Presynaptic proteins involved in exocytosis inDrosophila melanogaster: A genetic analysis

Neuronal communication involves the fusion of neurotransmitter filled synaptic vesicles with the presynaptic terminal. This exocytotic event depends upon proteins present in three separate compartments: the synaptic vesicle, the synaptic cytosol, and the presynaptic membrane. Recent data indicate that the basic components of exocytotic pathways, including those used for neurotransmitter release, are conserved from yeast to human. Genetic dissection of the secretory pathway in yeast, identification of the target proteins cleaved by the clostridial neurotoxins and biochemical characterization of the interactions of synaptic proteins from vertebrates have converged to provide the SNARE (soluble NSF attachment protein receptor) hypothesis for vesicle trafficking. This model proposes that proteins present in the vesicle (v-SNAREs) interact with membrane receptors (t-SNAREs) to provide a molecular scaffold for cytosolic proteins involved in fusion. The hypothesis that these mechanisms function at the synapse relies largely uponin vitro evidence. Recently, genetic approaches in mice, C.elegans and the fruitfly,Drosophila melanagaster, have been used to dissect thein vivo function of numerous proteins involved in synaptic transmission. This review covers recent progress and insights provided by a genetic dissection of neurotransmitter release inDrosophila. In addition, we will provide evidence that the mechanisms for synaptic communication are highly conserved from invertebrates to vertebrates, makingDrosophila an ideal model system to further unravel the intricacies of synaptic transmission.     

Analysis of peptides from known proteins: Clusterization in sequence space

A combinatorial sequence space (CSS) model was introduced to represent sequences as a set of overlapping k-tuples of some fixed length which correspond to points in the CSS. The aim was to analyze clusterization of protein sequences in the CSS and to test various hypotheses about the possible evolutionary basis of this clusterization. The authors developed an easy-to-use technique which can reveal and analyze such a clusterization in a multidimensional CSS. Application of the technique led to an unexpectedly high clusterization of points in the CSS corresponding to k-tuples from known proteins. The clusterization could not be inferred from nonuniform amino acid frequencies or be explained by the influence of homologous data. None of the tested possible evolutionary and structural factors could explain the clusterization observed either. It looked as if certain protein sequence variations occurred and were fixed in the early course of evolution. Subsequent evolution (predominantly neutral) allowed only a limited number of changes and permitted new variants which led to preservation of certain k-tuples during the course of evolution. This was consistent with the theory of exon shuffling and protein block structure evolution. Possible applications of sequence space features found were also discussed.Correspondence to: H.A. Lim     

Diurnal cycles of rhizosphere acidification byPinus contorta seedlings

The pH of the nutrient solution bathing the roots of four-month-oldPinus contorta var.latifolia Englm. seedlings was monitored continuously between additions of nutrients. Nitrogen was supplied in the form of NH₄NO₃, and was added three times per week in amounts relative to seedling fresh weight. No pH change was associated with the nutrient addition cycle; however, extinguishing of the lights at night resulted in a decrease in pH of almost half a pH unit in the first hour. The pH reverted to normal within a few hours. Re-illumination resulted in a pH increase of a smaller magnitude, but over a similar time span. Estimation of the proton extrusion rate gave values of about 17 µmol (g FW root)^–1 h^–1.     

Influence of copper on proton efflux from Saccharomyces cerevisiae and the protective effect of calcium and magnesium

Abstract The inhibitory effect of Cu on glucose-dependent H⁺ efflux from Saccharomyces cerevisiae was manifest at low (micromolar) concentrations, with the time period between the addition of glucose and commencement of H⁺ efflux, H⁺ efflux rate and duration all being affected with increasing Cu concentration (5–100 μM). Ca, at a concentration of 0.5 mM, completely removed the inhibitory effect of Cu at concentrations up to 50 μM and considerably reduced it at higher concentrations (up to 150 μM). Mg exhibited a similar but weaker protective effect against the influence of Cu. The protective effect of Ca against 50 μM Cu was evident at low Ca concentrations (2.5–5 μM), whereas Mg was effective at ≥50 μ M. In order to prevent the inhibitory effect of Cu, it was necessary to add Ca or Mg to the cell suspension before Cu addition. It is concluded that the protective effect of Ca and Mg is mediated by competitive and stabilizing interactions at the cell surface as well as physiological functions of Ca and Mg.     

Bio-availability of phosphorus in sediments of the western Dutch Wadden Sea

The purpose of this study was to make a prognosis of the effects of extended purification of terrestrial waste water, reaching the Wadden Sea by the River Rhine and Lake IJssel, on the phosphate concentration in the western Wadden Sea.The quantities of different phosphorus fractions in intertidal and subtidal sediments of the Marsdiep tidal basin (western Dutch Wadden Sea) were measured. Different methods are applied to determine the amount of phosphorus that can be released from these sediments. The direct bioavailability is determined by inoculating sediment suspensions with a natural mixture of precultured micro-organisms from the sampling area. A second approach is the measurement of the phosphate release under different redox conditions. Sequential extraction of sediment samples with different solvents is also applied. Under the present conditions and compared to the nutrient loads from fresh water (Lake IJssel) and from the North Sea, the phosphorus stored in the sediments of the western Dutch Wadden Sea plays a minor role in the total supply to micro-algae and bacteria. The bulk of the biologically available phosphorus in the sediments originates from the metal-associated fraction. Releasable phosphate may contribute to the local annual primary production to an extent of ca 45 to ca 150 g C m^–2 a^–1. The total amount of phosphorus in the sediment (mainly calcite associated) is twice to 6 times the biologically available amount.     

STADEERS: a software package for the statistical design of experiments pertaining to the estimation of parameters in rate expressions that describe enzyme-catalyzed processes

This paper describes a computational algorithm (STADEERS-STAtisticalDesign of Exeriments in Enzyme ReactorS) for the statisticaldesign of biochemical engineering experiments. The type of experimentthat qualifies for this package involves a batch reaction catalyzedby a soluble enzyme where the activity of the enzyme decayswith time. Assuming that both the catalytic action and the deactivationof the enzyme obey known rate expressions, the present codeis helpful in the process of obtaining estimates of the kineticparameters by providing as output the times at which samplesshould be withdrawn from the reacting mixture. Starting D-optimaldesign is used as a basis for the statistical approach. ThisBASIC code is a powerful tool when fitting a rate expressionto data because it increases the effectiveness of experimentationby helping the biochemical kineticist obtain data points withthe largest possible informa tional content.