed in mice for analysis of lipid fluxes and lipoprotein composition.     

Modelling ontogenetic changes of nitrogen and water content in lettuce

BACKGROUND AND AIMS: It is well established that the nitrogen content of plants, including lettuce, decreases with time. It has also been observed that water content of lettuce increases between planting and harvest. This paper is an attempt at modelling these observations. METHODS: An existing dynamic model (Nicolet), designed to predict growth and nitrate content of glasshouse lettuce, is modified to accommodate the ontogenetic changes of reduced-nitrogen and water contents (on a dry matter basis). The decreasing reduced-N content and the increasing water content are mimicked by dividing the originally uniform plant into 'metabolically active' tissue and 'support' tissue. The 'metabolic' tissue is assumed to contain a higher nitrogen content and a lower water content than the 'support' tissue. As the plants grow, the ratio of 'support' to 'metabolic' tissue increases, resulting in an increased mean water content and a decreased reduced-N content. Simulations with the new model are compared with experimental glasshouse data over four seasons. KEY RESULTS: The empirical linear relationship between water and reduced-N contents, matches, to a good approximation, the corresponding relationship based on the model. The agreement between the two makes it possible to effectively uncouple the estimation of the 'ontogenetic' parameters from the estimation of the other parameters. The growth and nitrate simulation results match the data rather well and are hardly affected by the new refinement. The reduced-N and water contents are predicted much better with the new model. CONCLUSION: Prediction of nitrogen uptake for the substantial nitrate pool of lettuce depends on the water content. Hence, the modified model may assist in making better fertilization decisions and better estimates of nitrogen leaching.     

Theory of force regulation by nascent adhesion sites

The mechanical coupling of a cell with the extracellular matrix relies on adhesion sites, clusters of membrane-associated proteins that communicate forces generated along the F-Actin filaments of the cytoskeleton to connecting tissue. Nascent adhesion sites have been shown to regulate these forces in response to tissue rigidity. Force-regulation by substrate rigidity of adhesion sites with fixed area is not possible for stationary adhesion sites, according to elasticity theory. A simple model is presented to describe force regulation by dynamical adhesion sites.