Amplitude,frequency and phase determinants of perceived rotations and rigidity in the kinetic depth effect

In a previous experiment the author has shown how perceived rotations, in the kinetic depth effect, decrease as a function of temporal frequency. It was argued that many of the ambiguous motion effects, and the temporally limited nature of the phenomenon, are due to the inability to discriminate curvature and torsion information as well as the finite time required to extract these latter sequentially dependent image parameters. In this paper we extend the investigation to consider the perception of rotations and rigidity as a function of complexity, including amplitude and phase differences between image elements. Results indicate that perceived rigidity is specifically a function of phase information, or relative motion components, and that rotations decrease as a function of complexity. In this way the curvature and torsion extraction processes are integrated with the sinusoidal nature of the image motion.     

Defaults in stereoscopic and kinetic depth perception.

This study presents three findings concerning the mechanisms of depth perception. First, the shape of the three-dimensional percept evoked by two-frame motion is defined solely by the rotation component around an axis in the frontoparallel plane; the visual system assigns a default value to this rotation component to arrive at a unique solution. Second, when the visual axes of two eyes are almost parallel, the visual system uses a default vergence value to reconstruct stereoscopic depth. Third, the default vergence and default rotation angles are highly correlated across subjects. This correlation implies that the two modalities share a common scaling default at an internal level.     

Interrelation of kinetic and stereoscopic depth: behavior and physiology in vertebrates

The target article gathers compelling behavioral evidence that motion parallax provides depth information in a variety of animal species. A more general evaluation of kinetic depth cues subserving depth perception would call attention to recent studies in monkeys, demonstrating the interrelation of kinetic and stereoscopic depth cues both on a behavioral and physiological level. Furthermore, it is argued that binocularity in birds has a clear function in stereopsis.     

The water effect on the kinetic of the bovine liver catalase

Catalase is an enzyme that occurs in almost all aerobic organisms. Its main metabolic function is to prevent oxidative damage to tissues induced by hydrogen peroxide which is a strong oxidizing agent. Catalase is very effective in performing this task, since it has the highest turnover rate among all the enzymes. The properties of catalase have been investigated extensively for many years; however, the role of the solvent molecules in the catalytic reaction of this enzyme has not yet been investigated. Therefore, the objective of this work was to investigate the contribution of the solvent molecules on the catalytic reaction of bovine liver catalase with its substrate H2O2 by the osmotic stress method. As a probe for protein structural changes in solution, the differential number of water molecules released during the transition from free to bound form of the enzyme was measured. These assays were correlated with protein structural data provided by the SAXS technique and crystallographic structures of free and CN(-) bonded enzymes. The results showed that the difference in surface accessible area of the crystal structures does not reflect the variation that is observed in solution. Moreover, catalase is not influenced by the solvent during the catalytic reaction, which represents a lower energy barrier to be crossed in the overall energetics of the reaction, a fact that contributes to the high turnover rate of catalase.     

Analytic determination of the depth effect in stereokinetic phenomena without a rigidity assumption

When a circular disk with an eccentric dot is set in slow rotary motion a compelling impression of a three-dimensional cone is observed. Similarly a line segment of constant length, a bar, rotating on the frontal plane appears slanted in depth. The two stereokinetic phenomena cannot be explained on the basis of Ullman's method of extracting depth from 2-D moving stimuli i.e. the rigidity assumption. A new analytic model is here presented based on the hypothesis that the visual system minimizes the relative velocity differences among all the points of the moving pattern. Two different methods of calculating the depth displacement are described: the velocity field method and the trajectories method. Both lead to the same results. A comparison of the theoretical results with the experimental ones supports the validity of the model.     

Steady-state kinetic properties of FoF1-ATPase: the pH effect.

1. The kinetic properties of FoF1-ATPase from submitochondrial particles isolated from rat heart were studied, with emphasis to the pH effect. The velocity data were treated according to the Hill equation, and the results were discussed on the basis of the knowledge on the soluble F1-ATPase properties. 2. Three kinetic phases were observed in the range of pH 6.0-8.5, with apparent dissociation constant values (K0.5) of 0.001, 0.04 and 1.5 mM (respectively sites I, II and III) at pH 7.0. Their contribution to the total activity of the enzyme were pH-dependent on the range of 6.0-7.0, but not from 7.0 to 8.5, where the maximal velocity (V) for site III was some 4-fold larger than for site II, and the total V of sites II and III was some 40-fold larger than V assumed for site I. Therefore, two catalytic sites seem to participate significantly in the catalysis at steady-state condition. 3. Azide increased the sites II and III K0.5 values as well as decreased the site III V. In the presence of bicarbonate these two sites were not distinguishable, and the kinetic parameters at pH 7.0 were similar to those for sites II and III combined. Both azide and bicarbonate did not have a significant effect on site I, and this behavior was not pH-dependent. 4. The studies on the effect of pH on the kinetic parameters showed the following results: (1) the optimum pH for V was around 8.5; (2) decrease in the K0.5 values at pH below 7.0 for site II, and increase at pH over 7.0 for sites II and III; (3) in the pH range of 6.0-8.5 the Hill coefficient increased for site II, decreased for site III, and an intermediary effect was observed for the sites II and III combined, with a Michaelis-Menten behavior in the highest affinity pH, which was found in the physiological range.     

On the difficulties of fitting the double Michaelis-Menten equation to kinetic data

The double Michaelis-Menten equation describes the reaction kinetics of two independent, saturable uptake mechanisms. The use of this equation to describe drug uptake has been reported several times in the literature, and several methods have been published to fit the equation to data. So far, however, confidence intervals on the fitted kinetic parameters have not been provided. We present a grid-search method for fitting the double Michaelis-Menten equation to kinetic uptake data, and a Monte-Carlo procedure for estimating confidence intervals on the fitted parameters. We show that the fitting problem is extremely ill-conditioned, and that very accurate data are required before any confidence can be placed in the fitted parameters.     

The effect of antiglaucoma drugs on the depth of the anterior chamber (I)

The Authors have taken into account the most common effect of antiglaucomatous drugs on the depth of the anterior chamber. The modifications of the anterior chamber have been evaluated utilizing a Jaeger Pachymeter. The values were obtained before the drug instillation and an hour afterwards. The results are presented as the mean and standard deviation. Among the examined drugs, only miotics have brought about a notable decrease, whereas the others have shown no significant effects.     

The effect of snow depth on overwinter survival in Lobelia inflata

The snowpack in high altitude and latitude regions provides thermal insulation during the cold season. Recent climate change has resulted in a decrease in both the duration and the reliability of this snowpack and may thus affect overwinter survival of biota. Here we use a manipulation approach to ask how snow depth affects ground surface temperatures and how this in turn affects survival of the overwintering rosette stage in the monocarpic plant Lobelia inflata. A shallow but consistent insulation layer (R‐value of 3) was sufficient to reduce temperature fluctuations and the accumulation of sub‐zero degree‐days substantially. For all treatments >R3 these measures were negligible. Survival results are consistent with a crucial role of thermal insulation to successful overwintering of Lobelia inflata rosettes: without a consistent snowpack survival was low (11%); with an insulation effect of R3 or greater survival increased dramatically (81%). The winter prior to the manipulation study was characterized by an anomalous absence of snow at the onset of cold temperatures. This resulted in substantially greater accumulation of sub‐zero degree‐days at the soil surface and almost 100% rosette mortality in the field. This study shows that inconsistent and reduced snowpack – a prediction of climate change – will have critical effects on plant survival because of increased temperature fluctuations and extreme temperatures experienced at the soil surface.     

Quantum chemical modeling of the kinetic isotope effect of the carboxylation step in RuBisCO

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the most important enzyme for the assimilation of carbon into biomass, features a well-known isotope effect with regards to the CO₂ carbon atom. This kinetic isotope effect α = k ₁₂/k ₁₃ for the carboxylation step of the RuBisCO reaction sequence, and its microscopic origin, was investigated with the help of cluster models and quantum chemical methods [B3LYP/6-31G(d,p)]. We use a recently proposed model for the RuBisCO active site, in which a water molecule remains close to the reaction center during carboxylation of ribulose-1,5-bisphosphate [B. Kannappan, J.E. Gready, J. Am. Chem. Soc. 130 (2008), 15063]. Alternative active-site models and/or computational approaches were also tested. An isotope effect alpha for carboxylation is found, which is reasonably close to the one measured for the overall reaction, and which originates from a simple frequency shift of the bending vibration of ¹²CO₂ compared to ¹³CO₂. The latter is the dominant mode for the product formation at the transition state.     

The effect of temperature change on the kinetic behaviour of yeast phosphofructokinase.

Yeast phosphofructokinase does not exhibit any cold sensitivity. The kinetic properties of the enzyme have been investigated in the range between 10 degrees C and 30 degrees C in dependence on fructose 6-phosphate and ATP. Although a significant increase in the enzyme activity with rising temperature does not occur, the shape of the ATP velocity curves is not markedly altered. With increasing concentrations of fructose-6-phosphate the efficiency of temperature on the catalytic process increases, indicating a small temperature effect on the shape of the fructose-6-phosphate velocity curves. The results are interpreted in terms of an adequate kinetic model.     

gamma-Glutamylcyclotransferase: inhibition by D-beta-aminoglutaryl-L-alanine and analysis of the solvent kinetic isotope effect

Spin-echo NMR spectroscopy was used to record the cleavage of a gamma-glutamyl--amino-acid by (5-L-glutamyl)-L-amino-acid 5-glutamyltransferase (cyclizing) (gamma-glutamylcyclotransferase) in human erythrocyte hemolysates. The Michaelis-Menten steady-state kinetic parameters were obtained by fitting the integrated Michaelis-Menten equation to the reaction time curves. The product, L-5-oxoproline, was shown to be an inhibitor of the reaction. The active site of the enzyme was probed by studies of the inhibition by D- and L-beta-aminoglutaryl-L-alanine which are the beta-amino-acid isomers of D- and L-gamma-glutamyl-L-alanine (the latter being a natural substrate of the enzyme); the D-isomer was the more potent inhibitor (Ki = 0.30 +/- 0.02 mmol/l water). When the alanyl alpha-carboxyl of the inhibitor was reduced to a hydroxyl (i.e. to give D-beta-aminoglutaryl-L-alaninol) the potency of inhibition was reduced. The previously reported kinetic isotope effect of solvent 2H2O on the enzyme-catalyzed reaction has been further studied using a proton inventory. We propose that the solvent kinetic isotope effect is due to an intramolecular proton transfer between the glutamyl amino group and the peptide bond nitrogen.     

Tritium secondary kinetic isotope effect on phenylalanine ammonia-lyase-catalyzed reaction.

The mechanism by which phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) catalyzes the reversible elimination of ammonia from phenylalanine yielding (E)-cinnamic acid has gained much attention in the recent years. Dehydroalanine is essential for the catalysis. It was assumed that this prostetic group acts as the electrophile, leading to a covalently bonded enzyme-intermediate complex with quarternary nitrogen of phenylalanine. Recently, an alternative mechanism has been suggested in which the enzyme-intermediate complex is formed in a Friedel-Crafts reaction between dehydroalanine and orthocarbon of the aromatic ring. Using semiempirical calculations we have shown that these two alternative mechanisms can be distinguished on the basis of the hydrogen secondary kinetic isotope effect when tritium label is placed in the orthopositions. Our calculations indicated also that the kinetic isotope effect measured using ring-labeled d(5)-phenylalanine could not be used to differentiate these alternative mechanisms. Measured secondary tritium kinetic isotope effect shows strong dependence on the reaction progress, starting at the inverse value of k(H)/k(T) = 0.85 for 5% conversion and reaching the normal value of about 1.15 as the conversion increases to 20%. This dependence has been interpreted in terms of a complex mechanism with initial formation of the Friedel-Crafts type intermediate.     

Substrate specificity and kinetic isotope effect analysis of the Eschericia coli ketopantoate reductase

Ketopantoate reductase (EC 1.1.1.169), an enzyme in the pantothenate biosynthetic pathway, catalyzes the NADPH-dependent reduction of alpha-ketopantoate to form D-(-)-pantoate. The enzyme exhibits high specificity for ketopantoate, with V and V/K for ketopantoate being 5- and 365-fold higher than those values for alpha-ketoisovalerate and 20- and 648-fold higher than those values for alpha-keto-beta-methyl-n-valerate, respectively. For pyridine nucleotides, V/K for beta-NADPH is 3-500-fold higher than that for other nucleotide substrates. The magnitude of the primary deuterium kinetic isotope effects on V and V/K varied substantially when different ketoacid and pyridine nucleotide substrates were used. The small primary deuterium kinetic isotope effects observed using NADPH and NHDPH suggest that the chemical step is not rate-limiting, while larger primary deuterium isotope effects were observed for poor ketoacid and pyridine nucleotide substrates, indicating that the chemical reaction has become partially or completely rate-limiting. The pH dependence of (D)V using ketopantoate was observed to vary from a value of 1.1 at low pH to a value of 2.5 at high pH, while the magnitude of (D)V/K(NADPH) and (D)V/K(KP) were pH-independent. The value of (D)V is large and pH-independent when alpha-keto-beta-methyl-n-valerate was used as the ketoacid substrate. Solvent kinetic isotope effects of 2.2 and 1.2 on V and V/K, respectively, were observed with alpha-keto-beta-methyl-n-valerate. Rapid reaction analysis of NADPH oxidation using ketopantoate showed no "burst" phase, suggesting that product-release steps are not rate-limiting and the cause of the small observed kinetic isotope effects with this substrate pair. Large primary deuterium isotope effects on V and V/K using 3-APADPH in steady-state experiments, equivalent to the isotope effect observed in single turnover studies, suggests that chemistry is rate-limiting for this poorer reductant. These results are discussed in terms of a kinetic and chemical mechanism for the enzyme.