Effects of light regime and oxygen profile on transformation of oxolinic acid in pond sediment

This study investigated the effects of light (visible light - 5800 lux, 24 h) or dark regime and aerobic or anaerobic condition on the decay of added oxolinic acid (OA) at 5, 10 and 20 mg L⁻¹ in eel pond sediment. An asymptotic decaying exponential model C_t = C_min + C_o × exp (−k × t) was used to facilitate quantitative approach to OA transformation, where C_t is the concentration of OA after t days, C_min the estimated level-off concentration of OA residue, C_o the concentration of added OA and k the decaying coefficient. OA decayed faster under light (C_min = 4.6 mg L⁻¹) than under dark (C_min = 7.8 mg L⁻¹) and also decayed faster under aerobic (C_min = 4.0 mg L⁻¹) than under anaerobic condition (C_min = 8.5 mg L⁻¹). C_min increased with C_o. Sundrying and tilling eel pond bottom should be able to reduce OA residue significantly.     

The diffusion coefficient for PGK folding in eukaryotic cells

We compare the folding kinetics of a fluorescent phosphoglycerate kinase construct in 30 mammalian cells with that in aqueous buffer. In both environments, the kinetics can be fitted to the functional form exp[−(t/τ)^β]. A histogram of τ shows that the average folding relaxation time in cells is only twice as long as in aqueous buffer. Consideration of the folding free energy and of β reveals that only some of the variation in τ arises from perturbation of the protein's energy landscape. Thus, the diffusion that controls barrier crossing during protein folding is nearly as fast in cells as in vitro, even though translational diffusion of phosphoglycerate kinase in the cell is slow compared to in vitro.     

Cross-Correlation Functions for a Neuronal Model

Cross-correlation functions, R_XY(t,τ), are obtained for a neuron model which is characterized by constant threshold θ, by resetting to resting level after an output, and by membrane potential U(t) which results from linear summation of excitatory postsynaptic potentials h(t). The results show that: (1) Near time lag τ = 0, R_XY(t,τ) = f_U [θ-h(τ), t + τ] {h′(τ) + E_U [u′(t + τ)]} for positive values of this quantity, where f_U(u,t) is the probability density function of U(t) and E_U [u′(t + τ)] is the mean value function of U′(t + τ). (2) Minima may appear in R_XY(t,τ) for a neuron subjected only to excitation. (3) For large τ, R_XY(t,τ) is given approximately by the convolution of the input autocorrelation function with the functional of point (1). (4) R_XY(t,τ) is a biased estimator of the shape of h(t), generally over-estimating both its time to peak and its rise time.     

Analogue tracers and lumped constant in capillary beds

The lumped constant is a proportionality factor for converting a tracer analogue's metabolic rate to that of its mother substance. In a uniform system, it is expressed as the ratio of the tracer analogue's extraction fraction (E^?) to the extraction fraction of its mother substance (E).Here we show that, in capillary beds perfused by unidirectional blood flow, unequal concentration gradients of the tracer analogue and of the mother substance influence extraction fractions both locally and across the organ and that the direct proportionality of E^? and E must be replaced by ln(1−E^?)/ln(1−E) to yield Λ, i.e. the lumped constant derived from first principles of bi-substrate enzyme and membrane kinetics. In other words, at a given capillary blood flow (F), the ratio of systemic clearances (FE^?/FE), often used in compartmental kinetic analysis, must be replaced by the ratio of the intrinsic clearances, [−F ln(1−E^?)]/[−F ln(1−E)].The conclusion is supported by 2-[¹⁸F]fluoro-2-deoxy-d-galactose removal kinetics in pig liver in vivo from previous publications by the dependence of E^?/E and the independence of Λ, on blood galactose concentration. Moreover, our corrections to the results of compartmental kinetics are quantified for comparing extraction fractions in different regions of interest (e.g. by positron emission tomography) and for calculating Λ using whole-organ E^? and E measured by arteriovenous concentration differences.     

Inferring the effect of therapy on tumors showing stochastic Gompertzian growth

The present work deals with a Gompertz-type diffusion process, which includes in the drift term a time-dependent function C(t) representing the effect of a therapy able to modify the dynamics of the underlying process. However, in experimental studies is not immediate to deduce the functional form of C(t) from a treatment protocol. So a statistical approach is proposed in order to estimate this function when a control group and one or more treated groups are observed. In order to validate the proposed strategy a simulation study for several interesting functional forms of C(t) has been carried out. Finally, an application to infer the net effect of cisplatin and doxorubicin+cyclophosphamide in actual murine models is presented.     

Multiple source pools for Galápagos plant species richness: a critical analysis of the line of sight connectivity index

An index (C_i*E) combining the number of line‐of‐sight islands (C_i) within a radius i and target island elevation (E) has been proposed as an improved predictive model of plant species richness (S_t) in the Galápagos Archipelago. We examined this index critically and found that several major flaws preclude it from being a useful predictive tool for the archipelago. Although the number of collecting trips to an island was reported over 20 years ago to have substantial predictive value for reported plant species richness in the Galápagos Islands, this relationship was ignored in multiple regression analyses of the index. When we included the number of collecting trips in different multiple regression analyses of the index, C_i*E had less predictive power than collecting trips or ceased to be significant at all. Additionally, the strong significant relationship between elevation and area in the Galápagos Archipelago results in area having a major confounding influence on the C_i*E index. When elevation is removed from the C_i*E index, the predictive power of C_i is far less than area alone. Finally, the data used to construct and correlate the C_i*E index with (S_t) were based only on a subset of the islands and species lists that were incomplete or out of date. Species richness on islands can be related to the interaction of different factors, so development and testing of indices like C_i*E is not inappropriate. However, it is important to examine the interrelationships among the components of these indices thoroughly, and not ignore the effect of factors already known to have high predictive power. We propose several ways in which more meaningful indices of source pool(s) capacity can be constructed.     

The rate of allelism of lethal genes in a geographically structured population

The expected rate of allelism, E[I(x)], of lethal genes between two colonies with distance x in a structured population is studied by using one- and two-dimensional stepping-stone models. It is shown that E[I(x)] depends on the magnitude of selection in heterozygous condition (h), the rate of migration among adjacent colonies (m), the number of loci which produce lethal mutations (n) and the effective population size of each colony (N).——E[I(x)] always decreases with distance x. The rate of decrease is affected strongly by the magnitude of m. The rate of decrease is faster when m is small. E[I(x)] also decreases with increasing N and n. The effect of h on E[I(x)] is somewhat complicated. However, E[I(0)] is always smaller when h is small than when it is large.——For large x, the following approximate formulae may be obtained: (see PDF) where q and Var (q) are the mean and the variance of gene frequencies in each colony, t is approximated as t=h, (see PDF), -h for the partially recessive, completely recessive, and overdominant lethals, respectively, and C₀ is a function of m and t. It is clear that E[I(x)] declines exponentially with x in a one-dimensional habitat. The decrease E[I(x)] is faster in a two-dimensional habitat than in a one-dimensional habitat. The present result is applied to some of the existing data and the estimation of population parameters is also discussed.     

Optimum temperature policy for batch reactors performing biochemical reactions in the presence of enzyme deactivation

A necessary condition is found for the optimum temperature policy which leads to the minimum reaction time for a given final conversion of substrate in a well stirred, enzymatic batch reactor performing an enzyme-catalyzed reaction following Michaelis-Menten kinetics in the presence of first order enzyme decay. The reasoning, which is based on Euler's classical approach to variational calculus, is relevant for the predesign steps because it indicates in a simple fashion which temperature program should be followed in order to obtain the maximum advantage of existing enzyme using the type of reactor usually elected by technologists in the fine biochemistry field. In order to highlight the relevance and applicability of the work reported here, the case of optimality under isothermal operating conditions is considered and a practical example is worked out.List of Symbols C _E mol.m^–3 concentration of active enzyme - C _E ^* dimensionless counterpart of C_E - C _E,0 mol.m^–3 initial concentration of active enzyme - C _E,b mol.m^–3 final concentration of active enzyme - C _E,opt ^* optimal dimensionless counterpart of C_E - C _smol.m^–3 concentration of substrate - C _S ^Emphasis>/* dimensionless counterpart of C_S - C _S,0mol.m^–3 initial concentration of substrate - C _S,bmol.m^–3 final concentration of substrate - E enzyme in active form - E ₃ ^* dimensionless counterpart of E_a,3 - E _a,1J.mol^–1 activation energy associated with k₁ - E _a,3J.mol^–1 activation energy associated with k₃ - E _d enzyme in deactivated form - ES enzyme/substrate complex - k ₁ s^–1 kinetic constant associated with the enzyme-catalyzed transformation of substrate - k _1,0 s^–1 preexponential factor associated with k₁ - k ₂ mol^–1.m³s^–1 kinetic constant associated with the binding of substrate to the enzyme - k _–2 s^–1 kinetic constant associated with the dissociation of the enzyme/substrate complex - K _2,0 mol.m^–3 constant value of K₂ - K _2,0 ^* dimensionless counterpart of K_2,0 - k ₃ s^–1 kinetic constant associated with the deactivation of enzyme - k _3,0 s^–1 preexponential factor associated with k₃ - k _3,0 ^* dimensionless counterpart of k_3,0 - P product - R J.K^–1.mol^–1 ideal gas constant - S substrate - t s time since start-up of reaction - T K absolute temperature - T ^* dimensionless absolute temperature - T _i,opt ^* optimal dimensionless isothermal temperature of operation - T _opt ^* optimal dimensionless temperature of operation - t _b s time of a batch - t _b ^* dimensionless counterpart of t_b - t _b,min ^* minimum value of the dimensionless counterpart of t_b Greek Symbols dimensionless counterpart of C_E,0 - dimensionless counterpart of C_E,b - dummmy variable of integration - dummy variable of integration - auxiliary dimensionless variable - ^* dimensionless variation of k₁ with temperature - _i ^* dimensionless value of k₁ under isothermal conditions - _opt ^* optimal dimensionless variation of k₁ with temperature     

Pore formation kinetics in membranes, determined from the release of marker molecules out of liposomes or cells

We discuss the efflux of entrapped marker material from liposomes or cells through pores in the membrane, being monitored by the time course of a certain signal F (e.g., fluorescence emission). This is expressed in terms of an appropriate normalized function of time, the so-called efflux function E(t). Under conditions frequently encountered in practice the measured E(t) can be easily related to the forward rate of pore formation if the liposomes/cells are monodisperse in size. In the basic case of a time-independent rate law it turns out that E(t) must be single exponential. Deviations from such a simple functional behavior might be due to a fairly broad distribution of liposome/cell sizes and/or a more complicated pore formation mechanism. A relevant evaluation of original data is demonstrated making use of experimental results obtained with small unilamellar lipid vesicles where pores are induced by the antibiotic peptide alamethicin. This includes the application of a general method to eliminate the effect of a given liposome/cell size distribution.     

On indicator dilution and perfusion heterogeneity: A stochastic model

Unidirectional extraction of a substrate S in the capillaries following the arterial injection of a bolus containing S and a reference tracer R is assumed to follow first-order kinetics. If C_R and C_S denote normalized venous effluent concentrations of R and S, respectively, let L(t)=ln[C_R(t)⧸C_S(t)]. We derive a formula which expresses the experimental L(t) data in terms of the mean μ(t) and variance of the transit times of those capillaries which are contributing indicators at each sample time t. We examine the information thus contained in the L data about capillary and noncapillary transit times under several kinematic assumptions. We show that if the capillary and noncapillary transit times are stochastically independent with frequency functions h_c(t) and h_av(t), respectively, then the shapes of the graphs of L(t) and μ(t) depend on the variances and skewnesses of h_c(t) and h_av(t). Specifically, let r₂ be the ratio of the variance of h_c(t) to the variance of h_av(t), and let r₃ be the ratio of skewnesses in the same order. Then the graph of μ(t) is concave downward if r₂⧸r₃ > 1, concave upward if r₂⧸r₃< 1, and linear if r₂⧸r₃ = 1. If the fraction of S extracted is not too large, L(t) has nearly the same shape as μ(t), and therefore, L(t) contains information about h_c(t) and h_av(t).     

Effect of collisions on Van Kampen waves

The time evolution of Van Kampen waves is analyzed by solving the kinetic equation for the plasma particle distribution function. The damping law for Van Kampen waves, ∝Bexp(?C(Ωt)³), obtained earlier from qualitative considerations, is confirmed. The values of the constants B and C are found, and comparison with the previous analysis is made.     

Electrostatic charging of an electrically insulated metal body streamlined by a plasma flow

Electrostatic charging of an electrically insulated metal body streamlined by a plasma flow is investigated theoretically. The physical processes occurring in the vicinity of the body are considered. The electric currents resulting in the charging or discharging of the body are determined. The electric charge Q(t), electric field E(t), and potential φ(t) of a metal sphere are estimated taking into account the adopted conditions and parameters of the problem. The physical phenomena that take place in the vicinity of a charged body after Q(t) reaches a certain threshold value are discussed. The obtained values of Q(t), E(t), and φ(t) are compared with the corresponding values for a body streamlined by an atmospheric air flow.     

Packing requirements and short-range interactions as structure-directing forces in the intercluster compounds based on silver clusters

Although being composed of high valent ions, the crystal structures of four new supramolecular intercluster compounds, presented in this article, display a major contribution of short-range intermolecular interactions, i.e., aromatic π-π interactions. These structure-directing forces has lead to the formation of an distorted NaCl-type packing in [Ag₅(2,2′-bipyridine)₄(CCtBu)₂][PW₁₂O₄₀] and [Ag₅(2,2′-bipyridine)₄(CCtBu)₂][PMo₁₂O₄₀], and a CsCl-type packing in [Ag₈(2,2′-bipyridine)₆(CCtBu)₄(C₃H₇NO)₂][SiW₁₂O₄₀] and [Ag₈(2,2′-bipyridine)₆(CCtBu)₄(C₃H₇NO)₂][SiMo₁₂O₄₀].     

Ordering Dynamics in Neuron Activity Pattern Model: An Insight to Brain Functionality

We study the domain ordering kinetics in d = 2 ferromagnets which corresponds to populated neuron activities with both long-ranged interactions, V(r) ∼ r ⁻ⁿ and short-ranged interactions. We present the results from comprehensive Monte Carlo (MC) simulations for the nonconserved Ising model with n ≥ 2, interaction range considering near and far neighbors. Our model results could represent the long-ranged neuron kinetics (n ≤ 4) in consistent with the same dynamical behaviour of short-ranged case (n ≥ 4) at far below and near criticality. We found that emergence of fast and slow kinetics of long and short ranged case could imitate the formation of connections among near and distant neurons. The calculated characteristic length scale in long-ranged interaction is found to be n independent (L(t) ∼ t ^1/(n−2)), whereas short-ranged interaction follows L(t) ∼ t ^1/2 law and approximately preserve universality in domain kinetics. Further, we did the comparative study of phase ordering near the critical temperature which follows different behaviours of domain ordering near and far critical temperature but follows universal scaling law.     

Acrylonitrile Quenching of Trp Phosphorescence in Proteins: A Probe of the Internal Flexibility of the Globular Fold

Quenching of Trp phosphorescence in proteins by diffusion of solutes of various molecular sizes unveils the frequency-amplitude of structural fluctuations. To cover the sizes gap between O₂ and acrylamide, we examined the potential of acrylonitrile to probe conformational flexibility of proteins. The distance dependence of the through-space acrylonitrile quenching rate was determined in a glass at 77 K, with the indole analog 2-(3-indoyl) ethyl phenyl ketone. Intensity and decay kinetics data were fitted to a rate, k(r) = k₀ exp[−(r − r₀)/r_e], with an attenuation length r_e = 0.03 nm and a contact rate k₀ = 3.6 × 10¹⁰ s⁻¹. At ambient temperature, the bimolecular quenching rate constant (kq) was determined for a series of proteins, appositely selected to test the importance of factors such as the degree of Trp burial and structural rigidity. Relative to kq = 1.9 × 10⁹ M⁻¹s⁻¹ for free Trp in water, in proteins kq ranged from 6.5 × 10⁶ M⁻¹s⁻¹ for superficial sites to 1.3 × 10² M⁻¹s⁻¹ for deep cores. The short-range nature of the interaction and the direct correlation between kq and structural flexibility attest that in the microsecond-second timescale of phosphorescence acrylonitrile readily penetrates even compact protein cores and exhibits significant sensitivity to variations in dynamical structure of the globular fold.     

A batch decolorization and kinetic study of Reactive Black 5 by a bacterial strain Enterobacter sp. GY-1

An Enterobacter strain (GY-1) with high activity of decolorization of Reactive Black 5 (RB 5) was isolated from textile wastewater treating sludge. The kinetic characteristics of dye decolorization by the strain GY-1 were determined quantitatively using the diazo dye, RB 5. Effects of different operation parameters (inoculum size, pH, temperature and salinity) and various electron donors on decolorization of the azo dye by GY-1 were systematically investigated to reveal the primary factors that determine the performance of the azo dye decolorization. The decolorization of RB 5 was attributed to extracellular enzymes. A kinetic model was established giving the dependence of decolorization rate on cell mass concentration (first order). Decolorization rate increased with increasing temperature from 20 to 35 °C, which can be predicted by Arrhenius equation with the activation energy (E_a) of 8.50 kcal mol⁻¹ and the frequency factor (A₀) of 6.28 × 10⁷ mg l g MLSS⁻¹ h⁻¹. Michaelis-Menten kinetics and Eadie-Hofstee plot were used to determine V_max, 1.05 mg l⁻¹ h⁻¹ and K_m, 24.06 mg l⁻¹.     

Influence of CH3 group of μ-N-C-S ligand on the properties of [Fe2(C4H5N2S)2(NO)4] complex

Bi-nuclear neutral sulfur-nitrosyl iron complex [Fe₂(SR)₂(NO)₄] (I) has been obtained by replacement of thiosulfate ligands in dianion [Fe₂(S₂O₃)₂(NO)₄]²⁻ by 1-methyl-imidazole-2-yl. From X-ray analysis data, the complex has centrosymmetrical dimeric structure, with the iron atoms being linked via μ-N-C-S bridge. From Mossbauer spectroscopy, isomeric shift δ_Fe is 0.180(1) mm/s and quadrupole splitting ΔE_Q is 0.928(2) mm/s at T = 290 K. By comparative studying the mass-spectra in the gaseous phase of solid samples decomposition and kinetics of NO release in 1% aqueous solutions of dimethylsulfoxide, using of the ligand with CH₃ substituent in position 1 of imidazole-2-thiol was shown to yield a more stable donor of nitrogen monoxide than earlier obtained analog with imidazole-2-thiol, [Fe₂(C₃H₃N₂S)₂(NO)₄].     

Reaction of the Co(II)-substrate radical pair catalytic intermediate in coenzyme B12-dependent ethanolamine ammonia-lyase in frozen aqueous solution from 190 to 217 K

The decay kinetics of the aminoethanol-generated Co^II-substrate radical pair catalytic intermediate in ethanolamine ammonia-lyase from Salmonella typhimurium have been measured on timescales of <10⁵ s in frozen aqueous solution from 190 to 217 K. X-band continuous-wave electron paramagnetic resonance (EPR) spectroscopy of the disordered samples has been used to continuously monitor the full radical pair EPR spectrum during progress of the decay after temperature step reaction initiation. The decay to a diamagnetic state is complete and no paramagnetic intermediate states are detected. The decay exhibits three kinetic regimes in the measured temperature range, as follows. i), Low temperature range, 190 ≤ T ≤ 207 K: the decay is biexponential with constant fast (0.57 ± 0.04) and slow (0.43 ± 0.04) phase amplitudes. ii), Transition temperature range, 207 < T < 214 K: the amplitude of the slow phase decreases to zero with a compensatory rise in the fast phase amplitude, with increasing temperature. iii), High temperature range, T ≥ 214 K: the decay is monoexponential. The observed first-order rate constants for the monoexponential (k_obs,m) and the fast phase of the biexponential decay (k_obs,f) adhere to the same linear relation on an lnk versus T⁻¹ (Arrhenius) plot. Thus, k_obs,m and k_obs,f correspond to the same apparent Arrhenius prefactor and activation energy (logA_app,f (s⁻¹) = 13.0, E_a,app,f = 15.0 kcal/mol), and therefore, a common decay mechanism. We propose that k_obs,m and k_obs,f represent the native, forward reaction of the substrate through the radical rearrangement step. The slow phase rate constant (k_obs,s) for 190 ≤ T ≤ 207 K obeys a different linear Arrhenius relation (logA_app,s (s⁻¹) = 13.9, E_a,app,s = 16.6 kcal/mol). In the transition temperature range, k_obs,s displays a super-Arrhenius increase with increasing temperature. The change in E_a,app,s with temperature and the narrow range over which it occurs suggest an origin in a liquid/glass or dynamical transition. A discontinuity in the activation barrier for the chemical reaction is not expected in the transition temperature range. Therefore, the transition arises from a change in the properties of the protein. We propose that a protein dynamical contribution to the reaction, which is present above the transition temperature, is lost below the transition temperature, owing to an increase in the activation energy barrier for protein motions that are coupled to the reaction. For both the fast and slow phases of the low temperature decay, the dynamical transition in protein motions that are obligatorily coupled to the reaction of the Co^II-substrate radical pair lies below 190 K.     

Design and synthesis of glucose-templated proline-lysine chimera: polyfunctional amino acid chimera with high prolyl cis amide rotamer population

We describe the synthesis of two glucose-templated proline-lysine chimeras (GlcTProLysCs) that differ in the stereochemistry of the hydroxymethyl substituent at the C-5′ position of the pyrrolidine ring. The key synthetic steps involve C-glycosylation of an exocyclic glucose-based epoxide with allyltributylstannane, which affords functionalized C-ketosides containing an α-hydroxy ester moiety; introduction of an amino group at C-2 through stereoselective reductive amination; and regioselective installation of the azide group at C-6 on the glucose scaffold. Incorporation of these chimeras into the model peptides Ac-GlcTProLysC-NHMe and Ac-GlcTProLysC-OMe demonstrates that the stereochemistry of the hydroxymethyl substituent at the C-5′ position has a profound effect on the equilibrium constant of prolyl amide cis/trans isomerization. The equilibrium constant K_c/t for the peptide mimic Ac-GlcTProLysC-NHMe with C-5′(R) stereochemistry was determined to be 3.03 ± 0.04, while the K_t/c for the C-5′(S) diastereoisomer was 0.56 ± 0.04 in D₂O. Temperature coefficient experiments indicate that the origin of these effects is derived from two critical hydrogen bonds involving the C-5′ hydroxymethyl substituent: one to the N-terminal amide carbonyl group, and the other to the primary amino group in the glucose moiety.