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PubMed2006

[Research advances in the relationships between biodiversity and invasiveness within plant communities].

This paper reviewed the theoretical, observational, and experimental studies on the relationships between biodiversity and invasiveness within plant communities. The contradictory conclusions made from these studies were summarized and analyzed, and suggestions were put forward to improve future researches. In theoretical studies, models were highly simplified and depended on unrealistic assumptions, e. g., single mechanism of biodiversity formation, balance between communities status, and similar characters of alien and native species, which limited the credibility of research conclusions. Most of the observational studies were not directly exploring the relationships between biodiversity and invasiveness, but inferring from invasion patterns occurred in nature. Different research scales always resulted in contradictory conclusions. In small-scale research where some biotic factors dominated species interaction, the relationships between biodiversity and invasiveness might be negative, while in larger-scale research, other co-varying extrinsic factors might override those biotic factors in small-scale research, and the relationships between biodiversity and invasiveness might be positive. Although most experimental studies were conducted in small scale and extrinsic influences were ruled out, some mistakes might still happen when constructing biodiversity gradients in the experimental communities. Among these mistakes, sampling effect was the most common one, and the others included building communities with same species abundance but varying richness and density. Some suggestions were put forward on improving the study of the relationships between biodiversity and invasiveness in plant communities. In future researches, we should integrate observational study with experimental study, pay more attention to research scale, avoid sampling effect, and couple model with experimental design.

Biodiversity↗

PubMed2006

Biological exposure indicators: quantification of biological variability using toxicokinetic modeling.

Compartmental and physiologically based toxicokinetic modeling coupled with Monte Carlo simulation were used to quantify the impact of biological variability (physiological, biochemical, and anatomic parameters) on the values of a series of bio-indicators of metal and organic industrial chemical exposures. A variability extent index and the main parameters affecting biological indicators were identified. Results show a large diversity in interindividual variability for the different categories of biological indicators examined. Measurement of the unchanged substance in blood, alveolar air, or urine is much less variable than the measurement of metabolites, both in blood and urine. In most cases, the alveolar flow and cardiac output were identified as the prime parameters determining biological variability, thus suggesting the importance of workload intensity on absorbed dose for inhaled chemicals.

Air Pollutants, Occupational↗

PubMed1985

Waste disposal technologies for polychlorinated biphenyls.

Improper practices in the disposal of polychlorinated biphenyl (PCB) wastes by land burial, chemical means and incineration distribute these chemicals and related compounds such as polychlorinated dibenzofurans (PCDFs) and polychlorinated dibenzodioxins (PCDDs) throughout the environment. The complete range of methods for disposal that have been proposed and are in use are examined and analyzed, with emphasis given to the two most commonly used methods: land burial and incineration. The understanding of aquifer contamination caused by migration of PCBs from subsurface burial sites requires a description of the physical, chemical and biological processes governing transport in unsaturated and saturated soils. For this purpose, a model is developed and solved for different soil conditions and external driving functions. The model couples together the fundamental transport phenomena for heat, mass, and moisture flow within the soil. To rehabilitate a contaminated aquifer, contaminated groundwaters are withdrawn through drainage wells, PCBs are extracted with solvents or activated carbon and treated by chemical, photochemical or thermal methods. The chemical and photochemical methods are reviewed, but primary emphasis is devoted to the use of incineration as the preferred method of disposal. After discussing the formation of PCDFs and PCDDs during combustion from chloroaromatic, chloroaliphatic, as well as organic and inorganic chloride precursors, performance characteristics of different thermal destructors are presented and analyzed. To understand how this information can be used, basic design equations are developed from governing heat and mass balances that can be applied to the construction of incinerators capable of more than 99.99% destruction with minimal to nondetectable levels of PCDFs and PCDDs.

Benzofurans↗

PubMed2001

Kinetic analysis of inhibitory substrate degradation in bioaugmented activated sludge process.

A steady-state model coupling Haldane kinetics and mass conservative principles was developed herein to depict the degradation of a single inhibitory substrate in a bioaugmented activated sludge reactor. The substrate toxicity impact on the bioaugmentation was evaluated for three levels of inhibition coefficient Ki: 0.1, 10, and 1000 mg/L. Under high toxicity conditions of Ki = 0.1 mg/L, the input biomass markedly enhanced the substrate removal. However, at less toxicity of Ki > 10 mg/L, the input biomass was ineffective. The sensitivity study confirmed the parameters of k, Ks, and bd has no connection with Ki, but depends on the amounts of degradative bacteria inside the reactor. Alternatively, parameter Y is important only when Ki is greater than 10 mg/L and the bacteria significantly utilize the substrate. In addition, a novel indicator of marginal solids retention time examines the economic advantages of adding biomass as compared to extending the solids retention time.

Bacteria↗

PubMedDate not supplied

Iron catalyst chemistry in modeling a high-pressure carbon monoxide nanotube reactor.

The high-pressure carbon monoxide (HiPco) technique for producing single-wall carbon nanotubes (SWNTs) is analyzed with the use of a chemical reaction model coupled with flow properties calculated along streamlines, calculated by the FLUENT code for pure carbon monoxide. Cold iron pentacarbonyl, diluted in CO at about 30 atmospheres, is injected into a conical mixing zone, where hot CO is also introduced via three jets at 30 degrees with respect to the axis. Hot CO decomposes the Fe(CO)5 to release atomic Fe. Then iron nucleates and forms clusters that catalyze the formation of SWNTs by a disproportionation reaction (Boudouard) of CO on Fe-containing clusters. Alternative nucleation rates are estimated from the theory of hard sphere collision dynamics with an activation energy barrier. The rate coefficient for carbon nanotube growth is estimated from activation energies in the literature. The calculated growth was found be about an order of magnitude greater than measured, regardless of the nucleation rate. A study of cluster formation in an incubation zone prior to injection into the reactor shows that direct dimer formation from Fe atoms is not as important as formation via an exchange reaction of Fe with CO in FeCO.

Carbon Monoxide↗

PubMed1999

Dynamics of Japanese encephalitis--a study in mathematical epidemiology.

An S-->I-->R-->S (susceptible-infective-recovered-susceptible) epidemiological model coupling the dynamics of the spread of Japanese encephalitis (JE) in two populations, human and reservoir animals (pigs, cattle, equines, birds, etc.) through a vector population (a particular species of mosquitos, Culex vishnui, Culex tritaeniorhynchus, etc.) is discussed. We assume that there is a constant recruitment rate of the susceptibles into both the populations, whereas the death rates are proportional to the population sizes, which are hence variables. We also assume that the human population is regulated by the disease. Conditions for the existence of a unique endemic equilibrium were found, and the endemicity of the disease is discussed. The threshold values determine whether the disease dies out or approaches an endemic equilibrium. The persistence of disease and disease-related death can lead to a new equilibrium population size. The criteria for eradication of the disease have been worked out. The analytical results corresponding to the solutions of our system are verified by numerical analysis and computer simulation. The dynamics of disease transmission of JE during 1948-1956 in Japan were also investigated with the help of available data.

Animals↗

PubMed1995

Cardiac quick-release contraction mechanoenergetics analysis using a cardiac muscle cross-bridge model.

Huxley's sliding filament cross-bridge muscle model coupled with parallel and series elastic components was simulated to examine the conflicting reports on the amount of energy saved by quick release at the peak contraction time. Cross-bridge energy utilization was determined by considering the ATP hydrolysis for the cross-bridge cycling. The quick-release cases were simulated by letting the muscle fiber suddenly shorten to the resting fiber length at peak systole, and then the contraction was allowed to continue at the resting length. Simulation results demonstrated that, using realistic parameter values, typically approximately 15% of the muscle fiber energy is used after peak systole (and approximately 30% of the cross-bridge energy), but this is also a function of the muscle fiber properties characterized by cross-bridge association and dissociation rate constants. Increasing the kinetic rate constants, the series elasticity, the initial fiber length, or the time of peak intracellular calcium will increase the amount of energy left, which may explain some of the discrepancies in the literature. Cardiac muscle hypertrophy will increase the fraction of muscle fiber energy left after peak systole to approximately 30%. The strongest indicator of the percent energy left at peak systole was the time the fiber reached peak systole, and as the fiber reached peak systole faster, the amount of energy saved by quick release increased.

Animals↗

PubMed2004

Loss of synchronization in partially coupled Hodgkin-Huxley equations.

We study the loss of synchronization of two partially coupled space-clamped Hodgkin-Huxley equations, with symmetric coupling. This models the coupling of two cells through an electrical synapse. For strong enough coupling it is known that all solutions of the equations approach a state where the two cells are perfectly synchronized, having the same behaviour at each moment. We describe the local bifurcations that arise when the coupling strength is reduced, using a mixture of analytical and numerical methods. We find that perfect synchrony is retained for very small positive values of the coupling strength, for almost all initial conditions. Although perfect synchrony is lost for negative values of the coupling constant, the system always retains some degree of synchronization until it becomes totally unstable. This happens in two ways: in many cases for almost all initial conditions the solutions still approach a perfectly synchronized state. Even when this is not true, the attracting solutions are still synchronized, with a half-period phase shift.

Kinetics↗

PubMed2007

Simulations of chemotaxis and random motility in 2D random porous domains.

We discuss a generic computational model of eukariotic chemotaxis in 2D random porous domains. The model couples the fully time-dependent finite-difference solution of a reaction-diffusion equation for the concentration field of a chemoattractant to biased random walks representing individual chemotactic cells. We focus in particular on the influence of consumption of chemoattractant by the boundaries of obstacles with irregular shapes which are distributed randomly in the domain on the chemotactic response of the cells. Cells are stimulated to traverse a field of obstacles by a line source of chemoattractant. We find that the reactivity of the obstacle boundaries with respect to the chemoattractant strongly determines the transit time of cells through two primary mechanisms. The channeling effect arises because cells are effectively repelled from surfaces which consume chemoattractant, and opposing surfaces therefore act to keep cells in the middle of channels. This reduces traversal times relative to the case with unreactive boundaries, provided that the appropriate Péclet number relating the strength of reactivity to diffusion in governing chemoattractant transport is neither too low nor too high. The dead-zone effect arises due to a realistic threshold on the chemotactic response, which at steady state results in portions of the domain having no detectable gradient. Of these two, the channeling effect is responsible for 90% of the sensitivity of transit times to boundary reactivity. Based on these results, we speculate that it may be possible to tune the rates of cellular penetration into porous domains by engineering the reactivity of the internal surfaces to cytokines.

Chemotactic Factors↗

PubMed2006

Enhanced de novo neurogenesis and dopaminergic neurogenesis in the substantia nigra of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced Parkinson's disease-like mice.

Research reports on de novo neurogenesis, particularly dopaminergic (DA) neurogenesis in the adult mammalian substantia nigra (SN), remain very controversial. For this reason, we used the nestin second intron enhancer-controlled LacZ reporter transgenic mouse model coupled with the 1-methyl-4-phyenyl-1,2,3,6-tetrahydropyridine (MPTP) lesion system to investigate whether there are neurogenesis and DA neurogenesis in the SN of the adult normal and Parkinson's disease (PD)-like mice. First, we demonstrated the presence of neural progenitor cells (NPCs), basal levels of neurogenesis, and DA neurogenesis in the normal adult mouse SN. Second, we showed that there is not only a significant increase in the number of NPCs but also a dramatic increase of neurogenesis from the NPCs in the SN and the midline region adjacent to the SN of the PD-like mice compared with that of normal controls. More importantly, we also demonstrated that there is an increase of DA neurogenesis in the SN of the MPTP-lesioned mice. Third, we showed that the increased DA neurogenesis in the MPTP-lesioned mice was derived from the NPCs and 5-bromodeoxyuridine-positive cells, suggesting that multiple stem cell lineages may contribute to the enhanced neurogenesis in the adult SN. Taken together, these results establish that there are basal levels, albeit low, and increased levels of de novo neurogenesis and DA neurogenesis in the SN of the adult normal and PD-like mice, respectively. The increased NPCs in the MPTP-lesioned mice further suggest that experimental approaches to promote de novo neurogenesis may provide an effective therapy for PD by functional replacement of degenerated DA neurons.

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

PubMed1996

PBPK modeling/Monte Carlo simulation of methylene chloride kinetic changes in mice in relation to age and acute, subchronic, and chronic inhalation exposure.

During a 2-year chronic inhalation study on methylene chloride (2000 or 0 ppm; 6 hr/day, 5 days/week), gas-uptake pharmacokinetic studies and tissue partition coefficient determinations were conducted on female B6C3F1, mice after 1 day, 1 month, 1 year, and 2 years of exposure. Using physiologically based pharmacokinetic (PBPK) modeling coupled with Monte Carlo simulation and bootstrap resampling for data analyses, a significant induction in the mixed function oxidase (MFO) rate constant (Vmaxc) was observed at the 1-day and 1-month exposure points when compared to concurrent control mice while decreases in glutathione S-transferase (GST) rate constant (Kfc) were observed in the 1-day and 1-month exposed mice. Within exposure groups, the apparent Vmaxc maintained significant increases in the 1-month and 2-year control groups. Although the same initial increase exists in the exposed group, the 2-year Vmaxc is significantly smaller than the 1-month group (p < 0.001). Within group differences in median Kfc values show a significant decrease in both 1-month and 2-year groups among control and exposed mice (p < 0.001). Although no changes in methylene chloride solubility as a result of prior exposure were observed in blood, muscle, liver, or lung, a marginal decrease in the fat:air partition coefficient was found in the exposed mice at p = 0.053. Age related solubility differences were found in muscle:air, liver:air, lung:air, and fat:air partition coefficients at p < 0.001, while the solubility of methylene chloride in blood was not affected by age (p = 0.461). As a result of this study, we conclude that age and prior exposure to methylene chloride can produce notable changes in disposition and metabolism and may represent important factors in the interpretation for toxicologic data and its application to risk assessment.

Administration, Inhalation↗

PubMed2000

Learning driver-response relationships from synchronization patterns.

We test recent claims that causal (driver-response) relationships can be deduced from interdependencies between simultaneously measured time series. We apply two recently proposed interdependence measures that should give results similar to cross predictabilities used by previous authors. The systems that we study are asymmetrically coupled simple models (Lorenz, Roessler, and Hénon models), the couplings being such that they lead to generalized synchronization. If the data were perfect (noise-free, infinitely long), we should be able to detect, at least in some cases, which of the coupled systems is the driver and which the response. This might no longer be true if the time series has finite length. Instead, estimated interdependencies depend strongly on which of the systems has a higher effective dimension at the typical neighborhood sizes used to estimate them, and causal relationships are more difficult to detect. We also show that slightly different variants of the interdependence measure can have quite different sensitivities.

Electroencephalography↗

PubMed2003

Rhodopsin crystal: new template yielding realistic models of G-protein-coupled receptors?

Molecular modelling is of major help to understand structure-function data on G-protein-coupled receptors (GPCRs). Since the first determination of the structure of rhodopsin, at high resolution, the view has emerged that it will be now easy to automatically obtain realistic models for any GPCR by homology modeling. Our experience on cholecystokinin CCK(1) receptor modelling together with available data on other GPCRs leads us to rule out this opinion. We believe that construction of realistic models of certain GPCRs still remains time-consuming and requires many refinements of the models in close association with experiments. This conclusion has important consequences for modelling orphan GPCRs.

Animals↗

PubMed1991

Stability properties of proliferatively coupled cell replication models.

To address the possibility that proliferative disorders may originate from interactions between multiple populations of proliferating and maturing cells, we formulate a model for this process as a set of coupled nonlinear first order partial differential equations. Using recent results for the asymptotic behaviour of the solutions to this model, we demonstrate that there exists a region of coupling coefficients, maturation rates, and proliferation rates that will guarantee the stable coexistence of coupled cellular populations. The analysis shows that increases in the coupling between populations may ultimately lead to a loss of stability. Furthermore, the analysis indicates that increases (decreases) in the maturation and/or proliferation rates above (below) critical levels will lead either to instability in the populations or the destruction of one population and the persistence of the other.

Cell Division↗

PubMed1997

Prediction and classification of alpha-turn types.

Tight turns play an important role in globular proteins from both the structural and functional points of view. Of tight turns, beta-turns and gamma-turns have been extensively studied, but alpha-turns were little investigated. Recently, a systematic search for alpha-turns was conducted by V. Pavone et al. [(1996) Biopolymers, Vol. 38, pp. 705-721] from 190 proteins (221 protein chains). They found 356 alpha-turns that were classified into nine different types according to their backbone trajectory features. In view of this new discovery, a sequence-coupled model based on Markov chain theory is proposed for predicting the alpha-turn types in proteins. The high rates of correct prediction by resubstitution test and jackknife test imply that that the formation of different alpha-turn types is evidently correlated with the sequence of a pentapeptide, and hence can be approximately predicted based on the sequence information of the pentapeptide alone, although the role of its interaction with the other part of a protein cannot be completely ignored. The algorithm presented here can also be used to conduct the prediction in which a distinction between alpha-turns and non-alpha-turns is also required.

Algorithms↗

PubMed1989

The RNA binding protein La influences both the accuracy and the efficiency of RNA polymerase III transcription in vitro.

The autoantigen La binds the U-rich 3' ends of all nascent RNA polymerase III transcripts. Here, we demonstrate that this abundant nuclear phosphoprotein not only binds these RNAs but appears to be required for their synthesis. HeLa cell extracts immunochemically depleted of La by either patient or mouse monoclonal antibodies lose greater than 99% of their transcription activity on class III genes. The few transcripts synthesized in the absence of La have fewer uridylate residues at their 3' ends than those made in its presence. Reconstitution of La-depleted extracts with biochemically purified HeLa La protein stimulates transcription levels and completely restores transcript length. A model coupling transcription levels to the action of La at the RNA polymerase III termination signal is presented.

Autoantigens↗

PubMed2006

Astrocytes refill intracellular Ca2+ stores in the absence of cytoplasmic [Ca2+] elevation: a functional rather than a structural ability.

Capacitative Ca(2+) entry (CCE) is a phenomenon triggered by depletion of Ca(2+) content in intracellular stores (ICS). Data about this phenomenon in astrocytes are limited. We analyzed CCE in astrocytes by means of fura-2 based digital imaging. We found that in astrocytes CCE is not associated with an increase of cytosolic Ca(2+) concentration ([Ca(2+)](i)), although ICS are efficiently refilled. We used Mn(2+), thapsigargin and prolonged ATP exposure to show that CCE is not associated with cytosolic diffusion of Ca(2+) entering astrocytes. Our data suggest that the ion is being quickly sequestered in the ICS by the smooth endoplasmic reticulum Ca(2+)-ATP-ase (SERCA). Several experiments were carried out with the goal of failing the efficient uptake in the endoplasmic reticulum (ER). In fact, inhibition of SERCA activity, increased extracellular [Ca(2+)](i) or pharmacologic potentiation of CCE all caused [Ca(2+)](i) elevation during CCE, suggesting that the control of this phenomenon could have physiologic and pathological relevance. The molecular components involved in CCE have been proposed to be organized in a multi-molecular complex tethered by cytoskeleton components and arranged via a secretion coupling model. We show here that the efficient routing of Ca(2+) into the ICS in astrocytes is not affected by disruption of cytoskeleton organization or Golgi's function, but it is instead linked to the high efficiency of SERCA. We conclude that depleted ICS in astrocytes are efficiently refilled by CCE activation, although Ca(2+) influx is not accompanied by elevation of [Ca(2+)](i). This ability seems to be functional rather than structural in nature.

Actins↗

PubMed2006

Chlorogenic acid is poorly absorbed, independently of the food matrix: A Caco-2 cells and rat chronic absorption study.

According to epidemiologic studies, dietary phenolic antioxidants, such as chlorogenic acid (CQA), could prevent coronary heart diseases and some cancers. Coffee is the main source of CQA in the human diet. The aim of this study was to assess the effect of usual coffee consumption conditions, such as the addition of milk, on CQA bioavailability. Interactions between CQA and milk proteins were shown, using an ultrafiltration technique. These interactions proved to be slightly disrupted during an in vitro digestion process. CQA absorption and bioavailability were then studied in vitro using a Caco-2 cell model coupled with an in vitro digestion process, and in vivo, in a chronic supplementation study in which rats were fed daily coffee or coffee and milk for 3 weeks. Both experiments showed that CQA absorption under its native form is weak, but unmodified by the addition of milk proteins, and slightly reduced by the addition of Maillard reaction products. These data show that there are some interactions between coffee phenolics and milk proteins, but these have no significant effect on CQA bioavailability from coffee in the rat. CQA is poorly absorbed under its native form in the body, when ingested in a realistic food matrix.

Absorption↗