Irradiation by electrons of tubulin solution in vitro causes tubulin assembly in absence of a magnesium cofactor

It was shown that irradiation of a tubulin solution (5 x 10(-6) mol/l) with electrons makes tubulin assemble to microtubules. The response of the system was monitored by the femtosecond laser technique. The assembly under these conditions occurs without Mg2+ (magnesium cofactor) and GTP. At 730 (the first harmonic) and 365 nm (the second harmonic), a rise in signal intensity occurs during the first 60-70 ns followed by the onset of tubulin assembly to microtubules, which was registered by the methods of spectrophotometry and electron spectroscopy. Theoretically this effect can be explained by the appearance of hydrated electrons in the solvated tubulin shell. Hydrated electrons are mostly in a long-living polaron state, which can be considered as an ensemble of quasi-dipoles of the electron-H3O+ type. The interaction of quasi-dipoles with the weak internal electrostatic field of tubulin leads, due to nonlinear effects, to a manifold rise in the intensity of the electrostatic field of the solvated shell of initially nonpolymerized tubulin chains. Finally, the increased field makes separate tubulin chains aggregate to microtubules. The effect observed is identical to the action of Mg2+ on the GTP site of beta-tubulin, which transfers it to a slightly perturbed triplet state.     

On the role of polarizability in QSAR

The polarizability of a molecule, an important physical property, is currently attracting our attention particularly in the area of QSAR for chemical-biological interactions. In this report, the polarizability effects on ligand-substrate interactions has been discussed in terms of NVE (number of valence electrons) using additive values for valence electrons and the formulation of a total number of 51 QSAR. The QSAR model can be illustrated by Eq. I. log 1/C = a(NVE) +/- constant     

ConFind: a robust tool for conserved sequence identification

SUMMARY: ConFind (conserved region finder) identifies regions of conservation in multiple sequence alignments that can serve as diagnostic targets. Designed to work with a large number of closely related, highly variable sequences, ConFind provides robust handling of alignments containing partial sequences and ambiguous characters. Conserved regions are defined in terms of minimum region length, maximum informational entropy (variability) per position, number of exceptions allowed to the maximum entropy criterion and the minimum number of sequences that must contain a non-ambiguous character at a position to be considered for inclusion in a conserved region. Comparison of the calculated entropy for an alignment of 95 influenza A hemagglutinin sequences with random deletions results in a 98% reduction in the average error in ConFind relative to the 'Find Conserved Regions' option in BioEdit. REQUIREMENTS: ConFind requires Python 2.3, but Python 2.4 or an upgrade of the optparse module to Optik 1.5 is suggested. The program is known to run under Linux and DOS.     

Parametric and semiparametric approaches to testing for seasonal trend in serial count data

We present two tests for seasonal trend in monthly incidence data. The first approach uses a penalized likelihood to choose the number of harmonic terms to include in a parametric harmonic model (which includes time trends and autogression as well as seasonal harmonic terms) and then tests for seasonality using a parametric bootstrap test. The second approach uses a semiparametric regression model to test for seasonal trend. In the semiparametric model, the seasonal pattern is modeled nonparametrically, parametric terms are included for autoregressive effects and a linear time trend, and a parametric bootstrap test is used to test for seasonality. For both procedures, a null distribution is generated under a null Poisson model with time trends and autoregression parameters.We apply the methods to skin melanoma incidence rates collected by the surveillance, epidemiology, and end results (SEER) program of the National Cancer Institute, and perform simulation studies to evaluate the type I error rate and power for the two procedures. These simulations suggest that both procedures are alpha-level procedures. In addition, the harmonic model/bootstrap test had similar or larger power than the semiparametric model/bootstrap test for a wide range of alternatives, and the harmonic model/bootstrap test is much easier to implement. Thus, we recommend the harmonic model/bootstrap test for the analysis of seasonal incidence data.     

Theory of harmonic generation in a plasma produced by the photoionization of gas atoms with electrons in the <Emphasis Type="Italic">np</Emphasis> states

For a plasma produced by the photoionization of hydrogen-like atoms with electrons in the np states, a theory is developed that describes the nonlinear plasma polarizability due to electron-ion collisions, which governs the bremsstrahlung-induced coherent harmonic generation. The effective partial collision frequencies are obtained as functions of the pump field intensity for the first four p states of hydrogen-like atoms and for the third, fifth, seventh, ninth, and eleventh harmonics. These analytic results make it possible to establish the scalings of the collision frequencies with pump field intensity, the principal quantum number, and the number of the generated harmonic. In the case of pump fields of comparatively low intensities, some qualitative differences are revealed between these scalings and the corresponding scalings obtained for the Bethe regime of suppression of the photoionization barrier in a gas of hydrogen-like atoms with electrons in the ns states.     

Activation and extinction models for platelet adhesion

Adherent platelets are an important part of both thrombus formation and in certain stages of atherogenesis. Platelets can be activated by potent chemicals released from adherent platelets and adhere far more readily than unactivated ones. An analytical and numerical model is presented utilising high Peclet number for the activation and adhesion of platelets in shear flows. The model uses a similarity transformation, which characterises the relationship between convective, diffusive transport and the bulk platelet activating reaction mechanism. A first order surface reaction mechanism is used to model platelet adhesion at the wall (cell) surface. The reduced Damk?hler number, M, characterises the importance of the bulk reaction and includes both convective and diffusive terms. For a high rate of blood flow (M-->0) the activation of platelets can effectively be terminated. In contrast, for (M-->infinity) an inner layer of activated platelets exists with an infinitesimally thin reaction sheet separating activated and non-activated platelets. This characterisation by the Damk?hler number highlights results found clinically, in that thrombus forms in areas of low shear (high M) and in some cases an increased blood flow (low M) can inhibit the activation of platelets completely. The model shows the critical balance that exists between convection, diffusion and reaction.     

Association of the minor groove binding drug Hoechst 33258 with d(CGCGAATTCGCG)2: volumetric, calorimetric, and spectroscopic characterizations

We employed ultrasonic velocimetry, high-precision densimetry, circular dichroism and fluorescence spectroscopy, and isothermal titration calorimetry to characterize the binding of Hoechst 33258 to the d(CGCGAATTCGCG)(2) oligomeric duplex at 25 degrees C. We used this experimental combination to determine the full thermodynamic profile for the binding of Hoechst 33258 to the DNA. Specifically, we report changes in binding free energy, enthalpy, entropy, volume, and adiabatic compressibility accompanying the binding. We interpret our volumetric data in terms of hydration and evaluate the number of waters of hydration that become released to or taken up from the bulk. Our calorimetric data reveal that the drug-DNA binding event studied in this work is entropy-driven and proceeds with an unfavorable change in enthalpy. The favorable binding entropy predominantly results from hydration changes. In contrast to a large and positive change in hydrational entropy, the binding-induced change in configurational entropy is insignificant. The latter observation is consistent with the "lock-and-key" mode of minor groove binding.     

The spatial metric of brain underlying the temporal metric of EEG and thought

Multiplying memory span by mental speed, we obtain the information entropy of short-term memory capacity, which is rate-limiting for cognitive functions and corresponds with EEG power spectral density. From psychometric and EEG data follows a fundamental of about 3.14 Hz. The number of harmonics (n = 1, 2,...,9) is identical with memory span, and the eigenvalues of the EEG impulse response are represented by the zero-crossings up to the convolved fundamental, the P300. The difference T of 4.42 ms between the 8th and the 9th harmonic is the smallest time window of conscious information processing. Shannon's sampling theorem allows the replacement of any band-limited signal by m discrete sequences of T without loss of any information. Brain architecture can be understood in terms of sequences of delaying chains. Acting as a wavefront tracking array, scaled in relation of mT and in such a way also expressing the metric of eigenvalues, widths of orientation columns match with phase reversal after a zero-crossing and lengths of dendritic trees with run-length of travelling harmonics.     

Postirradiation long-range energy transfer in a single crystal of cytosine monohydrate: an EPR study.

Thiocytosine molecules incorporated in the cytosine monohydrate crystal lattice act as traps for both electrons and holes. The radiation-induced cytosine ion radicals, C(+) and C(-), release their charge upon heating. The excess electrons and holes migrate long distances in the crystal lattice. The migration of holes has been demonstrated by the postirradiation, thermally activated accumulation of thiocytosine cation radicals, T(+), and the migration of electrons by formation of the S-centered radicals of an anionic nature. It is estimated that the migration length of the holes is at least 30 interbase distances, and the migration length of the electrons is more than 100 interbase distances. The selective formation of the cationic and anionic trap radicals, depending on the trap concentration, is discussed in terms of differences between the migration of electrons and holes.     

Chemical modification of horseradish peroxidase. Preparation and characterization of tracer enzymes with different isoelectric points.

Horseradish peroxidase (HRP), a plant glycoprotein with a molecular weight of 40,000 D and a molecular radius (ae) of 30 A, has been modified chemically to prepare tracer molecules with different molecular charge. Modification of free carboxyl groups on the enzyme is achieved by carbodiimide activation and subsequent reaction of activated carboxyl groups with a nucleophile; uncharged groups or radicals containing additional positively charged moieties are introduced into the protein molecule resulting in an increased net positive charge of the tracer. Amino groups in the protein molecule are modified by acetylation or succinylation; this reaction will increase the net negative charge of the enzyme by either introducing an uncharged group or an additional carboxyl radical. The tracer molecules so obtained are then characterized in terms of molecular size and charge by column chromatography and isoelectric focusing respectively. The enzymatic activity as measured by 3,3'-diaminobenzidine reaction, the pH optimum and the absorption spectra for the modified enzymes remain virtually unchanged.     

The response of murine intestinal crypts to short-range promethium-147 beta irradiation: deductions concerning clonogenic cell numbers and positions

An exteriorized loop of mouse intestine was exposed to 147Pm low-energy electrons, where the dose rate decreased by a factor of 5 from the base of the crypt to the top of the proliferative zone. A crypt survival curve was obtained, expressed in terms of exposure time. The shape of the curve was interpreted in terms of survival parameters for colony-forming cells (clonogens) derived using 137Cs gamma rays and the depth-dose curve measured for 147Pm electrons. It is concluded that the shape of the crypt survival curve using 147Pm electrons is inconsistent with the notion of either the presence of a large number of clonogens or a small number near the top of the proliferative zone. A computer fitting procedure showed that the best agreement between predicted and observed curves was achieved with 2.7 +/- 0.5 clonogens at cell position 5.6 +/- 0.6, in the putative stem-cell zone.     

Entropy and convergence in dynamics and demography

Demographic dynamics is formally equivalent to the dynamics of a Markov chain, as is true of some nonlinear dynamical systems. Convergence to demographic equilibrium can be studied in terms of convergence in the Markov chain. Tuljapurkar (1982) showed that population entropy (Kolmogorov-Sinai entropy) provides information on the rate of this convergence. This paper begins by considering finite state Markov chains, providing elementary proofs of the relationship between convergence rate and entropy, and discusses in detail the uses and limitations of entropy as a convergence measure; these results also apply to Markovian dynamical systems. Next, new qualitative and quantitative arguments are used to discuss the demographic meaning of entropy. An exact relationship is established giving population entropy in terms of the eigenvalues of the Leslie matrix characteristic equation. Finally, the significance of imprimitive and periodic limits is discussed in relation to population entropy.     

Oxytocinergic and serotonergic systems involvement in sodium intake regulation: satiety or hypertonicity markers?

Previous studies demonstrated the inhibitory participation of serotonergic (5-HT) and oxytocinergic (OT) neurons on sodium appetite induced by peritoneal dialysis (PD) in rats. The activity of 5-HT neurons increases after PD-induced 2% NaCl intake and decreases after sodium depletion; however, the activity of the OT neurons appears only after PD-induced 2% NaCl intake. To discriminate whether the differential activations of the 5-HT and OT neurons in this model are a consequence of the sodium satiation process or are the result of stimulation caused by the entry to the body of a hypertonic sodium solution during sodium access, we analyzed the number of Fos-5-HT- and Fos-OT-immunoreactive neurons in the dorsal raphe nucleus and the paraventricular nucleus of the hypothalamus-supraoptic nucleus, respectively, after isotonic vs. hypertonic NaCl intake induced by PD. We also studied the OT plasma levels after PD-induced isotonic or hypertonic NaCl intake. Sodium intake induced by PD significantly increased the number of Fos-5-HT cells, independently of the concentration of NaCl consumed. In contrast, the number of Fos-OT neurons increased after hypertonic NaCl intake, in both depleted and non-depleted animals. The OT plasma levels significantly increased only in the PD-induced 2% NaCl intake group in relation to others, showing a synergic effect of both factors. In summary, 5-HT neurons were activated after body sodium status was reestablished, suggesting that this system is activated under conditions of satiety. In terms of the OT system, both OT neural activity and OT plasma levels were increased by the entry of hypertonic NaCl solution during sodium consumption, suggesting that this system is involved in the processing of hyperosmotic signals.     

Game theory and evolution: finite size and absolute fitness measures

This article is concerned with the characterization and existence of evolutionarily stable strategies (ESS) in Games against Nature, a class of models described by finite size populations and absolute fitness measures. We address these problems in terms of a new formalism which revolves around the concept evolutionary entropy, a measure of the diversity of options associated with a strategy pure - strategies have zero entropy, mixed strategies positive entropy. We invoke this formalism to show that ESS are characterized by extremal states of entropy. We illustrate this characterization of ESS by an analysis of the evolution of the sex ratio and the evolution of seed size.     

Interpretation of Tracer Data: Significance of the Number of Terms in Specific Activity Functions

It has already been shown that the number of pools in an open system in the steady state cannot be determined from the number of exponential terms in the specific activity function of a pool, even if the data were free from experimental error. However, some information is conveyed by the number of exponential terms. The information is different depending upon whether the data are obtained from the pool into which the tracer is introduced or from another pool. In the latter case, the number of exponential terms is shown to indicate the maximum number of intermediate pools involved in the shortest path of transfer of material from the injected pool to the pool in question. With regard to the former case, this paper is restricted to functions with two exponential terms and shows which systems of n pools (n >/= 2) are consistent with such data. Consequently, biexponential experimental curves can be interpreted in terms of models consisting of an unrestricted number of pools in which each pool is defined in terms of fast mixing. The generalization to cases of functions with more than two exponential terms can be carried out in a similar manner.     

RNA bulge entropies in the unbound state correlate with peptide binding strengths for HIV-1 and BIV TAR RNA because of improved conformational access.

For the binding of peptides to wild-type HIV-1 and BIV TAR RNA and to mutants with bulges of various sizes, changes in the DeltaDelta G values of binding were determined from experimental K d values. The corresponding entropies of these bulges are estimated by enumerating all possible RNA bulge conformations on a lattice and then applying the Boltzmann relationship. Independent calculations of entropies from fluctuations are also carried out using the Gaussian network model (GNM) recently introduced for analyzing folded structures. Strong correlations are seen between the changes in free energy determined for binding and the two different unbound entropy calculations. The fact that the calculated entropy increase with larger bulge size is correlated with the enhanced experimental binding free energy is unusual. This system exhibits a dependence on the entropy of the unbound form that is opposite to usual binding models. Instead of a large initial entropy being unfavorable since it would be reduced upon binding, here the larger entropies actually favor binding. Several interpretations are possible: (i) the higher conformational freedom implies a higher competence for binding with a minimal strain, by suitable selection amongst the set of already accessible conformations; (ii) larger bulge entropies enhance the probability of the specific favorable conformation of the bound state; (iii) the increased freedom of the larger bulges contri-butes more to the bound state than to the unbound state; (iv) indirectly the large entropy of the bound state might have an unfavorable effect on the solvent structure. Nonetheless, this unusual effect is interesting.     

Effects of hydrated water on protein unfolding

The conformational stability of a protein in aqueous solution is described in terms of the thermodynamic properties such as unfolding Gibbs free energy, which is the difference in the free energy (Gibbs function) between the native and random conformations in solution. The properties are composed of two contributions, one from enthalpy due to intramolecular interactions among constituent atoms and chain entropy of the backbone and side chains, and the other from the hydrated water around a protein molecule. The hydration free energy and enthalpy at a given temperature for a protein of known three-dimensional structure can be calculated from the accessible surface areas of constituent atoms according to a method developed recently. Since the hydration free energy and enthalpy for random conformations are computed from those for an extended conformation, the thermodynamic properties of unfolding are evaluated quantitatively. The evaluated hydration properties for proteins of known transition temperature (Tm) and unfolding enthalpy (delta Hm) show an approximately linear dependence on the number of constituent heavy atoms. Since the unfolding free energy is zero at Tm, the enthalpy originating from interatomic interactions of a polypeptide chain and the chain entropy are evaluated from an experimental value of delta Hm and computed properties due to the hydrated water around the molecule at Tm. The chain enthalpy and entropy thus estimated are largely compensated by the hydration enthalpy and entropy, respectively, making the unfolding free energy and enthalpy relatively small. The computed temperature dependences of the unfolding free energy and enthalpy for RNase A, T4 lysozyme, and myoglobin showed a good agreement with the experimental ones.(ABSTRACT TRUNCATED AT 250 WORDS)