Variety Of Test Systems Research Articles

Local Temperature Measurement in Molecular Dynamics Simulations with Rigid Constraints.

Constraining molecules in simulations (such as with constant bond lengths and/or angles) reduces their degrees of freedom (DoF), which in turn affects temperature calculations in those simulations. When local temperatures are measured, e.g., from a set of atoms in a subvolume or from velocities in one Cartesian direction, the result can appear to unphysically violate equipartition of the kinetic energy if the local DoF are not correctly calculated. Here, we determine how to correctly calculate local temperatures from arbitrary Cartesian component kinetic energies, accounting for general geometric constraints, by self-consistently evaluating the DoF of atoms subjected to those constraints. The method is validated on a variety of test systems, including systems subject to a temperature gradient and those confined between walls. It is also shown to provide a sensitive test for the breakdown of kinetic energy equipartition caused by the approximate nature of numerical integration or insufficient equilibration times. As a practical demonstration, we show that kinetic energy equipartition between C and H atoms connected by rigid bonds can be violated even at the commonly used time step of 2 fs and that this equipartition violation appears to usefully indicate configurational overheating.

Automated Adaptive Absolute Binding Free Energy Calculations.

Alchemical absolute binding free energy (ABFE) calculations have substantial potential in drug discovery, but are often prohibitively computationally expensive. To unlock their potential, efficient automated ABFE workflows are required to reduce both computational cost and human intervention. We present a fully automated ABFE workflow based on the automated selection of λ windows, the ensemble-based detection of equilibration, and the adaptive allocation of sampling time based on inter-replicate statistics. We find that the automated selection of intermediate states with consistent overlap is rapid, robust, and simple to implement. Robust detection of equilibration is achieved with a paired t-test between the free energy estimates at initial and final portions of a an ensemble of runs. We determine reasonable default parameters for all algorithms and show that the full workflow produces equivalent results to a nonadaptive scheme over a variety of test systems, while often accelerating equilibration. Our complete workflow is implemented in the open-source package A3FE (https://github.com/michellab/a3fe).

Nonlocal Effective Medium (NLEM) for Quantitative Modelling of Nanoroughness in Spectroscopic Reflectance

Spectroscopic reflectance is a versatile optical methodology for the characterization of transparent and semi-transparent thin films in terms of thickness and refractive index. The Fresnel equations are used to interpret the measurements, but their accuracy is limited when surface roughness is present. Nanoroughness can be modelled through a discretized multi-slice and effective medium approach, but to date, this offered mostly qualitative and not quantitative accuracy. Here we introduce an adaptive and nonlocal effective medium approach, which considers the relative size and environment of each discretized slice. We develop our model using finite-difference time-domain simulation results and demonstrate its ability to predict nanoroughness size and shape with relative errors < 3% in a variety of test systems. The accuracy of the model is directly compared to the prediction capabilities of the Bruggeman and Maxwell–Garnett models, highlighting its superiority. Our model is fully parametrized and ready to use for exploring the effects of roughness on reflectance without the need for costly 3D simulations and to be integrated into the Fresnel simulator of spectroscopic reflectance tools.

Development of OPLS-AA/M Parameters for Simulations of G Protein-Coupled Receptors and Other Membrane Proteins.

G protein-coupled receptors (GPCRs) and other membrane proteins are valuable drug targets, and their dynamic nature makes them attractive systems for study with molecular dynamics (MD) simulations and free energy approaches. Here, we report the development, implementation, and validation of OPLS-AA/M force field parameters to enable simulations of these systems. These efforts include the introduction of post-translational modifications including lipidations and phosphorylation. We also modify previously reported parameters for lipids to be more consistent with the OPLS-AA force field standard and extend their coverage. These new parameters are validated on a variety of test systems, with the results compared to high-level quantum mechanics calculations, experimental data, and simulations with other force fields. The results demonstrate that the new parameters reliably reproduce the behavior of membrane protein systems.

Recovering dynamic correlation in spin flip configuration interaction through a difference dedicated approach.

This article introduces the restricted-active-space n-spin flip configuration interaction models, RAS(S)-SF and RAS(S,2h,2p)-SF, which provide highly correlated, yet low cost approaches for treating polyradical systems. These levels of theory add electronic degrees of freedom beyond those of previous spin flip approaches in order to achieve accurate ground and excited state energetics. The effects of additional dynamic correlation were investigated by comparing these two techniques to the prior RAS(h,p)-SF method on a variety of test systems, including multiple electronic states of methylene, tetramethyleneethane, three binuclear transition metal complexes, and a tetracene dimer. RAS(S,2h,2p)-SF significantly improves state descriptions in all cases and provides high accuracy even when using a minimal number of spin flips. Furthermore, this correlated level of theory is shown to be extensible to the large systems involved in singlet fission, where the multi-excitonic states in tetracene dimers are difficult to simulate with standard methods and therefore are still a matter of debate. Using a triple-zeta basis, the double triplet state, 1(TT), is predicted to be unbound. This result contradicts lower levels of theory and provides important insight into tetracene's ability to undergo efficient singlet fission.

Parameterization of linear supply functions in nonlinear AC electricity market equilibrium models - Part II: Case studies

This study utilizes the primal-dual nonlinear interior point algorithm formulated in Part I of this two-series paper, to obtain electricity market supply function equilibrium solutions for the bi-level market problem of nonlinear power systems with AC meshed networks. The strategic offers of the market players are modeled by parameterizing the generation marginal cost functions using any of the four available parameterization methods to obtain profit-maximizing linear supply function bids. The analysis takes into account a variety of test systems and examines the relation between the equilibrium solutions obtained from the different parameterization methods and the role of network complexity. An analysis of multiple equilibria in AC network constrained systems is also provided.

Sesamol: An Efficient Antioxidant with Potential Therapeutic Benefits

Sesamol has been shown earlier to exhibit antimutagenic (reactive oxygen mediated) and antiageing activity in our lab and it has also been found to exert chemopreventive effect. Here we report the in vitro antioxidant activity of sesamol. As most of the antioxidants act due to their property to auto-oxidise and the pro- or antioxidant activity would depend on the concentration of the agent used and the free radical source, at least 6 dilutions in concentration range of 5-1000 nmoles of sesamol were selected for each test system. Further the antioxidant activity was compared with a water soluble antioxidant (ascorbic acid). Eventhough some preliminary studies on the antioxidant activity of sesamol have been reported in DPPH assay & inhibition of lipid peroxidation, it is not complete. We, here in report comprehensively (both in terms of the no. of doses and also a variety of test systems being employed) on the antioxidant activity of sesamol. Furthermore, since all the data has been generated by the same workers and under same laboratory conditions, hence is scientifically significant. Also the process of dose selection as discussed earlier is more scientific; and the data treatment, i.e. calculation of IC(50) values and comparisons with ascorbic acid has been statistically validated. In conclusion, sesamol was found to be an efficient scavenger of the entire range of ROS in several test systems pointing towards the potential of sesamol to be developed as a possible therapeutic.

Origins of linewidth in H1 magic-angle spinning NMR

A detailed study of the factors determining the linewidth (and hence resolution) in H1 solid-state magic-angle spinning NMR is described. Although it has been known from the early days of magic-angle spinning (MAS) that resolution of spectra from abundant nuclear spins, such as H1, increases approximately linearly with increasing sample rotation rate, the difficulty of describing the dynamics of extended networks of coupled spins has made it difficult to predict a priori the resolution expected for a given sample. Using recently developed, highly efficient methods of numerical simulation, together with experimental measurements on a variety of test systems, we propose a comprehensive picture of H1 resolution under MAS. The “homogeneous” component of the linewidth is shown to depend primarily on the ratio between an effective local coupling strength and the spin rate, modified by geometrical factors which loosely correspond to the “dimensionality” of the coupling network. The remaining “inhomogeneous” component of the natural linewidth is confirmed to have the same properties as in dilute-spin NMR. Variations in the NMR frequency due to chemical shift effects are shown to have minimal impact on H1 resolution. The implications of these results for solid-state NMR experiments involving H1 and other abundant-spin nuclei are discussed.

Functional downregulation of the neurokinin 1 receptor by antidepressant, neuroleptics and mood stabilizers

Neurokinin–1/–2-receptor antagonists have some efficiency in the treatment of affective and anxiety disorders. However, recent data from clinical trials are disappointing since large phase III studies could not confirm previous data. Nevertheless, animal models have shown clear „antidepressant“ and „anxiolytic“ effects of these substances in a wide variety of test systems. In the present study, we investigated acute effects (stimulation for 1h up to 2 days) of the antidepressants imipramine and fluvoxamine, the antipsychotics clozapine and haloperidol as well as the mood stabilizers valproic acid, lithium and carbamazepine on NK–1-receptor expression and receptor binding in human astrocytoma cells, which highly express the NK–1-receptor. We found that imipramine and fluvoxamine, haloperidol as well as valproic acid strongly downregulated NK–1-receptor mRNA-expression (quantitative RT-PCR) and protein synthesis (Western Blot). Furthermore, these drugs also decreased functional activity of the receptor as they downregulated substance P-induced gene expression and led to a decrease of SP binding sites as shown by binding assay studies using 3H-SP. In summary, we have shown that certain antidepressants, antipsychotics and mood stabilizers are able to downregulate the NK–1-receptor with the consequence of decreased SP binding to the receptor and decreased functional activity. This may indicate a new mechanism by which psychopharmacological agents exert their psychotropic effects.

Aflatoxin Cause DNA Damage

Aflatoxins are food-borne secondary toxic fungal metabolites produced during the growth of Aspergillus flavusand A. parasiticus. Aflatoxins are well known hepatotoxic, hepatocarcinogenic and mutagenic agents. These effects are mainly due to adduct formation with DNA, RNA and protein. In addition, it also causes lipid peroxidation as well as oxidative damage to DNA. AFB1 possess genotoxic potential in a variety of test systems. Other aflatoxin has not been so extensively investigated, but in a variety of studies B2, G1, G2 and M1 have all shown evidence of genotoxicity.

ISIM: A Program for Grand Canonical Monte Carlo Simulations of the Ionic Environment of Biomolecules

In this work we present a new software package (ISIM), which represents a flexible, computational tool for simulations of electrolyte solutions via a grand canonical Monte Carlo procedure (GCMC) with a specific capability of treating biomolecules in solution. The GCMC method provides a powerful tool for studying the ionic environments of highly charged macromolecules with attention to the atomic detail of both the solute and the mobile counterions. The ISIM software differs from previous schemes mainly by treating different ion types independently and offering a new parameterization procedure for calibrating excess chemical potentials and bulk ion concentrations. Additionally, ISIM leverages the APBS software package to provide accurate descriptions of the biomolecular electrostatic potential through the efficient solution of Poisson's equation. ISIM has been validated on a variety of test systems; we successfully reproduce elementary properties of electrolyte solutions as well as theoretical and experimental results for challenging test systems like Calmodulin and DNA.

Hydrophobic similarity between molecules: a MST-based hydrophobic similarity index.

A similarity index based on the hydrophilic/hydrophobic properties of molecules is presented. Such an index is defined based on the fractional partition of the free energy of solvation developed within the framework of the self-consistent reaction field MST model, which divides the free energy of solvation or the free energy of transfer into contributions assigned to the surface elements defining the solute/solvent interface. These surface contributions can be integrated to derive atomic or group contributions. The suitability of the index to compute the molecular similarity based on hydrophobic/hydrophilic properties is examined by considering their application in a variety of test systems, including structure-activity relationships, absorption properties, and molecular recognition. The similarity index is expected to be a very powerful tool in molecular similarity studies for compounds of chemical, biochemical, and pharmaceutical interest.

Mechanisms of inhibitors of mutagenesis and carcinogenesis

For a rational implementation of chemoprevention strategies it is essential not only to assess the efficacy and safety of putative inhibitors by using a variety of test systems but also to understand the mechanisms involved. This article proposes a detailed classification of mechanisms along with pertinent examples of agents which may be potentially exploited in the host-addressed prevention of cancer and other mutation-related diseases. The classification, presented in tabulated form, covers a variety of mechanisms interfering with different phases of mutagenesis and carcinogenesis. However, the reported sequence of events is not meant to follow a rigid scheme, and several mechanisms are reiterated throughout evolution of these processes. Similarly, a number of protective agents are shown to work through multiple and often interconnected mechanisms.

Inhibition of methotrexate‐induced chromosomal damage by vanillin and chlorophyllin in V79 cells

Methotrexate (MTX), a chemotherapeutic agent used to treat cancer, produces cytogenetic damage and has a cytostatic effect in a variety of test systems. Several antigenotoxic agents have been studied in various in vitro and in vivo systems. However, data are limited regarding their ability to modulate MTX-induced genotoxicity. In the present study, vanillin (VA) and chlorophyllin (CHL) were used as antigenotoxic agents to study their ability to minimize the DNA damage caused by MTX. Exponentially growing V79 Chinese hamster lung cells were treated with MTX at five different concentrations (5–100 μg/ml) with S9 activation for 6 h and post-treated with two concentrations of either VA (50 or 100 μg/ml) or CHL (50 or 100 μg/ml) for 40 h. Cytochalasin B was added for the micronucleus (MN) assay along with antigenotoxic agents to evaluate MN in binucleated cells. Chromosomal aberrations were also evaluated in parallel cultures. Results indicate that MTX alone induced a dose-dependent decrease in the nuclear division index (NDI) and the mitotic index (MI). A significant increase in percent micronucleated binucleated cells (MNBN) and percent aberrant cells (Abs) was observed. Studies using VA as an antigenotoxic agent showed a decrease in the number of MNBN (26.3–83.1%) and Abs (16.0–87.5%) with the addition of either 50 or 100 μg VA/ml. The addition of CHL also significantly reduced the number of MNBN (53.0–91.5%) at both concentrations tested. Chromosomal aberrations were also significantly reduced (41.0–83.0). These studies indicate that both VA and CHL are capable of effectively minimizing MTX-induced chromosomal damage. Teratogenesis Carcinog. Mutagen. 17:313–326, 1997/98. © 1998 Wiley-Liss, Inc.

Inhibition of methotrexate-induced chromosomal damage by vanillin and chlorophyllin in V79 cells

Methotrexate (MTX), a chemotherapeutic agent used to treat cancer, produces cytogenetic damage and has a cytostatic effect in a variety of test systems. Several antigenotoxic agents have been studied in various in vitro and in vivo systems. However, data are limited regarding their ability to modulate MTX-induced genotoxicity. In the present study, vanillin (VA) and chlorophyllin (CHL) were used as antigenotoxic agents to study their ability to minimize the DNA damage caused by MTX. Exponentially growing V79 Chinese hamster lung cells were treated with MTX at five different concentrations (5-100 micrograms/ml) with S9 activation for 6 h and post-treated with two concentrations of either VA (50 or 100 micrograms/ml) or CHL (50 or 100 micrograms/ml) for 40 h. Cytochalasin B was added for the micronucleus (MN) assay along with antigenotoxic agents to evaluate MN in binucleated cells. Chromosomal aberrations were also evaluated in parallel cultures. Results indicate that MTX alone induced a dose-dependent decrease in the nuclear division index (NDI) and the mitotic index (MI). A significant increase in percent micronucleated binucleated cells (MNBN) and percent aberrant cells (Abs) was observed. Studies using VA as an antigenotoxic agent showed a decrease in the number of MNBN (26.3-83.1%) and Abs (16.0-87.5%) with the addition of either 50 or 100 micrograms VA/ml. The addition of CHL also significantly reduced the number of MNBN (53.0-91.5%) at both concentrations tested. Chromosomal aberrations were also significantly reduced (41.0-83.0). These studies indicate that both VA and CHL are capable of effectively minimizing MTX-induced chromosomal damage.

The genotoxicity profile of atorvastatin, a new drug in the treatment of hypercholesterolemia

While HMG-CoA reductase inhibitors such as fluvastatin, lovastatin, pravastatin and simvastatin demonstrate lack of in vitro and in vivo mutagenicity and clastogenicity in bacterial and mammalian cells, long term rodent carcinogenicity studies resulted in an increased incidence in neoplasms at high doses. These effects may be attributable to an exaggeration of the desired biochemical effect of the drug and/or a tumor promoting effect. The genotoxicity of atorvastatin, a newly developed HMG-CoA reductase inhibitor, was evaluated in a variety of test systems. In bacterial mutagenicity tests, the E. coli tester strain WP2(uvrA) and S. typhimurium strains TA98, TA100, TA1535, TA1537, and TA1538 were exposed to concentrations of atorvasatin as high as 5000 μg/plate both in the absence (S9-) and presence (S9+) of metabolic activation. Atorvastatin was not mutagenic in either E. coli or S. typhimurium. Chinese hamster lung V79 cell cultures were exposed to atorvastatin at concentrations of 50–300 μg/ml (S9-) and 100–300 μg/ml (S9+) and structural chromosome aberrations were assessed. Mutation at the hgprt locus was assessed at concentrations of 100–300 μg/ml (S9-) and 150–275 μg/ml (S9+). Atorvastatin was neither mutagenic nor clastogenic in the absence or presence of S9. The lack of in vitro genotoxicity was corroborated in vivo in a mouse micronucleus study in which single oral doses of atorvastatin were administered to male and female CD-1 mice at 1, 2500, or 5000 mg/kg. No biologically significant increases in the frequency of micronucleated polychromatic erythrocytes in bone marrow at 24, 48, or 72 h postdosing were observed. Thus, atorvastatin, as with the other tested HMG-CoA reductase inhibitors, is not genotoxic.

HZE particle effects in space

Among the various particulate components of ionizing radiation in space, heavy ions (the so-called HZE particles) have been of special concern to radiobiologists. To understand the ways by which HZE particles of cosmic radiation interact with biological systems, methods have been developed to precisely localize the trajectory of an HZE particle relative to the biological object and to correlate the physical data of the particle with the biological effects observed along its path. In a variety of test systems, injuries were traced back to the traversal of a single HZE particle, such as somatic mutations and chromosomal aberrations in plant seeds, development disturbances and malformations in insect and salt shrimp embryos, or cell death in bacterial spores. In the latter case, a long-ranging killing effect around the particle's track was observed. Whereas, from spaceflight experiments, substantial information has been accumulated on single HZE particle effects in resting systems and in a few embryonic systems, there is a paucity of data on cosmic radiation effects in whole tissues or animals, especially mammalians.

Signs of central nervous activation during mental practice in seniors

This report outlines the activity of a new thromboxane synthase inhibitor sodium, 5-(3-pyridinymethyl)-2-benzofurancarboxylate, (U-63557A). U-63557A is a potent inhibitor of the thromboxane synthase in human platelets in vitro, as well as in rhesus monkey platelets ex vivo. A single oral dose of 3.0 mg/kg U-63557A inhibits the platelet thromboxane synthase in rhesus monkeys approximately 80% for at least 12 hrs. U-63557A has been administered to monkeys twice a day, (10 mg/kg) for 14 days, without evidence of drug tachyphylaxis or rebound. U-63557A does not inhibit thrombin-stimulated PGI2 biosynthesis in human endothelial cells, the 5-lipoxygenase in human neutrophils, or the cyclo-oxygenase in a variety of test systems. In anesthetized dogs, U-63557A injected i.v. at 0.1 at 5 mg/kg prevented the blockage of stenosed coronary arteries caused platelet aggregation,. Similar effects were obtained by oral administration of 1–5 mg/kg. The thromboxane synthase inhibitor was more efficacious than cyclooxgenase inhibitors and equal to PGI2 in efficacy. Under appropriate conditions the protective effects of U-63557A could be reversed by i.v. cylooxygenase inhibitors suggesting that its efficacy dependened in part of endogenous PGI2 formation. Due to its specificity, oral activity, and extended duration of action, U-63557A is a promising compound for the evaluation of the role of thromboxane synthase in a variety of patho[hysiological states.

Carcinogenicity, mutagenicity and cancer preventing activities of flavonoids: a structure-system-activity relationship (SSAR) analysis.

Flavonoids and related phenolic compounds are widely distributed among vascular plants and are found in numerous fruits, grains vegetables and other parts of higher plants [1–3]. Isolation and structural determination of flavonoids have been employed in plant taxonomy [1, 2]. Because of the wide range of chemical structures of flavonoids, coupled with a variety of test systems and different dose levels used, sometimes conflicting reports have been published in the literature regarding their numerous pharmacological and toxicological activities. This prompted us to conduct a literature survey and a structure-system-activity-relationship (SSAR) analysis of existing data, with particular emphasis on the carcinogenicity/mutagenicity and cancer preventive aspects of the flavonoids.KeywordsMutagenic ActivityGenic DerivativeFlavonol GlycosideNational Toxicology ProgramSwiss Male MouseThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Epitopes of the HIV-1-Negative Factor (nef) Reactive with Murine Monoclonal Antibodies and Human HIV-1-Positive Sera

Murine monoclonal antibodies (MAbs) raised against a recombinant nef protein fragment of human immunodeficiency virus type 1 (HIV-1) strain BH10 were characterized by an epitope mapping system using overlapping decapeptides. Four different immunogenic regions were identified. Ten human HIV-1-positive sera were tested in the same epitope mapping system, seven of these were reactive with four immunogenic regions. Two of the nef-specific epitopes recognized by human sera overlapped with the epitopes defined by the murine monoclonal antibodies. The reactivity of the monoclonal antibodies with the recombinant nef protein and with infected and uninfected cells were investigated in a variety of test systems. The results are discussed with respect to homologous regions of nef and cellular proteins.