Interaction function gamma(x) for Chinese hamster cells treated with hypertonic phosphate-buffered saline after irradiation

The repair of potentially lethal damage (PLD) in stationary-phase V79 Chinese hamster cells, which was expressible by a postirradiation treatment with hypertonic (0.5 M NaCl) phosphate-buffered saline (PBS), was analyzed within the framework of the theory of dual radiation action. The interaction function gamma(x) was estimated for cells permitted to repair PLD for various intervals of time. The experimental data indicated that 50-60% of the lethal lesions produced at the time of irradiation were repaired in 120 min. The repair of PLD was implicitly involved in the probability of the interaction of sublesions. That is, g(x,trep) was defined as the probability that two sublesions separated by distance x interact to produce a lethal lesion which will not be repaired until the fixation by treatment with hypertonic PBS at time trep after irradiation. It is concluded that the time dependence of the repair of PLD is not independent of the interaction distance x. Three conclusions are drawn: (1) The repair of a lesion produced by a long distance interaction is not detectable by postirradiation treatment with hypertonic PBS. (2) A lesion produced by a short distance interaction is rapidly repaired in about 20 min. (3) A lesion produced by the interaction of sublesions separated by a distance of about 100 nm is repaired slowly.     

Correlated hit probability and cell transformation in an effect-specific track length model applied to in vitro alpha irradiation

In estimating the risk from low doses of alpha particles such as those emitted by radon progeny, it is important to consider the correlation between cellular inactivation and transformation that can exist at the cellular level. A phenomenological model of radiation- induced cellular inactivation and transformation at this level is presented here which incorporates aspects of a state vector model of radiation carcinogenesis and of correlated hit probabilities for inactivation and transformation. The general form of the model assumes that both inactivation and initial initiation damage are produced through the interaction of sublesions induced by radiation passing through cell nuclei, with the production of sublesions governed by hit probabilities and a characteristic probability-per-unit track length. The inactivation and initiation events are partially correlated through the use of hit probabilities. In addition, promotional events are incorporated for the case of cellular transformation based on a previously published state vector model. The model provides good fits to available data on the relationship between inactivation, transformation and LET for doses of alpha above 0.1 Gy in the range of LETs commonly produced by radon and progeny; by ”good fits” we mean here the ability to yield the correct shapes of dose-response data using parameter values that vary smoothly with LET and using inactivation parameters that are applied consistently between inactivation and transformation assays. The resulting model correctly predicts recent findings indicating an increased transformation frequency per surviving cell when a population receives a distribution of hits compared to irradiation where all cells receive the same number of hits. Received: 1 June 2001 / Accepted: 7 September 2001     

Compound dual radiation action. I. General aspects.

The theory of dual radiation action (A. M. Kellerer and H. H. Rossi, Curr. Top. Radiat. Res. Q. 8, 85-158, 1972) has attributed the effects of ionizing radiation on eukaryotes to the production of molecular changes (sublesions) that combine pairwise to produce injury (lesions) responsible for radiation effects. If the yield of sublesions is independent of radiation quality (as is currently assumed), dual radiation action results in the well-known proportionality between the average yield of lesions and alpha D+beta D2, where beta is a radiation-independent quantity. It has, however, been observed that beta changes with radiation type. In this paper we propose an explanation of this discrepancy. Specifically, we suggest that dual radiation action-type processes where beta is variable are the result of a mechanism--termed compound dual radiation action--which consists of a sequence of simple dual radiation action processes, each process being the causative agent for the next one. The sequence, single-strand DNA breaks, double-strand DNA breaks (chromosome breaks), and exchange-type chromosomal aberrations, is one such example examined in the paper.     

Mathematical modeling of synergistic interaction of sequential thermoradiation action on mammalian cells

Data obtained by other authors for mammalian cells treated by sequential action of ionizing radiation and hyperthermia were used to estimate the dependence of synergistic enhancement ratio on the ratio of damages induced by these agents. Experimental results were described and interpreted by means of the mathematical model of synergism in accordance with which the synergism is expected to result from the additional lethal damage arising from the interaction of sublesions induced by both agents.     

Multiple components of split-dose repair in plateau-phase mammalian cells: a new challenge for phenomenological modelers

Split-dose experiments using starved plateau-phase Chinese hamster ovary cells have been used to investigate the kinetics of repair, expressed in terms of enhancement of reproductive survival. The results show two distinct components of repair, one having a characteristic time of just over 1 h for the removal of a lesion, the other, about 18 h. The rate at which each component removes damage and the fraction of the total damage that each removes appear to be independent of the initial amount of damage produced, i.e., dose. This lack of dose dependence is not consistent with some simple models of ionizing radiation damage and repair, such as those which assume that saturation of a repair process, depletion of enzyme pools, or the interaction of pairs of sublesions is responsible for the curvature in the dose-response relationship. However, the relationship between the amounts of each type of damage and dose appears to be consistent with models that assume that only a portion of the initial damage is directly accessible to the repair systems or that the initial damage consists of a mixture of potentially lethal and sublethal lesions.     

Mathematical modeling of the synergistic effects of sequential thermoradiation action on mammalian cells

In order to estimate the dependence of the synergistic enhancement ratio on the damage level induced by ionizing radiation and hyperthermia, data obtained by other authors for mammalian cells treated with sequential thermoradiation were used. The experimental results were described and interpreted by means of the mathematical model of synergism, according to which synergism is determined by additional lethal damage arising from the interaction of nonlethal sublesions induced by individual damaging agents.     

Locations of radiation-produced DNA double strand breaks along chromosomes: a stochastic cluster process formalism.

Ionizing radiation produces DNA double strand breaks (DSBs) in chromosomes. For densely ionizing radiation, the DSBs are not spaced randomly along a chromosome: recent data for size distributions of DNA fragments indicate break clustering on kbp-Mbp scales. Different DSB clusters on a chromosome are typically made by different, statistically independent, stochastically structured radiation tracks, and the average number of tracks involved can be small. We therefore model DSB positions along a chromosome as a stationary Poisson cluster process, i.e. a stochastic process consisting of secondary point processes whose locations are determined by a primary point process that is Poisson. Each secondary process represents a break cluster, typically consisting of 1-10 DSBs in a comparatively localized stochastic pattern determined by chromatin geometry and radiation track structure. Using this Poisson cluster process model, which we call the randomly located clusters (RLC) formalism, theorems are derived for how the DNA fragment-size distribution depends on radiation dose. The RLC dose-response relations become non-linear when the dose becomes so high that DSB clusters from different tracks overlap or adjoin closely. The RLC formalism generalizes previous models, fits current data adequately and facilitates mechanistically based extrapolations from high-dose experiments to the much lower doses of interest for most applications.     

Substrate Specifity of Chymotrypsin. Study of Induced Strain by Molecular Mechanics

Acylenzyme intermediates, produced by transfer of the acyl portions of selected natural substrates onto the catalytic serine hydroxyl of the serine protease chymotrypsin, were modeled with the AMBER force field. The obtained structures were used to calculate interaction and deformation energies. A set of 32 geometry variables were extracted out of each structure. They describe deformation effects specific for each substrate. It is shown by statistical analyses, that the interaction and deformation energies correspond to measured substrate reactivities. The extracted geometry variables are able to reproduce this dependency through multivariante statistical methods. These analyses suggest that there exist specific deformations of both the substrate and the enzyme portion, which are related to substrate reactivity. The geometry changes observed for high specific substrates are interpreted in terms of mechanistical requirements of the enzymatic reaction. The obtained model validates the hypothesis of induced strain as possible source of substrate specifity of chymotrypsin.     

A pulse radiolytic study of the interaction of nitroxyls with free-radical adducts of purines: consequences for radiosensitization

Using the technique of pulse radiolysis, it has been demonstrated that the radicals, produced on interaction of the hydroxyl radical with purine nucleotides/nucleosides, interact with the nitroxyls, TMPN and NPPN. It has been possible to discern the various interactions in terms of the known redox properties of the various OH-radical adducts of the purines based upon spectral and kinetic data. It has been confirmed that the properties of the radical produced on interaction of Br2-. with dGMP, based upon its subsequent interactions with nitroxyls, are quantitatively the same as those for the .OH-radical adduct of dGMP with oxidizing properties. The implications of these findings are presented in terms of the potential competition between nitroxyls and cellular radiation modifiers for the various DNA radicals with different redox potentials, and thereby assess the potential importance of the reactivity of the oxidizing-purine radicals towards nitroxyls in radiobiological studies.     

Transition modes in Ising networks: an approximate theory for macromolecular recognition.

For a statistical lattice, or Ising network, composed of N identical units existing in two possible states, 0 and 1, and interacting according to a given geometry, a set of values can be found for the mean free energy of the 0-->1 transition of a single unit. Each value defines a transition mode in an ensemble of nu N = 3N - 2N possible values and reflects the role played by intermediate states in shaping the energetics of the system as a whole. The distribution of transition modes has a number of intriguing properties. Some of them apply quite generally to any Ising network, regardless of its dimension, while others are specific for each interaction geometry and dimensional embedding and bear on fundamental aspects of analytical number theory. The landscape of transition modes encapsulates all of the important thermodynamic properties of the network. The free energy terms defining the partition function of the system can be derived from the modes by simple transformations. Classical mean-field expressions can be obtained from consideration of the properties of transition modes in a rather straightforward way. The results obtained in the analysis of the transition mode distributions have been used to develop an approximate treatment of the problem of macromolecular recognition. This phenomenon is modeled as a cooperative process that involves a number of recognition subsites across an interface generated by the binding of two macromolecular components. The distribution of allowed binding free energies for the system is shown to be a superposition of Gaussian terms with mean and variance determined a priori by the theory. Application to the analysis of the biologically interaction of thrombin with hirudin has provided some useful information on basic aspects of the interaction, such as the number of recognition subsites involved and the energy balance for binding and cooperative coupling among them. Our results agree quite well with information derived independently from analysis of the crystal structure of the thrombin-hirudin complex.     

Flexible docking using tabu search and an empirical estimate of binding affinity

This article describes the implementation of a new docking approach. The method uses a Tabu search methodology to dock flexibly ligand molecules into rigid receptor structures. It uses an empirical objective function with a small number of physically based terms derived from fitting experimental binding affinities for crystallographic complexes. This means that docking energies produced by the searching algorithm provide direct estimates of the binding affinities of the ligands. The method has been tested on 50 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. All water molecules are removed from the structures and ligand molecules are minimized in vacuo before docking. The lowest energy geometry produced by the docking protocol is within 1.5 Å root-mean square of the experimental binding mode for 86% of the complexes. The lowest energies produced by the docking are in fair agreement with the known free energies of binding for the ligands. Proteins 33:367–382, 1998. © 1998 Wiley-Liss, Inc.     

Dependence of synergism of the combined effect of ultrasound and hyperthermia upon intensity of ultrasound

The inactivation of wild-type yeast Saccharomyces cerevisiae was studied after simultaneous treatment with ultrasound and hyperthermia. A temperature range was established within which ultrasound and hyperthermia exert a synergistic action. The effect was shown to depend on ultrasound intensity and the temperature at which the treatment takes place. The temperature range enhancing the ultrasound effect shifted forward higher temperature with increasing ultrasound intensity. For every intensity value, an optimal temperature exists at which the synergetic effect is maximum. The biophysical interpretation of the results obtained is based on the assumption that synergism is due to an additional lethal damage, which arises from the interaction of some sub-lesions induced by both agents. These sublesions are considered non-lethal if the agents are applied separately.     

Mechanisms and Physiologic Significance of Microwave Action on the Auditory System

Studies conducted by the authors and their coworkers on the mechanisms and physiologic significance of radiofrequency hearing effects are reviewed. Results of these studies demonstrate that 1) thermoelastic expansion of fluids and structures within the inner ear is the main mechanism by which auditory stimuli are produced by microwave pulses; 2) the frequency spectra of these stimuli are indistinguishable from the spectra of rectangular pulses with the same durations as the microwave pulses; 3) exposure to continuous-wave (CW) microwave radiation evokes an increase in the metsbolic activities of nuclei in the ascending auditory pathway and also decreases the latency and increases the magnitude of brainstem-evoked responses produced by acoustic clicks; and 4) the mechanism of the effects of CW microwave radiation on the auditory system is intracochlear heating. The significance of these findings is discussed in terras of potential applications of microwave stimuli in basic research on the auditory system and in terms of interpreting the results of past studies that demonstrate behavioral sensitivity to CW microwave fields.     

A possible energetic role of mineral surfaces in chemical evolution

The postulated roles of clays and other minerals in chemical evolution and the origin of life are reconsidered in terms of the interaction of these minerals with penetrating sources of energy such as ionizing radiation and mechanical stress. This interaction, including such facets as excitation, degradation, storage, and transfer, is considered here with regard to its profound potential for altering the capabilities of minerals to serve both as substrates for prebiological chemistry and as inorganic prototypic life forms. The interaction of minerals and energy in relationship to surface chemistry is discussed in terms of the spectroscopic properties of minerals, the interaction of energy with condensed phases, some commonly accepted concepts of heterogeneous catalysis in the absence of electronic energy inputs, and some commonly accepted and novel means by which surface activity might be enhanced in the presence of energy inputs.An estimation is made of the potential contribution of two poorly characterized prebiotic energy sources, natural radioactive decay and triboelectric energy. These estimates place a conservative lower limit on their prebiotic abundance. Also some special properties of these energy sources, relative to solar energy, are pointed out which might give them particular suitability for driving reactions occurring under geological conditions.Skeletal support for this broadly defined framework of demonstrated and potential relationships between minerals, electronic excitation, and surface reactivity, as applied to chemical evolution, is provided from the results of our studies on 1/1 clays. We have discovered and partially characterized a number of novel luminescent properties of these clays, that indicate energy storage and transfer processes in clays. These luminescent properties are interpreted in relationship to the electron spin resonance phenomena, to provide a basis for estimating the potential significance of energy storage and transduction in monitoring or driving clay surface chemistry.Consideration of the electronic structure of abundant minerals in terms of band theory and localized defect centers provides a predictive theoretical framework from which to rationalize the capacity of these materials to store and transduce energy. The bulk crystal is seen as a collecting antenna for electronic energy, with the defect centers serving as storage sites.The clay properties produced by isomorphic substitution appear to be intimately associated with all of the life-mimetic chemical processes that have been attributed to clays. It appears sensible to postulate that the energetic properties of these substitutional defect centers may also be influential in these biomimetic processes: the promotion of surface reactions, storage of information, replication with transfer of information, and asymmetric separation of electrical charges, as well as their more recently hypothesized roles in energy storage and transduction. The identity of the sites implicated in all of the biomimetic functions of clays as well as their capacity for energy storage is seen to offer significant potential for coupling these functions to an environmental energy source. A yet more specific and experimentally testable hypothesis is offered for a new biomimetic process performed by clays. This hypothesis is that energy stored near isomorphically substituted sites provides the energetic basis for the coupled transport of electrical charge and/or electronic energy through the clay layer, which operates via environmental activation of electron/hole mobility. This is to say that mobility of charge/electronic excitation between defect centers serves as the basis for a primordial inorganic electron transport chain.     

Modeling of metal interaction geometries for protein-ligand docking

The accurate modeling of metal coordination geometries plays an important role for structure-based drug design applied to metalloenzymes. For the development of a new metal interaction model, we perform a statistical analysis of metal interaction geometries that are relevant to protein-ligand complexes. A total of 43,061 metal sites of the Protein Data Bank (PDB), containing amongst others magnesium, calcium, zinc, iron, manganese, copper, cadmium, cobalt, and nickel, were evaluated according to their metal coordination geometry. Based on statistical analysis, we derived a model for the automatic calculation and definition of metal interaction geometries for the purpose of molecular docking analyses. It includes the identification of the metal-coordinating ligands, the calculation of the coordination geometry and the superposition of ideal polyhedra to identify the optimal positions for free coordination sites. The new interaction model was integrated in the docking software FlexX and evaluated on a data set of 103 metalloprotein-ligand complexes, which were extracted from the PDB. In a first step, the quality of the automatic calculation of the metal coordination geometry was analyzed. In 74% of the cases, the correct prediction of the coordination geometry could be determined on the basis of the protein structure alone. Secondly, the new metal interaction model was tested in terms of predicting protein-ligand complexes. In the majority of test cases, the new interaction model resulted in an improved docking accuracy of the top ranking placements.     

DNA lesions that signal the induction of radioresistance and DNA repair in yeast

DNA recombinational repair, and an increase in its capacity induced by DNA damage, is believed to be the major mechanism that confers resistance to killing by ionizing radiation in yeast. We have examined the nature of the DNA lesions generated by ionizing radiation that induce this mechanism, using two different end points: resistance to cell killing and ability of the error-free recombinational repair system to compete for other DNA lesions and thereby suppress chemical mutation. Under the various conditions examined in this study, the "maximum" inducible radiation resistance was increased approximately 1.5- to 3-fold and suppression of mutation about 10-fold. DNA lesions produced by low-LET gamma rays at doses greater than about 20 Gy given in oxygen were shown to be more efficient, per unit dose, at inducing radioresistance to killing than were lesions produced by neutrons (high-LET radiation). This suggests that DNA single-strand breaks are more important lesions in the induction of radioresistance than DNA double-strand breaks. Oxygen-modified lesions produced by gamma rays (low-LET radiation) were particularly efficient as induction signals. DNA damage due to hydroxyl radicals (OH.) derived from the radiolytic decomposition of H2O produced lesions that strongly induced this DNA repair mechanism. Similarly, OH. derived from aqueous electrons (e-aq) in the presence of N2O also efficiently induced the response. Cells induced to radioresistance to killing with high-LET radiation did not suppress N-methyl-N'-nitro-N-nitrosoguanidine (MNNG)-generated mutations as well as cells induced with low-LET radiation, supporting the conclusion that the type of DNA damage produced by low-LET radiation is a better inducer of recombinational repair. Surprisingly, however, cells induced with gamma radiation in the presence of N2O that became radioresistant to killing were unable to suppress MNNG mutations. This result indicates that OH. generated via e-aq (in N2O) may produce unusual DNA lesions which retard normal repair and render the system unavailable to compete for MNNG-generated lesions. We suggest that the repairability of these unique lesions is restricted by either their chemical nature or topological accessibility. Attempted repair of these lesions has lethal consequences and accounts for N2O radiosensitization of repair-competent but not incompetent cells. We conclude that induction of radioresistance in yeast by ionizing radiation responds variably to different DNA lesions, and these affect the availability of the induced recombinational repair system to deal with subsequent damage.     

Ways of Asking,Ways of Telling

The interpretive understanding that can be derived from interviews is highly influenced by methods of data collection, be they structured or semistructured, ethnographic, clinical, life-history or survey interviews. This article responds to calls for research into the interview process by analyzing data produced by two distinctly different types of interview, a semistructured ethnographic interview and the Structured Clinical Interview for DSM, conducted with participants in the Navajo Healing Project. We examine how the two interview genres shape the context of researcher-respondent interaction and, in turn, influence how patients articulate their lives and their experience in terms of illness, causality, social environment, temporality and self/identity. We discuss the manner in which the two interviews impose narrative constraints on interviewers and respondents, with significant implications for understanding the jointly constructed nature of the interview process. The argument demonstrates both divergence and complementarity in the construction of knowledge by means of these interviewing methods.     

Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models

A new method for normal mode analysis is reported for all-atom structures using molecular geometry restraints (MGR). Similar to common molecular mechanics force fields, the MGR potential contains short- and long-range terms. The short-range terms are defined by molecular geometry, i.e., bond lengths, angles and dihedrals; the long-range term is similar to that in elastic network models. Each interaction term uses a single force constant parameter, and is determined by fitting against a set of known structures. Tests on proteins/non-proteins show that MGR can produce low frequency eigenvectors closer to all-atom force-field-based methods than conventional elastic network models. Moreover, the “tip effect”, found in low frequency eigenvectors in elastic network models, is reduced in MGR to the same level of the modes produced by force-field-based methods. The results suggest that molecular geometry plays an important role, in addition to molecular shape, in determining low frequency deformational motions. MGR does not require initial energy minimization, and is applicable to almost any structure, including the one with missing atoms, bad contacts, or bad geometries, frequently observed in low-resolution structure determination and refinement. The method bridges the two major representations in normal mode analyses, i.e., the molecular mechanics models and elastic network models.