Continuous representations of time-series gene expression data.

We present algorithms for time-series gene expression analysis that permit the principled estimation of unobserved time points, clustering, and dataset alignment. Each expression profile is modeled as a cubic spline (piecewise polynomial) that is estimated from the observed data and every time point influences the overall smooth expression curve. We constrain the spline coefficients of genes in the same class to have similar expression patterns, while also allowing for gene specific parameters. We show that unobserved time points can be reconstructed using our method with 10-15% less error when compared to previous best methods. Our clustering algorithm operates directly on the continuous representations of gene expression profiles, and we demonstrate that this is particularly effective when applied to nonuniformly sampled data. Our continuous alignment algorithm also avoids difficulties encountered by discrete approaches. In particular, our method allows for control of the number of degrees of freedom of the warp through the specification of parameterized functions, which helps to avoid overfitting. We demonstrate that our algorithm produces stable low-error alignments on real expression data and further show a specific application to yeast knock-out data that produces biologically meaningful results.     

Presynaptic Nicotinic Receptors Stimulate Increases in Intraterminal Calcium of Chick Sympathetic Neurons in Culture

Abstract: Stimulation of chick sympathetic neurons in culture by the cholinergic agonists acetylcholine, nicotine, and 1,1-dimethyl-4-phenylpiperazinium (all at 10–1,000 µmol/L) induced concentration-dependent increases of free calcium levels measured by fura 2 fluorescence in neuronal processes. The response evoked by acetylcholine had both nicotinic and muscarinic components, whereas that induced by 1,1-dimethyl-4-phenylpiperazinium was purely nicotinic. Tetrodotoxin (0.3 µmol/L) blocked completely the increase of intraterminal free calcium level evoked by electrical stimulation. On the other hand, stimulation with 1,1-dimethyl-4-phenylpiperazinium still evoked 20–25% of the control response in the presence of tetrodotoxin. The concentration-response relationship of 1,1-dimethyl-4-phenylpiperazinium stimulation did not differ in the absence and in the presence of tetrodotoxin. The nicotinic antagonists d -tubocurarine (10 µmol/L) and mecamylamine (10 µmol/L), but not α-bungarotoxin (125 nmol/L), prevented the increase of intraterminal free calcium level evoked by 1,1-dimethyl-4-phenylpiperazinium (100 µmol/L) in the presence of tetrodotoxin. These observations indicate the presence of nicotinic receptors on neuronal processes that increase the intraterminal concentration of free calcium and probably modulate transmitter release. Their pharmacological properties are similar to those of nicotinic receptors located on neuronal cell bodies.     

The Lipid Peroxidation Product, 4-Hydroxy-2-trans-Nonenal, Alters the Conformation of Cortical Synaptosomal Membrane Proteins

Abstract: Alzheimer's disease (AD) is widely held to be a disorder associated with oxidative stress due, in part, to the membrane action of amyloid β-peptide (Aβ). Aβ-associated free radicals cause lipid peroxidation, a major product of which is 4-hydroxy-2- trans -nonenal (HNE). We determined whether HNE would alter the conformation of synaptosomal membrane proteins, which might be related to the known neurotoxicity of Aβ and HNE. Electron paramagnetic resonance spectroscopy, using a protein-specific spin label, MAL-6(2,2,6,6-tetramethyl-4-maleimidopiperidin-1-oxyl), was used to probe conformational changes in gerbil cortical synaptosomal membrane proteins, and a lipid-specific stearic acid label, 5-nitroxide stearate, was used to probe for HNE-induced alterations in the fluidity of the bilayer domain of these membranes. Synaptosomal membranes, incubated with low concentrations of HNE, exhibited changes in protein conformation and bilayer order and motion (fluidity). The changes in protein conformation were found to be concentration- and time-dependent. Significant protein conformational changes were observed at physiologically relevant concentrations of 1–10 µ M HNE, reminiscent of similar changes in synaptosomal membrane proteins from senile plaque- and Aβ-rich AD hippocampal and inferior parietal brain regions. HNE-induced modifications in the physical state of gerbil synaptosomal membrane proteins were prevented completely by using excess glutathione ethyl ester, known to protect neurons from HNE-caused neurotoxicity. Membrane fluidity was found to increase at higher concentrations of HNE (50 µ M ). The results obtained are discussed with relevance to the hypothesis of Aβ-induced free radical-mediated lipid peroxidation, leading to subsequent HNE-induced alterations in the structure and function of key membrane proteins with consequent neurotoxicity in AD brain.     

The ant’s path integration system: a neural architecture

 A model is developed by which path integration as observed in many animal species could be implemented neurobiologically. The proposed architecture is able to describe the navigation behaviour of Cataglyphis ants, and that of other social insects, at the level of interacting neurons. The basic idea of this architecture is the concept of activity patterns travelling along neural chains. Although experimental evidence has yet to be provided, this concept seems biologically plausible and not limited to the navigation problem. Neural chains are able to represent variables by activity patterns with high accuracy and temporal stability. Moreover, they are able to integrate incremental signals with high precision. Cyclical chains of neurons show superior performance as soon as cyclical variables are to be represented and integrated. Finally, representation of cyclical variables by travelling activity peaks allows simple approximations of goniometric functions as they are used in path integration systems. Received: 15 November 1994/Accepted in revised form: 30 May 1995     

l-NNA inhibits the histochemical NADPH-d reaction in rat spinal cord neurons

In nerve tissue the histochemical nicotinamide adenine dinucleotide phosphate-diaphorase (NADPH-d) reaction is considered a suitable marker for nitric oxide synthase (NOS) activity. We have previously shown that the NOS-specific inhibitorl-nitroarginine (l-NNA) can block NADPH-d staining in intermediolateral (IML) neurons of the rat spinal cord; such a reaction might serve as a control for the presence of a NOS-related catalytic activity, i.e.,l-NNA-dependent NO synthesis in these neurons. However,l-NNA inhibition of neuronal NADPH-d is inconsistent and is therefore disputed by others. This prompted us to reinvestigate the reaction conditions to provide a standardized protocol for inhibition experiments. In IML neurons of formaldehyde-fixed spinal cord tissue, inhibition of NADPH-d reaction was tested by preincubation of frozen sections with the flavin-binder diphenylene iodonium chloride (DPI, 10 M-1 mM) which blocked the NADPH-d reaction in a concentration-dependent way, suggesting an inverse relationship of inhibitor concentration and final reaction product generated. Preincubation with the NOS-specific inhibitorl-NNA in glycine-NaOH buffer (pH 8.5–9.5) but notl-nitroarginine methyl ester (l-NAME) revealed a concentration-dependent blocking effect on neuronal NADPH-d comparable to the effects seen with DPI, suggesting the existence of al-NNA sensitive NADPH-d activity. Blocking withl-NNA (100 M-10 mM) was prevented by excessl-arginine (10–100 mM), suggesting competitive binding sites. NADPH-d staining was not inhibited by 7-nitro indazole, another NOS inhibitor. Thus, in formaldehyde-fixed nervous tissue both DPI andl-NNA inhibit the NOS-associated catalytic NADPH-d activity, thereby preventing NADPH-dependent conversion of nitroblue tetrazolium to formazan.Presented in the Workshop Detection of NO-synthases at the XXXVI Symposium of the Society for Histochemistry on Oxy Radicals, 20–23 September 1994, Heidelberg, Germany     

Sucrose transport into vacuoles isolated from barley mesophyll protoplasts

Sucrose transport has been investigated in vacuoles isolated from barley mesophyll protoplasts. Rates of sucrose transfer across the tonoplast were even higher in vitro than in vivo indicating that the sucrose transport system had not suffered damage during isolation of the vacuoles. Sucrose transport is carrier-mediated as shown by substrate saturation of transport and sensitivity to a metabolic inhibitor and to competitive substrates. A number of sugars, in particular maltose and raffinose, decreased uptake of sucrose. Sorbitol was slowly taken up but had no effect on sucrose transport. The SH-reagent p-chloromercuribenzene sulfonate inhibited sucrose uptake completely. The apparent K_m of the carrier for sucrose uptake was 21 mM. Transport was neither influenced by ATP and pyrophosphate, with or without Mg²⁺ present, nor by protonophores and valinomycin (with K⁺ present). Apparently uptake was not energy dependent. Efflux experiments with preloaded vacuoles indicated that sucrose unloading from the isolated vavuoles is mediated by the same carrier which catalyses uptake. The vacuole of mesophyll cells appears to represent an intermediary storage compartment. Uptake of photosynthetic products into the vacuole during the light apparently minimizes osmotic swelling of the small cytosolic compartment of vacuolated leaf cells when photosynthetic productivity exceeds the capacity of the phloem for translocation of sugars.Abbreviations Hepes 4-(2-hydroxyethyl)-1-piperazincethane-sulfonic acid - pCMBS p-chloromercuribenzene sulfonate Dedicated to Professor Dr. W. Simonis on the occasion of his 75th birthday     

Zum Ortstreue-Verhalten des Trauerschn?ppers(Ficedula hypoleuca) im westlichen Randbereich seines mitteleurop?ischen Verbreitungsgebietes

Zusammenfassung 1974–1981 wurden in einem Lärchen-Versuchsforst (320 ha; 600 künstliche Nisthöhlen) in Niedersachsen (52.27 N/7.15 E) 529 Brutvögel des Trauerschnäppers beringt. Geburtsortstreue — auf das Versuchsgebiet bezogen — konnte bei 78 Individuen (=5,2 % der ausgeflogenen Nestlinge) festgestellt werden. Die geburtsortstreuen wurden in der Regel schon im ersten Jahr als Brutvogel nachgewiesen, während die Hälfte der geburtsortstreuen bei der ersten Erfassung ein Alter von mindestens 2 Jahren besaß. In der mittleren Entfernung zwischen Geburts- und erstbekannter Bruthöhle ergab sich zwischen den Geschlechtern kein gesicherter Unterschied ( : 883 m, : 798 m). Geschwister verhielten sich bezüglich Ansiedlungsalter und Ansiedlungs-entfernung nicht einheitlich. Von den als Brutvögel beringten Trauerschnäppern konnten 38,2 % der und 24,0 % der in einem späteren Jahr wiedergefangen werden. Bei den lagen die in aufeinanderfolgenden Jahren besetzten Nisthöhlen näher beieinander als bei den (Mittelwerte: 371 m bzw. 534 m). In der untersuchten Population war in allen Jahren bei den der Prozentsatz brutortstreuer Individuen höher und der Anteil an Zuwanderern geringer als bei den (Mittelwerte: 48 % gegenüber 30 % bzw. 45 % gegenüber 64 %). Diese Befunde wurden unter anderem im Hinblick auf die Lage des Untersuchungsgebietes am Rande des Trauerschnäpper-Areals diskutiert. Die Ortstreue war geringer ausgebildet als in mehreren anderen Populationen.

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On place-fidelity behaviour in the Pied Flycatcher(Ficedula hypoleuca) in the western border area of its Central European range

Summary The evaluation is based on findings from 1974 to 1981, in a 320 ha. experimental larch forest (52.27N, 7.15E), with 600 nestboxes, in western Lower Saxony, from a total of 529 breeding Pied Flycatchers. Fidelity to birthplace — recovery in the study area — was recorded for 78 individuals (=5.2 % of the fledged nestlings). faithful to birthplace were traced, as a rule, in the first year, while half of the who showed this fidelity were at least 2 years old when first recorded. There was no significant difference between sexes in the mean distance between the hole in which they were hatched and the first known breeding hole ( : 883 m, : 798 m). There was no uniformity among siblings in relation to age of settlement and distance of settlement. 38.2 % of and 24.0 % of Pied Flycatchers ringed as breeding birds were recaptured in a later year. Nest boxes occupied in successive years were closer together in the case of than (mean: 371 m and 534 m respectively). The percentage of individuals showing fidelity to birthplace was higher, in all years, and the number of immigrants smaller, in the than in (mean: 48 % against 30 % and 45 % against 64 % respectively). These findings are discussed in relation to the border situation of the study area. The rate of recoveries was lower than in some other populations.

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Gefördert mit Hilfe von Forschungsmitteln des Landes Niedersachsen.     

Structurally symmetrical,easily polarizable hydrogen bonds between side chains in proteins and proton-conducting mechanisms. III

(L -Cys)_n, (L -Lys)_n, and (L -Glu)_n were studied by ir spectroscopy in terms of their degree of deprotonation or protonation. It is shown that structurally symmetrical, easily polarizable SH ?S^? ? ^?S ?HS, N⁺H ?N ? N ?H⁺N, and OH ?O^? ? ^?O ?HO hydrogen bonds are formed between the side chains. The different wave number distributions of the ir continua caused by these hydrogen bonds show that the barrier in the double-minimum proton potential decreases in the series of these hydrogen bonds. The stability of these hydrogen bonds against hydration increases in this series. The OH ?O^? ? ^?O ?HO bonds are not broken by small amounts of water. With (L -Cys)_n the formation of easily polarizable hydrogen bonds and a β-structure–coil transition are strongly interdependent. As a result of this coupling effect, the β-structure–coil transition becomes cooperative. With (L -Glu)_n, the formation of the polarizable hydrogen bonds and the observed conformational change are independent processes. The (L -Glu)_n conformation changes from α-helix to coil only if more than 80% of the residues are deprotonated. Finally, on the basis of the various types of easily polarizable hydrogen bonds, charge shifts in active centers of enzymes and the proton-conducting mechanism through hydrophobic regions of biological membranes are discussed.