Characterization of the mobile charges in the membrane ofValonia utricularis

Summary An attempt for the characterization of the mobile charges has been made by investigation of the voltage relaxations following a charge pulse at various temperatures between 2 and 40°C. The translocation ratek, the membrane conductivity 1/R _m and the total concentration of mobile chargesN _t within the membrane were calculated from recently developed theory (U. Zimmermann. K.-H. Büchner and R. Benz,J. Membrane Biol. 67:183–197, 1982). Data from 21 cells show that the concentration of mobile charges does not change significantly over a temperature range of 5 to 34°C, whereas both the translocation rate and the membrane conductivity reveal a strong but reversible temperature dependence. In the temperature range of 18 to 5°C,k decreases by a factor of 10 to 20, while between 18 and 34°C the increase ink is only two- or threefold with a maximum around 25°C. In principle, the same temperature dependence was observed for the membrane conductivity. Hysteresis effects occurring in the low temperature range as well as at high temperatures indicate that a protein component is involved in the mobile charge system. Furthermore, addition of cycloheximide leads to a marked decrease in both the translocation rate and the membrane conductivity, however, leaving the concentration of mobile charges almost unchanged. Therefore, it is assumed that the mobile charges are coupled to, but not part of a carrier protein.     

Backbone 1H and 15N resonance assignments of the N-terminal SH3 domain of drk in folded and unfolded states using enhanced-sensitivity pulsed field gradient NMR techniques

Summary The backbone ¹H and ¹⁵N resonances of the N-terminal SH3 domain of the Drosophila signaling adapter protein, drk, have been assigned. This domain is in slow exchange on the NMR timescale between folded and predominantly unfolded states. Data were collected on both states simultaneously, on samples of the SH3 in near physiological buffer exhibiting an approximately 1:1 ratio of the two states. NMR methods which exploit the chemical shift dispersion of the ¹⁵N resonances of unfolded states and pulsed field gradient water suppression approaches for avoiding saturation and dephasing of amide protons which rapidly exchange with solvent were utilized for the assignment.Abbreviations 2D, 3D two-, three-dimensional - drkN SH3 N-terminal SH3 domain of Drosophila drk - HSQC heteronuclear single-quantum spectroscopy - NOE nuclear Overhauser enhancement - SH3 Src homology domain 3 - TOCSY total correlation spectroscopy     

Design,synthesis and in vitro biological evaluation of quinazolinone derivatives as EGFR inhibitors for antitumor treatment

Abstract

In this paper, a series of novel 3-methyl-quinazolinone derivatives was designed, synthesised and evaluated for antitumor activity in vitro on wild type epidermal growth factor receptor tyrosine kinase (EGFR^wt-TK) and three human cancer cell lines including A549, PC-3, and SMMC-7721. The results displayed that some of the compounds had good activities, especially 2-{4-[(3-Fluoro-phenylimino)-methyl]-phenoxymethyl}-3-methyl-3H-quinazolin-4-one (5?g), 2-{4-[(3,4-Difluoro-phenylimino)-methyl]-phenoxymethyl}-3-methyl-3H-quinazolin-4-one (5k) and 2-{4-[(3,5-Difluoro-phenylimino)-methyl]-phenoxymethyl}-3-methyl-3H-quinazolin-4-one (5?l) showed high antitumor activities against three cancer cell lines. Moreover, compound 5k could induce late apoptosis of A549 cells at high concentrations and arrest cell cycle of A549 cells in the G2/M phase at tested concentrations. Also, compound 5k could inhibit the EGFR^wt-TK with IC₅₀ value of 10?nM. Molecular docking data indicates that the compound 5k may exert inhibitory activity by forming stable hydrogen bonds with the R817, T830 amino acid residues and cation-Π interaction with the K72 residue of EGFR^wt-TK.     

An algorithm to equiprobably generate all directed trees withk labeled terminal nodes and unlabeled interior nodes

A computer algorithm is presented which equiprobably generates any member of the set of all directed trees withk labeled terminal nodes and unlabeled interior nodes. The algorithm requires roughlyk ² /2 storage locations. The one-time initialization requiresO(k ² ) time, while generating each tree requiresO(k) time. Contribution No. 477 in Ecology and Evolution, State University of New York at Stony Brook. This research was supported by Grant No. DEB8003508 from the National Science Foundation to Robert R. Sokal.     

A comparative study of critical temperature estimation of atomic fluid and chain molecules using fourth-order Binder cumulant and simplified scaling laws

Grand-canonical transition-matrix Monte Carlo simulation with histogram reweighting and finite-size scaling technique are used to calculate fourth-order Binder cumulant of order parameter along the vapour–liquid coexistence line to calculate the critical temperature of bulk and confined square-well fluid in slit pore of two pore sizes. Further, this approach is utilised to estimate the critical temperatures of relatively more complex fluids such as n-alkanes confined in graphite and mica slit pores of different slit widths. The estimated critical temperatures are compared with the critical temperature obtained for the same systems using simplified form of the scaling law. This investigation reveals that critical temperatures of simple and complex fluids in bulk state and under confinement, estimated using the scaling law, are within reasonable accuracy with that obtained using more accurate and rigorous approach of fourth-order Binder's cumulant.     

Doubly sensitivity-enhanced 3D TOCSY-HSQC

Summary Recently, strategies for double sensitivity enhancement in heteronuclear three-dimensional NMR experiments were introduced (Krishnamurthy, V.V. (1995) J. Magn. Reson., B106, 170–177; Sattler et al. (1995) J. Biomol. NMR, 6, 11–22; Sattler et al. (1995) J. Magn. Reson., B108, 235–242). Since a sensitivity enhancement of a factor 2^1/2 can be achieved for each indirect dimension, nD spectra can theoretically be enhanced up to a factor of 2^((n-1)/2). We propose and analyze a doubly enhanced three-dimensional TOCSY-HSQC sequence. The application of the doubly enhanced three-dimensional {¹⁵N, ¹H} TOCSY-HSQC sequence is shown for uniformly ¹³C-/¹⁵N- and ¹⁵N-labeled samples of the relatively large Azotobacter vinelandii flavodoxin II (179 amino acids). The main factors that contribute to the final signal-to-noise enhancement have been systematically investigated. The sensitivity enhancement obtained for the doubly enhanced TOCSY-HSQC pulse sequence as compared to the standard (unenhanced) version is close to the theoretically expected factor of two.     

Linear Discrete Population Models with Two Time Scales in Fast Changing Environments I: Autonomous Case

In this work we consider a structured population with groups and subgroups of individuals. The intra-group dynamics is assumed to be fast in comparison with the inter-group dynamics. We study linear discrete models where the slow dynamics is represented by a single matrix and the fast dynamics is described by means of the first k terms of a converging sequence of different matrices. The number k can be interpreted as the ratio between the two time scales.The aim of this work is to extend aggregation techniques to the case of fast changing environments. The main idea of aggregation is to build up a new system, with lower dimension, that summarizes the information concerning the fast process. This "aggregated" system provides essential information on the original one. It is shown that the asymptotic behavior of the original system can be approximated by the asymptotic behavior of the aggregated system when the ratio between the two time scales is large enough.We present an example of an age structured population in a patchy environment. The migration process is assumed to be fast in comparison with the demographic process. Numerical simulations illustrate that the asymptotic growth rate and the stable age distribution of the population in the original and the aggregated systems are getting closer as the ratio k increases.     

Generating Correlated Binary Variables with Complete Specification of the Joint Distribution

Most statistical methods for the analysis of correlated binary data are based on asymptotic theory. Therefore it is important to generate correlated binary data efficiently for Monte Carlo simulation studies to investigate the finite sample performance of these methods. This article provides a simple method for generating correlated binary data with a given joint distribution. The key idea is to consider k‐variate binary data as a multinomial distribution with 2^k possible outcomes.     

A singular dispersion relation arising in a caricature of a model for morphogenesis

In 1983 Oster et al. proposed a model for morphogenesis consisting of a system of partial differential equations in which the dispersion relation for the problem linearised about the zero solution has a singularity. That is, the initial growth rate of a small perturbation of wave number k from the zero solution tends to positive or negative infinity as k tends to some critical value k _c from above or below respectively. We consider here as a caricature of the model a single partial differential equation with a similar dispersion relation in a bounded one-dimensional domain. The wave number, or equivalently the domain size, may be thought of as a bifurcation parameter. For the Neumann problem a phenomenon arises in which, as the domain size l increases past a critical value l _l ,the linear stability of the n-th mode jumps from one solution to a remote solution. That is, for l _n the trivial solution is unstable and a certain non-trivial solution is stable to perturbations of mode n, whereas for l>l _n the opposite is true. For the Dirichlet or the Robin problem a linear stability change in the trivial solution occurs, but no corresponding change in any other solution has been found. The corresponding initial boundary value problems are then considered. An asymptotic analysis is performed in the weakly nonlinear limit in the particular case in which only one mode is unstable and gives an asymptotic solution for two classes of nonlinearity, one symmetric and the other asymmetric about u=0. A development of the method of harmonic balance is then used to obtain approximate solutions in the strongly nonlinear case and when more than one mode may be unstable.     

Thermal variations, between 1 and 3000 degrees K, of the specific heat of L-alanine, tri(L-alanine) and poly(L-alanine) for the alpha and beta forms]

The heat capacities of L -Alanine, tri(L -alanine), and poly (L -alanine) (α helicoidal form and β pleated sheet structure) have been measured between 1.5 and 300°K with a standard adiabatic calorimeter. In the solid state, the heat capacity is in general dut to three parts which are additive in first-order approximation. (1) The lattice vibrations or “acoustical modes” which are the largest at low temperatures. The low-temperature lattice specific heat is proportional to T, T², or T³ for an ideal one-, two- or three-dimensional solid, respectively. (2) The so-called group vibrations or “optical modes” which, due to their high frequencies, usually take effect only at higher temperatures. (3) The defects and unharmonic effects. The α-amino acid and its trimer present a specific heat thermal variation characteristic of molecular solids which is correctly fitted with an empirical law proposed by Kitaigorodskii. This author assumes that, for such solids, the molecular lattice point has six degrees of freedom (three of translation and three of rotation). Thus the lattice contribution of the specific heat satisfies the Debye approximation in agreement with the doubling of the number of degrees of freedom per molecule (compared with atomic crystals). The polypeptide behavior is, however, different. The specific heat for each form exhibits a thermal dependence connected with a strong vibrational anisotropy. The model proposed earlier by Tarasov accounts well for these results. In the case of the β form, we have observed the predicted three- and two-dimensional behavior due to the intermolecular H bondings responsible for the sheet structure. For the α form we observed a one-dimensional pattern at higher temperature, since each peptidic chain vibrates separately. The comparison with other spectroscopic and theoretical investigations shows a large discrepancy. However, we have attemped to account for the “optical contribution” to the specific heat of poly(L -alanine) by using a continuum of mean frequencies as suggested by Wunderlich. Vibrational frequency spectra are proposed to explain our results, but the overlapping of acoustical and optical branches in the case of the α form outlines the limits of macroscopic models. It is quite likely that the acoustical spectrum is greatly affected by the intramolecular H bonding. At low temperature the specific heat is a physical property sensitive to the long-range order of the macromolecule, and therefore further spectroscopic and theoretical investigations are necessary to explain correctly these experimental results.     

Molecular dynamics study of the aggregation rate for zwitterionic dodecyldimethylamine oxide and cationic dodecyltrimethylammonium chloride micelles

Abstract

We studied dynamic scaling law for the early stage domain growth in the micelle aggregation process of dispersed surfactant molecules in water for zwitterionic dodecyldimethylamine oxide (DDAO) and cationic dodecyltrimethylammonium chloride (DTAC) based on all-atomistic molecular dynamics calculations. For both surfactants, the aggregation number N increases in proportion to t^α′, where t and α′ are the simulation time and exponent of the dynamic scaling, respectively. When the aggregation is controlled by diffusion, it follows the well-known Lifshitz–Slyozov (LS) law giving the exponent α′ = 1. The values of α′ obtained for DDAO and DTAC are 0.6 and 0.3, respectively, indicating that the aggregation rate is suppressed compared with purely diffusion controlled LS process. The aggregation of DDAO and DTAC may be partly controlled by electrostatic interaction between the aggregates.     

Growth and mortality of bigeye tuna <Emphasis Type="Italic">Thunnus obesus</Emphasis> (Scombridae) in the eastern and central tropical Pacific Ocean

Biological parameters such as age, growth and age (or size) at maturity are vital for stock assessment and management. Aging is essential in yielding such information. However, limited aging studies have been conducted for large tropical pelagic species in the eastern and central tropical Pacific Ocean. The objective of this study is to conduct a length frequency analysis for estimating growth and mortality of bigeye tuna in the eastern and central tropical Pacific Ocean using samples from the Chinese longline fishery during February to November 2006. The von Bertalanffy growth parameters of asymptotic fork length L _∞ and growth coefficient k were estimated at L _∞ = 207.4 cm fork length, k = 0.23 year^-1, and theoretical age at zero length t ₀ = −0.40 year. The total mortality rate (Z) was estimated to be 0.60; the fishing mortality rate (F) and the natural mortality rate (M) were 0.25 year^-1 and 0.35 year^-1, respectively. The exploitation rate (E) was 0.16. This study provides the estimates of growth and mortality rate for bigeye tuna in the eastern and central tropical Pacific Ocean, which can be used as biological input parameters in further stock evaluations in this region. However, age analysis, further validation of the age composition and stock structure are needed for future studies.     

Steady-state viscosity of the liquid two-phase disperse system water-casein-sodium alginate

The steady-state viscosity (η^*) of the liquid two-phase disperse system water-casein-sodium alginate of varying composition, with a disperse particle diameter of about 30 μm, has been investigated in the shear rate range . The flow curves obtained are similar in shape. They are invariant in composition and can be fitted to the flow curve equation where η^*₀ is the Newtonian viscosity obtained from data at low shear stresses and k is an empirical parameter. Both η^*₀ and k depend on the composition of the two-phase system.The experimental dependence of the viscosity on the composition follows a logarithmic additivity law at high shear stresses, but at low shear stresses the observed viscosities are lower than would be predicted by this law. The experimental dependence of the ratio (the mean activation volume) on the composition is also not in agreement with the additivity law. These special features of the steady-state flow of the investigated disperse system are explained by the presence of a low-concentration interphase layer having a lower viscosity and less pronounced non-Newtonian behaviour than the disperse and continuous phases. This interphase layer exists in other two-phase systems which consist of a solvent and two incompatible polymers. For this reason, the rheological behaviour of the system investigated may be expected to be common for two-phase systems of this type, particularly protein-polysaccharide mixtures in water.     

The temperature‐size rule in Daphnia magna across different genetic lines and ontogenetic stages: Multiple patterns and mechanisms

Ectotherms tend to grow faster, but reach a smaller size when reared under warmer conditions. This temperature‐size rule (TSR) is a widespread phenomenon. Despite the generality of this pattern, no general explanation has been found. We therefore tested the relative importance of two proposed mechanisms for the TSR: (1) a stronger increase in development rate relative to growth rate at higher temperatures, which would cause a smaller size at maturity, and (2) resource limitation placing stronger constraints on growth in large individuals at higher temperatures, which would cause problems with attaining a large size in warm conditions. We raised Daphnia magna at eight temperatures to assess their size at maturity, asymptotic size, and size of their offspring. We used three clonal lines that differed in asymptotic size and growth rate. A resource allocation model was developed and fitted to our empirical data to explore the effect of both mechanisms for the TSR. The genetic lines of D. magna showed different temperature dependence of growth and development rates resulting in different responses for size at maturity. Also, at warm temperatures, growth was constrained in large, but not in small individuals. The resource allocation model could fit these empirical data well. Based on our empirical results and model explorations, the TSR of D. magna at maturity is best explained by a stronger increase in development rate relative to growth rate at high temperature, and the TSR at asymptotic size is best explained by a size‐dependent and temperature‐dependent constraint on growth, although resource limitation could also affect size at maturity. In conclusion, the TSR can take different forms for offspring size, size at maturity, and asymptotic size and each form can arise from its own mechanism, which could be an essential step toward finding a solution to this century‐old puzzle.     

Relationship between power law coefficients and major blood constituents affecting the whole blood viscosity

The present work concerns a quantitative analysis of parameters that affect apparent blood viscosity at different low shear rates, i.e, between 1 s⁻¹ and, 100 s⁻¹. Viscosity profile of a large number of blood samples from thromboembolic stroke cases and age and sex matched healthy controls were studied which confirmed non-Newtonian power law behaviour of blood. The power law coefficients,n andk, which are unique to each blood sample, were related with blood viscosity parameters in the form of a mathematical equation by performing non-linear regression analysis. It was possible to calculaten andk of power law model by supplying the values of major blood constituents in the equation obtained for stroke and controls. The calculation ofn andk of a blood sample using the equation obtained, provided a quick information on its apparent viscosity values at any given shear rate without viscometry. The calculated and the experimental viscosity were found in good agreement within a permissible error range. The relation obtained between power law coefficients and major blood constituents in the present investigation would give a quantification of different blood viscosity parameters contributing to the resistance to flow of blood. Such an analysis may be considered as a scientific basis for the study of blood fluidity in different disease conditions.     

2,4,5-Triphenylisothiazol-3(2H)-one 1,1-dioxides as inhibitors of human leukocyte elastase

A series of substituted 2,4,5-triphenylisothiazol-3(2H)-one 1,1-dioxides 9 was synthesized and investigated as inhibitors of human leukocyte elastase (HLE). All compounds were found to inhibit HLE in a time-dependent manner and most of them exhibited k_obs/[I] values > 300 M^{? 1}s^{? 1}. The most potent 3-oxosultam of this series was 9l (k_obs/[I] = 2440 M^{? 1}s^{? 1}). Kinetic investigations performed with 9g and different substrate concentrations did not allow to clearly distinguish between a competitive or noncompetitive mode of inhibition. A more complex interaction is supported by the failure of a linear dependency of k_obs values on the inhibitor concentration.     

Phase Equilibria of Quadrupolar Fluids by Simulation in the Gibbs Ensemble

Abstract

Vapour-liquid phase diagrams for pure fluids and mixtures of molecules with Lennard-Jones plus quadrupole-quadrupole interaction potentials were determined by Monte Carlo simulation in the Gibbs ensemble [1]. This is the first reported application of the method to molecular fluids. We have demonstrated that the Gibbs method works reliably for strongly interacting molecular fluids at liquid densities. Pure fluid calculations were performed for reduced quadrupole strengths, Q* = Q/(εσ⁵)^1/2 equal to 1 and √2, typical of molecules like C₂H₂ and C₂H₄. It was found that the critical temperature of the quadrupolar fluid increased rapidly with increasing quadrupolar strength, in good agreement with previous computer simulation and theoretical results. A single mixture with components characterized by identical Lennard-Jones parameters and Q*₁ = + 1, Q*₂ = - 1 was studied at three temperatures. A negative azeotrope was observed at the lowest temperature studied, as seen experimentally in the CO₂/C₂H₂ mixture. The perturbation theory calculations are in good agreement with the simulation results for all properties except coexisting liquid densities. The results illustrate some of the strengths and limitations of perturbation theories based on the Padé approximant for the free energy of polar fluids.     

An improved algorithm for statistical alignment of sequences related by a star tree

The insertion-deletion model developed by Thorne, Kishino and Felsenstein (1991, J. Mol. Evol., 33, 114–124; the TKF91 model) provides a statistical framework of two sequences. The statistical alignment of a set of sequences related by a star tree is a generalization of this model. The known algorithm computes the probability of a set of such sequences in O(l ^2k ) time, where l is the geometric mean of the sequence lengths and k is the number of sequences. An improved algorithm is presented whose running time is only O(2^2k l ^k).     

Preparation of extracellular domain 3 of human VEGF receptor‐2 and the monitoring of its real‐time binding to VEGF by biosensors

Vascular endothelial growth factor receptor‐2 (VEGFR‐2) plays an important role in stimulating the proliferation of endothelial cells and improving the permeability of blood vessels, which is involved in tumor angiogenesis, a process that is essential for tumor growth and metastasis. In this study, we describe a method for high yield of recombinant extracellular domain 3 (KDR3) of human VEGFR‐2 in an Escherichia coli system with further purification by cation exchange chromatography and immobilized metal affinity chromatography (IMAC). The biological activity of recombinant KDR3 was performed by sequestering VEGF in HUVEC proliferation assay. The real‐time binding of human VEGF to immobilized KDR3 was monitored by a label‐free biosensor, Optical waveguide lightmode spectroscopy (OWLS). Under the given experimental conditions, the association rate constant k_a was 4.2 × 10³ M^?1 s^?1 and the dissociation rate k_d was 5.1 × 10^?3 s^?1. The dissociation constant K_D was then calculated to be 1.2 × 10^?6 M. The obtained values will serve as baseline parameters for the design of improved versions of recombinant soluble VEGF receptors and the evaluation of developed anti‐KDR antibodies. In addition, such a scenario established by the use of OWLS will potentiate the kinetic study of ligand/receptor and antigen/antibody. The receptor discussed here, which block VEGF binding to cell membrane KDR, have potential clinical application in the treatment of cancer and other diseases where pathological angiogenesis is involved. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

Comparing body-size growth curves: the Gallucci-Quinn index,and beyond

Gallucci and Quinn suggested that the product L_￥ ·k {L_\infty } \cdot k is a sensible index to compare two growth curves (L _∞, k the usual Bertalanffy parameters). This paper gives four (interrelated) reasons why this index captures some essential features of body-size growth. It also notes that the product k ·L_￥³ k \cdot L_\infty^3 directly compares fish growth at the maximum growth rate.