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PubMed1991

Body composition in humans: advances in the development of multicompartment chemical models.

Until recently it was practical to divide body weight into only two or three chemical compartments in living subjects due to an inability to quantify directly total body mineral, protein, and fat in vivo. The six-compartment chemical model is now the cornerstone of research in human body composition. Advanced technologies, including neutron activation analysis systems and dual photon absorptiometry, now enable investigators to extend body composition estimates and to construct near-complete chemical models in vivo. These new or refined approaches will advance our knowledge of human body composition and will also improve our accuracy in calibrating simpler epidemiologic and bedside body-composition techniques.

Animals↗
PubMed1985

Physico-chemical model of a protocell.

A physico-chemical model of a self-maintaining unity or protocell is constructed on the basis of reaction and diffusion processes. The surface motion of the protocell is taken into account explicitly by a so-called Stefan condition, which leads to a nonlinear feedback to the reaction and diffusion processes. The spatio-temporal dynamics in the neighbourhood of the steady states is investigated in the framework of linear stability analysis with the use of an expansion in terms of spherical harmonics Ylm. It is shown that modes with l greater than or equal to 2 become successively unstable with increasing nutrient supply. The leading instability with l = 2 initiates a process of the nonlinear dynamics which is interpreted as the onset of division. A stabilizing effect of surface tension is also discussed.

Cell Division↗
PubMed2006

A stochastic regression approach to analyzing thermodynamic uncertainty in chemical speciation modeling.

Chemical speciation modeling is a vital tool for assessing the bioavailability of inorganic species, yet significant uncertainties in thermodynamic parameters and model form limit its potential for decision-making. In this paper we present a novel method for the quantification of thermodynamic parameter uncertainty and ionic strength correction model uncertainty using Bayesian Markov Chain Monte Carlo (MCMC) estimation methods. These methods allow for the inclusion of correlation modeling, which has not been present in previous work. The MCMC simulations are used to model a natural river water to determine the uncertainty in the calculated environmental speciation of ethylenediamenetetraacetate, a chelating agent that has attracted considerable environmental interest. The results indicate that incorporating correlation among related thermodynamic parameters into the uncertainty model is necessary to correctly quantify the overall system uncertainty. This result indicates the superiority of MCMC estimation methods overtraditional Monte Carlo methods when available data are used to estimate parameter uncertainty in systems with closely related model parameters.

Bayes Theorem↗
PubMed2005

Quantum chemical modeling of CO oxidation by the active site of molybdenum CO dehydrogenase.

The catalytic mechanism of molybdenum containing CO dehydrogenase has been studied using hybrid DFT methods with quite large chemical models. The recent high-resolution X-ray structure, showing the surprising presence of copper linked to molybdenum, was used as a starting point. A pathway was initially found with a low barrier for C-O bond formation and CO2 release. However, this pathway did not include the formation of any S-CO2 species, which had been suggested by experiments with an n-butylisocyanide inhibitor. When these SCO2 structures were studied they were found to lead to deep minima, making CO2 release much more difficult. A large effort was spent, including investigations of other spin states, varying the number of protons and electrons, adding water, etc., until a plausible pathway for S-C bond cleavage was found. In this pathway a water molecule is inserted in between molybdenum and the SCO2 group. Full catalytic cycles, including electron and proton transfers, are constructed both with and without S-C bond formation. When these pathways are extended to two full catalytic cycles it can be understood why the formation of the S-C bond actually makes catalysis faster, even though the individual step of CO2 release becomes much more difficult. These results agree well with experimental findings.

Aldehyde Oxidoreductases↗
PubMed1999

Biochemical evolution III: polymerization on organophilic silica-rich surfaces, crystal-chemical modeling, formation of first cells, and geological clues.

Catalysis at organophilic silica-rich surfaces of zeolites and feldspars might generate replicating biopolymers from simple chemicals supplied by meteorites, volcanic gases, and other geological sources. Crystal-chemical modeling yielded packings for amino acids neatly encapsulated in 10-ring channels of the molecular sieve silicalite-ZSM-5-(mutinaite). Calculation of binding and activation energies for catalytic assembly into polymers is progressing for a chemical composition with one catalytic Al-OH site per 25 neutral Si tetrahedral sites. Internal channel intersections and external terminations provide special stereochemical features suitable for complex organic species. Polymer migration along nano/micrometer channels of ancient weathered feldspars, plus exploitation of phosphorus and various transition metals in entrapped apatite and other microminerals, might have generated complexes of replicating catalytic biomolecules, leading to primitive cellular organisms. The first cell wall might have been an internal mineral surface, from which the cell developed a protective biological cap emerging into a nutrient-rich "soup." Ultimately, the biological cap might have expanded into a complete cell wall, allowing mobility and colonization of energy-rich challenging environments. Electron microscopy of honeycomb channels inside weathered feldspars of the Shap granite (northwest England) has revealed modern bacteria, perhaps indicative of Archean ones. All known early rocks were metamorphosed too highly during geologic time to permit simple survival of large-pore zeolites, honeycombed feldspar, and encapsulated species. Possible microscopic clues to the proposed mineral adsorbents/catalysts are discussed for planning of systematic study of black cherts from weakly metamorphosed Archaean sediments.

Animals↗
PubMed2005

The mathematical properties of the quasi-chemical model for microorganism growth-death kinetics in foods.

Knowledge of the mathematical properties of the quasi-chemical model [Taub, Feeherry, Ross, Kustin, Doona, 2003. A quasi-chemical kinetics model for the growth and death of Staphylococcus aureus in intermediate moisture bread. J. Food Sci. 68 (8), 2530-2537], which is used to characterize and predict microbial growth-death kinetics in foods, is important for its applications in predictive microbiology. The model consists of a system of four ordinary differential equations (ODEs), which govern the temporal dependence of the bacterial life cycle (the lag, exponential growth, stationary, and death phases, respectively). The ODE system derives from a hypothetical four-step reaction scheme that postulates the activity of a critical intermediate as an antagonist to growth (perhaps through a quorum sensing biomechanism). The general behavior of the solutions to the ODEs is illustrated by several examples. In instances when explicit mathematical solutions to these ODEs are not obtainable, mathematical approximations are used to find solutions that are helpful in evaluating growth in the early stages and again near the end of the process. Useful solutions for the ODE system are also obtained in the case where the rate of antagonist formation is small. The examples and the approximate solutions provide guidance in the parameter estimation that must be done when fitting the model to data. The general behavior of the solutions is illustrated by examples, and the MATLAB programs with worked examples are included in the appendices for use by predictive microbiologists for data collected independently.

Food Microbiology↗
PubMed2006

A mechano-chemical model for the passive swelling response of an isolated chondron under osmotic loading.

The chondron is a distinct structure in articular cartilage that consists of the chondrocyte and its pericellular matrix (PCM), a narrow tissue region surrounding the cell that is distinguished by type VI collagen and a high glycosaminoglycan concentration relative to the extracellular matrix. We present a theoretical mechano-chemical model for the passive volumetric response of an isolated chondron under osmotic loading in a simple salt solution at equilibrium. The chondrocyte is modeled as an ideal osmometer and the PCM model is formulated using triphasic mixture theory. A mechano-chemical chondron model is obtained assuming that the chondron boundary is permeable to both water and ions, while the chondrocyte membrane is selectively permeable to only water. For the case of a neo-Hookean PCM constitutive law, the model is used to conduct a parametric analysis of cell and chondron deformation under hyper- and hypo-osmotic loading. In combination with osmotic loading experiments on isolated chondrons, model predictions will aid in determination of pericellular fixed charge density and its relative contribution to PCM mechanical properties.

Biomechanical Phenomena↗
PubMed2005

Chemical models for ribozyme action.

Mechanistic studies of the action of catalytic ribonucleic acids, ribozymes, are highly challenging, because even a slight structural change can dramatically affect the chain folding. This, in turn, alters the binding properties of the catalytic core, making identification of the real origin of the observed influence on rate difficult. Unambiguous structure-reactivity correlations based on studies with structurally simplified chemical models may help to distinguish between alternative mechanistic interpretations. The results of such model studies are reviewed. The topics include intramolecular cleavage of RNA phosphodiester bonds by solvent-derived species, general acids/bases and metal ions, effect of molecular environment on their hydrolytic stability and trinucleoside monophosphates as models for large ribozymes.

Catalysis↗
PubMed2004

Female germ cell mutagenicity of model chemicals in Drosophila melanogaster: mechanistic information and analysis of repair systems.

In spite of differences between female and male germ cells, and although both of them contribute to the gene pool of future generations, most germ cell mutagenicity studies in higher eukaryotes have been carried out on males. To study the response of female germ cells to mutagen/carcinogen exposure, the mutagenicity of two model chemicals like diethyl sulfate (DES) and hexamethylphosphoramide (HMPA), and the monofunctional methylating chemotherapeutic drug streptozotocin (STZ), has been analysed on repair efficient females of Drosophila melanogaster. Results previously obtained with N-ethyl-N-nitrosourea (ENU), another model chemical, have also been included in the analysis. The activity of bypass tolerance mechanism (BTM; represented by the mus308 locus) and nucleotide excision repair (NER) on the removal of oxygen and nitrogen ethylations was studied by determining DES mutagenicity in NER deficient females, comparing it with existing results for ENU, and by analysing both chemicals on BTM deficient females. Results indicate that (1) all chemicals are mutagenic on repair efficient females; (2) a measure of mutagenic activity ranked from the lowest DES to STZ, HMPA, and ENU as the highest. This order correlates with the repair of the respectively induced DNA damages, and with the mutagenic and carcinogenic potency of these compounds, considering the toxicity of cross-linking agents; (3) NER efficiently repairs nitrogen ethylation damage and seems to contribute to the processing of oxygen damage in female germ cells; and (4) BTM is involved on the processing of oxygen ethylation damage, whereas the results on nitrogen ethylation are not clear. Finally, these results indicate that differences between male and female germ cells affect the response to chemical exposure, and therefore demonstrate the necessity of analysing also female cells in germinal mutagenicity studies. In addition, these studies can provide important mechanistic information about germ cell chemical mutagenesis, and even when the analysis of oogonia is not possible, since all female germ cells are pre-meiotic, studies of oocytes could be a model for pre-meiotic cells.

Animals↗
PubMed1997

Chemical model studies on the monoamine oxidase-B catalyzed oxidation of 4-substituted 1-methyl-1,2,3,6-tetrahydropyridines.

The MAO-B catalyzed alpha-carbon oxidation of amines has been proposed to proceed via either a single electron transfer (SET) or hydrogen atom transfer (HAT) pathway. In an attempt to distinguish between these pathways, we have examined the alpha-carbon oxidation of a series of 4-substituted 1-methyl-1,2,3,6-tetrahydropyridine derivatives, compounds which are MAO-B substrates, employing chemical models of the SET pathway [using the PF-6 salt of Fe+3 (1,10-phenanthroline)3 as the electron acceptor] and HAT pathway (using the tert-butoxyl radical as the hydrogen atom acceptor). The rates of oxidation and deuterium isotope effects observed with these compounds were similar with the two model reactions. Consequently, unlike their utility in modeling the related cytochrome P450 catalyzed alpha-carbon oxidation of N,N-dimethylaniline derivatives, it appears that these reagents will not distinguish between the proposed pathways.

1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine↗
PubMed1989

A chemical model of catechol-O-methyltransferase. Methylation of 3,4-dihydroxybenzaldehyde in aqueous solution.

The reaction of 3,4-dihydroxybenzaldehyde (LH2) and dimethylsulfate (DMS) to form the m- and p-O-methylated products (vanillin and isovanillin, respectively) in aqueous 2-(N-morpholino)ethane sulfonate buffer was studied kinetically. The products were determined by means of high-performance liquid chromatography. The O-methylation occurred principally at the p-hydroxyl group in the absence of divalent metal ions. In the presence of Cu(II), the m-methylation was promoted and became predominant. Zn(II) showed a similar but less pronounced effect. The effects were explained in terms of the complex formation of LH2. The second order rate constants for the m- and p-methylation of the species, LH2, CuL and CuL2-2 by DMS were calculated. The values and their ratio for the m-/p-reactions increased in the order of LH2 less than CuL less than CuL2-2. The reaction may serve as a chemical model for catechol-O-methyltransferase, which requires divalent metals and catalyzes the m-methylation.

Benzaldehydes↗
PubMed2005

Chemical models for aspects of the photosynthetic reaction centre: synthesis and photophysical properties of tris- and tetrakis-porphyrins that resemble the arrangement of chromophores in the natural system.

Tris-porphyrin and tetrakis-porphyrin arrays 1 and 2 are proposed as models for the arrangement of the chromophores that constitute photosynthetic reaction centres (PRC's). Their porphyrinic chromophores are similar in distance apart to the key chromophores of PRC's and the C2 symmetric arrangement of the macrocycles that constitute the 'special pair' where charge separation occurs is also incorporated. The use of zinc(II) and gold(III) chelation establishes an energy gradient for photoinduced electron transfer across each compound. Synthesis was achieved in good yields through a strategy that used the construction of biquinoxalinyl and Tröger's base linkages between the porphyrinoid components. Compounds which are bis-porphyrin molecular components of the arrays were also synthesised. Photophysical analyses indicate that long-range photoinduced energy and electron transfer processes occur in the extended arrays in addition to those occurring in the component bis-porphyrins. Evidence for step-wise electron transfer between terminal zinc(II)-chelated and gold(III)-chelated porphyrins has been detected in both porphyrins 1 and 2 in polar solvents, representing charge transfer across 35 A and 50 A, respectively. At 298 K, in deaerated benzonitrile, the lifetime of the charge transfer state of the tris-porphyrin 1 is 150 ns and the lifetime of the charge transfer state of tetrakis-porphyrin 2 is 59.4 micros; very long when compared to simpler chemical model systems, but still much shorter than the 1 s lifetime of the charge separated state of natural PRC's in cell membranes.

Gold↗
PubMed2004

A quasi-chemical model for the growth and death of microorganisms in foods by non-thermal and high-pressure processing.

Predictive microbial models generally rely on the growth of bacteria in laboratory broth to approximate the microbial growth kinetics expected to take place in actual foods under identical environmental conditions. Sigmoidal functions such as the Gompertz or logistics equation accurately model the typical microbial growth curve from the lag to the stationary phase and provide the mathematical basis for estimating parameters such as the maximum growth rate (MGR). Stationary phase data can begin to show a decline and make it difficult to discern which data to include in the analysis of the growth curve, a factor that influences the calculated values of the growth parameters. In contradistinction, the quasi-chemical kinetics model provides additional capabilities in microbial modelling and fits growth-death kinetics (all four phases of the microbial lifecycle continuously) for a general set of microorganisms in a variety of actual food substrates. The quasi-chemical model is differential equations (ODEs) that derives from a hypothetical four-step chemical mechanism involving an antagonistic metabolite (quorum sensing) and successfully fits the kinetics of pathogens (Staphylococcus aureus, Escherichia coli and Listeria monocytogenes) in various foods (bread, turkey meat, ham and cheese) as functions of different hurdles (a(w), pH, temperature and anti-microbial lactate). The calculated value of the MGR depends on whether growth-death data or only growth data are used in the fitting procedure. The quasi-chemical kinetics model is also exploited for use with the novel food processing technology of high-pressure processing. The high-pressure inactivation kinetics of E. coli are explored in a model food system over the pressure (P) range of 207-345 MPa (30,000-50,000 psi) and the temperature (T) range of 30-50 degrees C. In relatively low combinations of P and T, the inactivation curves are non-linear and exhibit a shoulder prior to a more rapid rate of microbial destruction. In the higher P, T regime, the inactivation plots tend to be linear. In all cases, the quasi-chemical model successfully fit the linear and curvi-linear inactivation plots for E. coli in model food systems. The experimental data and the quasi-chemical mathematical model described herein are candidates for inclusion in ComBase, the developing database that combines data and models from the USDA Pathogen Modeling Program and the UK Food MicroModel.

Bacteria↗
PubMed2000

Ricinine-elicited seizures. A novel chemical model of convulsive seizures.

The present investigation introduces ricinine-elicited seizures as a novel chemical model of convulsive seizure. Ricinine, a neutral alkaloid obtained from the plant Ricinus communis, induces seizures when administered to mice at doses higher than 20 mg/kg. Animals presenting seizures showed a marked preconvulsive phase followed by short duration hind limb myoclonus, respiratory spasms, and death. The lethal nature of ricinine seizures is also pointed out as a good model to study the events causing death in clonic seizures, particularly those related to respiratory spasms, which are also observed in some types of human epilepsy. The behavioral signs of ricinine-elicited seizures are accompanied by electrographic alterations more evident during the preconvulsive phase in the cerebral cortex and more intense during the ictal phase both in the cortex and in the hippocampus. The ricinine-elicited seizures may be inhibited by diazepam but not by phenobarbital, phenytoin, or ethosuximide. Micromolar concentrations of ricinine cause a small decrease in the binding of [3H]-flunitrazepam to cerebral cortex membranes, but do not alter the binding of other radioligands to AMPA, 5-HT(1A), muscarinic, and alpha(1)-adrenergic receptors. Although ricinine presents a cyanide radical, only higher doses of ricinine (4 mM) caused a small impairment of mitochondrial respiration. These results suggest that the mechanism of action of ricinine probably involves the benzodiazepine site in the GABA(A) receptor. This may represent a new mechanism of drug-elicited seizures that may contribute to a better understanding of epilepsy and to new therapeutic approaches to this disease.

Alkaloids↗
PubMed2004

Chemical models for simulating single-walled nanotube production in arc vaporization and laser ablation processes.

Chemical kinetic models for the nucleation and growth of clusters and single-walled carbon nanotube (SWNT) growth are developed for numerical simulations of the production of SWNTs. Two models that involve evaporation and condensation of carbon and metal catalysts, a full model involving all carbon clusters up to C80, and a reduced model are discussed. The full model is based on a fullerene model, but nickel and carbon/nickel cluster reactions are added to form SWNTs from soot and fullerenes. The full model has a large number of species--so large that to incorporate them into a flow field computation for simulating laser ablation and arc processes requires that they be simplified. The model is reduced by defining large clusters that represent many various sized clusters. Comparisons are given between these models for cases that may be applicable to arc and laser ablation production. Solutions to the system of chemical rate equations of these models for a ramped temperature profile show that production of various species, including SWNTs, agree to within about 50% for a fast ramp, and within 10% for a slower temperature decay time.

Carbon↗
PubMed1988

A self-organized chemical model and reaction cascade.

Some reaction cascades in biological systems are analyzed by a self-organized chemical model, an autocatalytic reaction. This model is described by the coupling of a primary system which stabilizes the initial stage of the reaction rapidly and a partial system which controls the primary system slowly. By the internal force caused by a trigger above the threshold, the coupled system in near-equilibrium is broken and changed into a new state. From the rate equation for the coupled system, a dimensionless nonlinear state equation, n = -n3 - un - v, is derived, where n is the concentration of intermediate, and u, v are dynamic variables of the system. This equation is similar to a nonequilibrium tri-molecular reaction. By using this chemical network theory, fibrin polymerization. F + F----fm----fp + X, where F is a fibrinogen molecule, fm is a fibrin monomer, fp is fibrin polymer, and X is small peptides released from fibrinogen, is discussed as an excellent example of the enzyme reaction cascade.

Blood Coagulation↗
PubMed2003

Mechanisms of ocular toxicity using the in vitro bovine lens and sodium dodecyl sulfate as a chemical model.

Previous work using the in vitro bovine lens as a model has shown a correlation between toxicity and lens optical function and showed much higher sensitivity in detecting irritancy of several surfactants at much lower concentrations than the Draize score. In the current study, cultured bovine lenses were used to study the effects of the surfactant sodium dodecyl sulfate (SDS) on lens optical properties and mitochondrial integrity. Bovine lenses were exposed to SDS (0.1 to 0.00625%) for 30 min and cultured for 24 h. Compared to controls (n = 17), loss of sharp focus was evident immediately following exposure to 0.1% SDS (n = 14, p < 0.0001). At 24 h loss of sharp focus became evident in all groups. Loss of lens transparency, significant increase in lens wet weight, and axial length were seen 24 h postexposure in lenses treated with 0.1 to 0.025% SDS. Confocal analysis 24 h postexposure showed SDS concentration-dependent decrease in number and length of the mitochondria in lens epithelial and superficial cortical fiber cells. The results of this study show a correlation between lens optical properties and metabolic function and together provide a sensitive in vitro model of ocular chemical toxicity. Results of confocal analysis suggest that the mitochondrial integrity of the superficial cortical fiber cells is most sensitive to damage caused by SDS. The results further suggest that recovery of lens metabolic function is necessary for the recovery of lens optical properties.

Animals↗