Voltage-stepping schemes for the simulation of spiking neural networks

The numerical simulation of spiking neural networks requires particular attention. On the one hand, time-stepping methods are generic but they are prone to numerical errors and need specific treatments to deal with the discontinuities of integrate-and-fire models. On the other hand, event-driven methods are more precise but they are restricted to a limited class of neuron models. We present here a voltage-stepping scheme that combines the advantages of these two approaches and consists of a discretization of the voltage state-space. The numerical simulation is reduced to a local event-driven method that induces an implicit activity-dependent time discretization (time-steps automatically increase when the neuron is slowly varying). We show analytically that such a scheme leads to a high-order algorithm so that it accurately approximates the neuronal dynamics. The voltage-stepping method is generic and can be used to simulate any kind of neuron models. We illustrate it on nonlinear integrate-and-fire models and show that it outperforms time-stepping schemes of Runge-Kutta type in terms of simulation time and accuracy.

Fluxes of bacterioplankton between a tidal estuary and the sea: returning to the “Outwelling Hypothesis”

The tidal dynamics of bacterioplankton communities at the outer part ofa shallow estuary (Ria de Aveiro, Portugal) were studied during 6 tidal cyclesat a fixed sampling site. Bacterial numbers (0.2–8.1 ×10⁹ cells l^–1), aminopeptidase activity(189–1662 nmol l^–1 h^–1),-glucosidase activity (1.7–67.0 nmoll^–1 h^–1) and potential glucoseincorporation (0.48–3.99 nmoll^–1 h^–1) followed a consistent patternof increase during ebb and decrease during flood.Fluxes of bacterioplankton populations and associated heterotrophic activitiesbetween the estuary and the coastal area during a tidal cycle were estimatedfrom the water flux as derived from a two-dimensional vertically-integratednumerical model. The net fluxes estimated for a tidal cycle ranged from–26.0 to –2.5 to × 10¹⁶ bacterial cells. The nettidal fluxes of potential heterotrophic activities ranged from –10 to–80 mol h^–1 for aminopeptidase, –0.33to –1.10 mol h^–1 for -glucosidase and–0.18 to +0.03 mol h^–1 for glucoseincorporation. Net fluxes were generally negative in sign indicating thetransfer of phyto- and bacterioplankton, as well as potential capacities for thedegradation and recycling of organic matter, from the outer estuarinecompartment to the sea.     

Inhibitory effects of GABA on synaptic excitation in isolated rat hippocampal slices

In research on -aminobutyric acid (GABA) used at different concentrations on the amplitude of EPSP within populations (PEPSP), as recorded from dentrites in isolated hippocampal slices, GABA induced a dose-dependent reversible reduction in PEPSP amplitude with no noticeable signs of desensitization. Highest sensitivity to GABA was shown by PEPSP in hippocampal zone CA1 (threshold concentration: 3×10^–5–2×10^–4 M; (concentration at which the effect equal to 1/2 of maximum occurs) IC₅₀: 5×10^–4–1×10^–3 M). The effects of GABA on PEPSP were not blocked by bicuculline, picrotoxin, or penicillin. Action of GABA on dendritic antidromic population spike (DAPS — postynaptic effects) were slightly diminished by these blockers. Baclofen inhibited PEPSP more powerfully than GABA (threshold concentration: 1×10^–6 M: IC₅₀: 3×10^–6 M), although it only produced a minor reduction in DAPS amplitude even at high concentrations. It is concluded that the inhibitory effect of GABA on PEPSP in hippocampal zone CA1 may be put down mainly to its presynaptic action mediated by GABA_B receptors on axonal terminals of Schaffer collaterals.A. A. Bogomolets Institute of Physiology, Academy of Sciences of the Ukrainian SSR, Kiev. Translated from Neirofiziologiya, Vol. 22, No. 5, pp. 627–633, September–October, 1990.     

Second-order nonlinear optical properties ofp-dimethylaminobenzylidene-1,3-indandione (DABI) measured by EFISH in dioxane

The second-order nonlinear optical properties of p-dimethylaminobenzylidene-1,3-indandione (DABI) have been measured using electric field-induced second-harmonic generation (EFISH) at wavelengths of 1064 nm and 1907 nm in dioxane. The absolute values of the microscopic hyperpolarizabilities are ^{1064 nm}=1064×10^–40 m⁴ V^–1 and ^{1907 nm}=150×10^–40 m⁴ V^–1.The condensation of 1,3-indandione with substituted aromatic aldehydes offers a pathway to a class of molecules with extended -electron systems. In the case of DABI, semiempirical calculations and a simple, two-level model indicate that the relatively high values of the microscopic hyperpolarizability are due to several factors which, in combination, positively enhance the electron donor-acceptor group-induced polarizability of DABI. The nonlinear optical properties of DABI are compared with experimental data for 2-methyl-4-nitroaniline (MNA).     

Lipolytic and adenyl-cyclase-stimulating activity of glucagon1–6: comparison with glucagon derivatives chemically modified in the 7–29 sequence

Glucagon_1–6 has a maximum lipolytic activity (L_max) in the rat adipocyte which is 66% of that of glucagon. The N-guanidyl derivative, modified at Lys₁₂ , has about the same L_max as glucagon_1–6. Modifying the carboxyl groups of glucagon with glycinamide or removing the COON-terminal residues with cyanogen bromide reduces L_max to less than 25% of the level of glucagon. The potency of each of these analogs (A₅₀) in M is as follows: glucagon 6×10^–3; glucagon^1–6 2 ×10^–2; N-guanidyl glucagon 9×10^–3; glycinamide glucagon 10^–2; cyanogen bromide peptide of glucagon 2 ×10^–1. The ability of all of the glucagon analogs to stimulate adenyl cyclase was somewhat less than their tipolytic activities with the exception of the glycin-amide derivative and the cyanogen bromide peptide, which were slightly more active in stimulating adenyl cyclase than in lipolysis. Glucagon_1–6 is much more potent in stimulating adipocyte than liver adenyl cyclase.     

In vitro propagation of the bamboo (Bambusa tulda Roxb.) through shoot proliferation

An efficient protocol has been developed for the in vitro propagation of Bambusa tulda through shoot proliferation. Shoots from 3-week-old aseptically grown seedlings were used to initiate cultures. Multiple shoots were obtained on liquid Murashige and Skoog (MS) medium supplemented with 6-benzylaminopurine (8×10^–6M) and kinetin (4×10^–6M). Continuous shoot proliferation at a rate of 4–5 fold every three weeks was achieved through forced axillary branching. More than 90% of the shoots could be rooted on a modified MS medium containing indoleacetic acid (1×10^–5M) and coumarin (6.8×10^–5M). Following simple hardening procedures, the in vitro raised plants were transferred to the soil with more than 80% success.Abbreviations BAP 6-benzylaminopurine - 2-ip 6-,-dimethylallylaminopurine - Kn kinetin - IAA 3-indoleacetic acid - IBA 3-indolebutyric acid - NAA 1-naphthaleneacetic acid     

Interactions of growth inhibitory factor with hydroxyl and superoxide radicals

To show the effects of growth inhibitory factor (Cu₄Zn₃MT-III) involved in the scavenging of reactive oxygen species (ROS), a pulse radiolytic study was employed using N₂O-saturated Cu₄Zn₃MT-III aqueous solutions. It was demonstrated that the oxidizing OH radical efficiently reacted with Cu₄Zn₃MT-III by forming a thiyl radical RS with a second-order constant of 1.46×10¹¹ mol l^–1s^–1, which was determined by competition kinetics against KSCN. The thiyl radical RS reacted rapidly and reversibly with a thiolate in Cu₄Zn₃MT-III to form radical anion RSSR ^– with a constant of 1.65×10⁹ mol lL^–1s^–1 per thiolate, while the constant of the decay of this radical anion was 2.72×10⁵ s^–1, and the equilibrium constant of the formation for RSSR ^– was 6.08×10³ mol^–1 l. These values were close to those of Cd₅Zn₂MT-II. The SOD activity of Cu₄Zn₃MT-III to quench O₂ ^–was assayed by the riboflavine-methionine-nitrobluetetrazolium (NBT) method which catalyzed the dismutation of superoxide (O₂ ^–) at pH 7.8 with an IC₅₀ value of 1.50×10^–6 M for Cu₄Zn₃MT-III and 1.62×10^–6 M for Cd₅Zn₂MT-II. Additionally, the down-regulation of GIF may be a main factor in the decrease of the scavenging ability for the free OH and O₂ ^–radicals, which is possibly associated with the pathogenesis of neurodegenerative disease.     

Peptidergic and adrenergic regulation of electrogenic ion transport in isolated gills of the flounder (Platichthys flesus L.)

Summary Electrogenic potentials measured in isolated gills of seawater-adaptedPlatichthys flesus conform to the current model proposed for salt secretion by teleost chloride cells. Gills perfused and bathed with identical salines maintained a stable potential (blood-side positive) thought to represent the activity of a chloride pump. Furosemide added to the perfusate (1×10^–4 and 5×10^–4 mol l^–1) caused a large inhibition of the transepithelial potential. Cyclic 8-(4-chlorophenylthio) adenosine-3:5-monophosphate (5×10^–5 mol l^–1) stimulated the transepithelial potential and decreased the arterial vascular resistance. The adenylate cyclase activator forskolin mimicked the effects of the cAMP derivative on branchial vascular resistance and, at low concentrations, on electrogenic ion transport. At high concentration (>5×10^–7 mol l^–1) forskolin inhibited the transepithelial potential. These results implicate cAMP as an important intracellualr regulator of both ionoregulatory and haemodynamic functions in the teleost gill.The -adrenergic agonist isoprenaline administered as injected doses in the perfusate produced a stimulation of the transepithelial potential and a decrease in the arterial vascular resistance. A dose-response analysis showed that half-maximal haemodynamic effects occurred at significantly lower doses of agonist than those required for half-maximal stimulation of the potential. The pancreatic hormone glucagon also caused dose-dependent stimulation of the transepithelial potential but had no effect on arterial vascular resistance. It is suggested that regulation of the rate of branchial monovalent ion excretion may be under peptidergic as well as adrenergic control.     

Kinetics of the potential-sensitive extrinsic probe oxonol VI in beef heart submitochondrial particles

Summary The interaction of the potential-sensitive extrinsic probe oxonol VI with beef heart submitochondrial particles has been investigated under time resolved and equilibrium conditions. The time course of the probe absorption spectrum red shift induced by ATP or NADH injection into a suspension of submitochondrial particles in a dye solution is biphasic, consisting of a faster process described by a second-order rate law withk ₂3×10⁵ m ^–1 sec^–1. For the ATP pulse experiments, the slower process follows first-order kinetics withk ₁0.3 sec^–1. In oxygen pulse experiments to an anaerobic dyeparticle system, the slower process is not significantly developed due to rapid depletion of the oxygen, but the faster process follows second-order kinetics with the same rate constant as for the ATP and NADH cases. Evidence for permeation of the submitochondrial particle membrane by oxonol VI has been obtained; the slower process is interpretable as describing the permeation of the membrane bilayer. The results of the time-resolved work are consistent with a mechanism involving a redistribution of the dye from the bulk phase to the particle membrane. The value of the second-order rate constant for passive binding of the dye to submitochondrial particles is not compatible with a mechanism proposed to explain the microsecond probe response times in bilayer and excitable membrane experiments nor are such rapid signals observed in the oxonol VI-submitochondrial particle system.     

Feeding rate inhibition in crowded Daphnia pulex

Feeding rates of Daphnia pulex fed a range of levels of the alga Chlamydomonas reinhardi of 15 °C are strongly density-dependent. At lower densities, Daphnia (30 1^–1) fed at higher rates than crowded (270 1^–1) Daphnia which manifest a relatively depressed saturation feeding response. At 30 individuals/liter, Daphnia consumed 8.5 – 15.7 × 10⁴ cells d^–1h^–1 (on a volume basis, 12.1 – 22.2 × 10⁶ m³), at 270 L^–1 3.7 – 3.9 × 10⁴ (5.2 – 5.5 = 10⁶ m³ cells d^–1h^–1 when feeding on algae at 80 000 cells ml^–1 (11.3 × 10⁶ m³ ml^–1). The feeding rate data best fit an Ivlev feeding function. An autoallelopath might be causing the repression. Water preconditioned with crowded Daphnia completely repressed feeding in uncrowded Daphnia after six hours.     

Refolding of trypsin-subtilisin inhibitor from marine turtle eggwhite

Trypsin-subtilisin inhibitor from marine turtle eggwhite refolded quantitatively from its fully reduced state atpH 8.5 in the presence of reduced and oxidized glutathione. The refolding process was studied by following the accompanying changes in inhibitory activity, fluorescence, sulfhydryl group titer, and hydrodynamic volume. The refolding process followed second-order kinetics with rate constants of 4.80×10² M^–1 sec^–1 for trypsin-inhibiting domain and 0.77× 10² M^–1 sec^–1 for subtilisin-inhibiting domain of the inhibitor at 30°C and their respective activation energies of the refolding process were 15.9 and 21.6 kcal/mol. Fluorescence intensity of the reduced inhibitor decreased with time of refolding until it corresponded to the intensity of the native inhibitor. The inhibitor contained 1–2%-helix, 40–42%-sheet, and 57–58% random coil structure. Refolded inhibitor gave a circular dichroic spectrum identical to that of the native inhibitor. A number of principal intermediates were detected as a function of the refolding time. Size-exclusion chromatography separated the intermediates differing in hydrodynamic volume (Stokes radius). The Stokes radius ranged from 23 Å (fully reduced inhibitor) to 18.8 Å (native inhibitor). Results indicated the independent refolding of two domains of the inhibitor and multiple pathways of folding were followed rather than an ordered sequential pathway.     

Is bacterioplankton production in the Ria de Aveiro influenced by salt marshes and bed sediment?

The contribution of potential export of materials from bottom sedimentsand salt marshes into the water column of a shallow estuarine system of Ria deAveiro to the observed high bacterial productivity in the mid section of thisestuary was evaluated. Vertical profiles of physical, chemical and bacterialvariables were studied in the marine and brackish water zones, and oftransversal profiles in the brackish zone only. Although the concentrations ofseston (17–241 mg l^–1), particulate organiccarbon (3–15.5 mg l^–1) and chlorophyll(1.2–7.0 g l^–1) varied widely, thevertical and transversal profiles were without much variation. Total bacterialnumber (0.2–8.5 × 10⁹ cellsl^–1) and the number of particle-attached bacteria(0.02–2.50 × 10⁹ cellsl^–1)along vertical and transversal profiles did not differ much, but the rate ofbacterial production (0.05–14.2 g C l^–1h^–1) and dissolved organic carbon concentration(6.0–69.2 mg l^–1) were frequently highernear the salt marsh margin at the brackish water transect. The increase inproductivity could not be associated with runoff of particulate matter butcoincided with the inputs of dissolved organic carbon. The results of verticaland transversal profiles point to a minor role of particulate matter additionsfrom the salt marsh area or from bed sediments.     

Acetylcholine activates a chloride channel as well as glutamate and GABA

Summary In conventional two microelectrode experiments, acetylcholine had qualitatively the same effect as GABA and glutamate on membrane potential and input resistance of muscle fibres of the opener and intrinsic stomach muscles of crayfish (Austropotamobius torrentium). In patch-clamp experiments, acetylcholine occasionally elicited single channel openings in cell-attached patches on these muscles. If outside-out patches were excised and the Cl^– concentration was high on both sides of the membrane, acetylcholine at concentrations of 1 nM regularly elicited single channel currents. The amplitude of single channel currents depended strongly on the intracellular concentration of Cl^–. The reversal potential of the channel, determined after replacing intracellular K⁺ with Cs⁺, corresponded to the Nernst potential for Cl^–. The voltage dependence and the reversal potential of single channel current amplitudes elicited by ACh, glutamate and GABA were identical. The distribution of life times of openings (>1 ms) elicited by ACh and glutamate could be fitted by a single exponential with a time constant of about 2.5 ms, corresponding to the mean open time. ACh and glutamate applied to the same outside-out patch showed cross-desensitization, and thus ACh and glutamate activate the same channels. An excitatory, cationic ACh-activated channel could not be identified. Permeabilities of the chloride channel were calculated according to the Goldman-Hodgkin-Katz equation at different membrane potentials. Negative single channel current amplitudes (inward currents) could be fitted with a permeability of ₂= 3.9×10^–14 cm³s^–1. For positive currents (outward) the channel had a permeability of ₁= 1.4× 10^–14 cm³s^–1. The permeability of the channel declined from 16×10^–14 cm³s^–1 to 2.3×10^–14 cm³s^–1 if the intracellular Cl^–-concentration was raised from 6 to 257 mM. The activation elicited by acetylcholine was inhibited by extracellular Ca⁺⁺. The mean current activated by ACh was reduced by a factor of 50 if the extracellular concentration of Ca⁺⁺ was raised from 0.1 mM to the physiological concentration of 13.5 mM.     

Enhanced paclitaxel production induced by the combination of elicitors in cell suspension cultures of Taxus chinensis

Taxus chinensis suspension cells were cultured in the modified Gamborg's B5 medium. Addition of 50 mg chitosan l^–1, 60 M methyl jasmonate and 30 M Ag⁺ resulted in the greatest paclitaxel production, at 25 mg l^–1 in the cultures, being almost 40 times higher than that of the control culture, 10 times higher than that of the culture exposed to Ag⁺, 6 times higher than that of the culture elicited by chitosan and almost double that of the culture elicited by methyl jasmonate.     

Kinetics and equilibrium studies of Tet repressor-operator interaction

Binding of a Tet repressor mutant containing a single Trp43 residue in the tet operator recognition -helix leads to the quenching of the protein fluorescence down to about 23% in the case of the tet O₁ operator and to 40% in the case of the tet O₂ operator. We have used fluorescence detection to describe the binding equilibrium and kinetics of the Tet repressor interaction with the 20-bp DNA operators tet O₁ and tet O₂. Stopped-flow measurements in an excess of the tet operators performed in 5 mM NaCl or 150 mM NaCl indicate that the reaction can be described by at least three exponentials characterized by different relaxation times. The mechanism of interaction for both operators as well as for two salt concentrations used can be described as TetR + Operator Complex 1 Complex 2 Complex 3. Only the much faster process can be described as a second-order reaction characterized by a bimolecular rate constant equal to 2.8 × 10⁶ M^–1 sec^–1 for both operators. The medium and slow processes may be described by relaxational times ranging from 50 msec to seconds. The results of the binding equilibrium measurements extrapolated to 1 M NaCl concentration, which reflects the specific nonionic interaction between TetR and tet operators, indicate K _as equal to 3.2 × 10⁴ and 4.0 × 10⁵ M^–1 for tet O₁ and tet O₂, respectively. The number of monovalent ions replaced upon binding can be calculated as about 5 and 3 for tet O₁ and tet O₂, respectively. The binding of Tet repressor to the operators leads to changes in the circular dichroism spectra of the DNA which could indicate transitions of B-DNA into A-like DNA structure.     

Ca2+-dependent Cl− efflux in tonoplast-free cells ofNitellopsis obtusa

Summary In order to demonstrate the presence of a Ca²⁺-activated Cl^–-channel in theNitellopsis plasmalemma, tonoplast-free cells were prepared and their intracellular Ca²⁺ concentration was modified by internal perfusion. An increase in the Ca²⁺ concentration caused a large Cl^– efflux with a concomitant depolarization of the membrane potential. These changes were for the most part reversible. The critical Ca²⁺ concentration was about 4.0 m. Neither the Cl^– efflux nor the membrane depolarization showed a time-dependent inactivation. A Cl^–-channel blocker, A-9-C (9-anthracenecarboxylic acid) reduced both the Cl^– efflux and the magnitude of the membrane potential depolarization. A small increase in the intracellular Ca²⁺ concentration, which is caused by membrane excitation of tonoplast-free cells is not sufficient to activate this Ca²⁺-dependent Cl^–-channel.     

Growth of the toxic dinoflagellate Alexandrium minutum (Dinophyceae) using high biomass culture systems

Toxic dinoflagellates are important in natural ecosystems and are ofglobal economic significance because of the impact of toxic blooms onaquaculture and human health. Both the organisms and the toxins they producehave potential for biotechnology applications. We investigated autotrophicgrowth of a toxic dinoflagellate, Alexandrium minutum, inthree different high biomass culture systems, assessing growth, productivityandtoxin production. The systems used were: aerated and non-aerated2-L Erlenmeyer flasks; 0.5-L glass aerated tubes; anda 4-L laboratory scale alveolar panel photobioreactor. A range ofindicators was used to assess growth in these systems. Alexandriumminutum grew well in all culture conditions investigated, with amarked increase in both biomass and productivity in response to aeration. Thehighest cell concentration (4.9 × 10⁵ cellsmL^–1) and productivity (2.6 ×10⁴cells mL^–1d^–1) was achieved inthe aerated glass culture tubes. Stable growth of A.minutum in the laboratory scale alveolar panel photobioreactor wasmaintained over a period of five months, with a maximum cell concentration of3.3 × 10⁵ cells mL^–1, a meanproductivity of 1.4 × 10⁴ cells mL^–1d^–1, and toxin production of approximately 20g L^–1 d^–1 with weeklyharvesting.     

Kinetics of conversion ofNeisseria gonorrhoeae to resistance to complement by cytidine 5′-monophospho-N-acetyl neuraminic acid

Freshly isolated gonococci upon subculture are readily lysed by normal human serum although a few strains remain inherently resistant to the complement activity. The sensitive gonococci can be converted to serum resistance by incubation with a host derived factor referred to as cytidine 5-monophospho-N-acetylneuraminic acid (CMP-NANA). These gonococci resist complement mediated killing due to their sialylation of an epitope structure on a component of lipo-oligosaccharide (LOS). In the present study, the kinetics of conversion to serum resistance by the action of sialyltransferase (STase) inNeisseria gonorrhoeae was followed with very low concentrations of CMP-NANA. This conversion could not be perceived at 2×10^–3 nmol.ml^–1 but was fully attainable from 8×10^–3 to 2×10^–2 nmol.ml^–1 CMP-NANA. When pretreated up to 100 min in presence of the very low concentration of 2×10^–3 nmol.ml^–1, a potentiating effect on the conversion of gonococci by 2×10^–2 nmol.ml^–1 was observed in relation to the time of preincubation. This action was abolished after exposure to a subinhibitory concentration of chloramphenicol (0.5 µg.ml^–1). The gonococci recovered their ability to convert to serum resistance following adequate washing. The potential for increase in STase activity should be of interest for understanding the conversion from a serum sensitive to a serum resistance state.     

Inward membrane current inChara inflata: I. A voltage- and time-dependent Cl− component

Summary An inward current which increases in magnitude over a period of seconds is activated when the membrane ofChara inflata (a green alga) in a K⁺-conductive state is hyperpolarized by a voltage clamp. The peak current and the half-time of activation are exponentially dependent on membrane potential difference. It was found by using an external Cl^– electrode that the component exponentially dependent on potential was due to an efflux of Cl^–. The measured current-voltage curves and the kinetics of deactivation of the current showed that other time-dependent components contributed to the net inward current. The punchthrough theory of Coster (Biophys. J. 5:669–686, 1965) does not adequately explain the inward current since a punchthrough potential could not be obtained, and the inward current was distinctly time dependent. The voltage and time dependence of the inward current strongly suggests that the Cl^– efflux activated by hyperpolarization is through voltage-gated channels which open more frequently as the membrane is hyperpolarized.