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At least 145 records · Page 8Linked to original sources
PubMed2006

Radioactive materials in biosolids: dose modeling.

The Interagency Steering Committee on Radiation Standards (ISCORS) has recently completed a study of the occurrence within the United States of radioactive materials in sewage sludge and sewage incineration ash. One component of that effort was an examination of the possible transport of radioactivity from sludge into the local environment and the subsequent exposure of humans. A stochastic environmental pathway model was applied separately to seven hypothetical, generic sludge-release scenarios, leading to the creation of seven tables of Dose-to-Source Ratios (DSR), which can be used in translating from specific activity in sludge into dose to an individual. These DSR values were then combined with the results of an ISCORS survey of sludge and ash at more than 300 publicly owned treatment works, to explore the potential for radiation exposure of sludge workers and members of the public. This paper provides a brief overview of the pathway modeling methodology employed in the exposure and dose assessments and discusses technical aspects of the results obtained.

Environmental Monitoring↗
PubMed2002

Modelling regulatory pathways in E. coli from time series expression profiles.

MOTIVATION: Cells continuously reprogram their gene expression network as they move through the cell cycle or sense changes in their environment. In order to understand the regulation of cells, time series expression profiles provide a more complete picture than single time point expression profiles. Few analysis techniques, however, are well suited to modelling such time series data. RESULTS: We describe an approach that naturally handles time series data with the capabilities of modelling causality, feedback loops, and environmental or hidden variables using a Dynamic Bayesian network. We also present a novel way of combining prior biological knowledge and current observations to improve the quality of analysis and to model interactions between sets of genes rather than individual genes. Our approach is evaluated on time series expression data measured in response to physiological changes that affect tryptophan metabolism in E. coli. Results indicate that this approach is capable of finding correlations between sets of related genes.

Adaptation, Physiological↗
PubMed1981

Permeability of Novikoff hepatoma cells to water and monohydric alcohols.

The permeability coefficients of Novikoff hepatoma ascites cell membranes for tritiated water (3HHO) and for a homologous series of monohydric alcohols (methanol through hexanol) were deduced from linear diffusion coefficients by means of a series-parallel pathway model (Redwood et al. (1974) J. Gen. Physiol. 64, 706-729). Membrane permeability coefficients for 3HHO at 20, 30 and 37 degrees C were (all x 10(-5)) 97, 125, and 163 cm . s-1, respectively, and were significantly smaller than the corresponding values for the alcohols tested. In the alcohols series, ethanol had the lowest permeability coefficient 198 x 10(-5) cm . s-1 at 20 degrees C. The apparent activation energy for water permeation was 6.7 +/- 1.9 S.E. kcal . mol-1. The apparent membrane diffusion coefficients for the alcohols were a complex function of molecular properties with less diffusional membrane resistance to the alcohols in the middle of the homologous series than would have been expected on the basis of oil-water partitioning or molar volume considerations. The conventional parallel aqueous lipophilic pathway model is not consistent with the present data which can be interpreted by consideration of parallel lipophilic pathways through the Novikoff hepatoma cell membrane.

Alcohols↗
PubMed2001

Nitrogen-containing bisphosphonates induce apoptosis of Caco-2 cells in vitro by inhibiting the mevalonate pathway: a model of bisphosphonate-induced gastrointestinal toxicity.

Bisphosphonates have become an important addition to the pharmacological armamentarium against postmenopausal osteoporosis. One of the major side effects of oral therapy with some nitrogen-containing bisphosphonates appears to be gastrointestinal (GI) intolerability, particularly esophageal irritation and ulceration. Because nitrogen-containing bisphosphonates can cause apoptosis in a variety of cell types in vitro, by inhibiting the mevalonate pathway, we hypothesized that the effect of these agents on the GI tract may be due to apoptosis or inhibition of growth of gut epithelial cells. A comparison between clodronate, etidronate, pamidronate, alendronate, and risedronate demonstrated that only the nitrogen-containing bisphosphonates were effective at inducing apoptosis or inhibiting proliferation of Caco-2 human epithelial cells in vitro, at concentrations of between 10 and 1000 micromol/L. The ability of nitrogen-containing bisphosphonates to cause apoptosis and inhibit Caco-2 cell proliferation was due to inhibition of the mevalonate pathway, because the addition of farnesol, oxidized low-density lipoprotein (LDL) cholesterol, or especially geranylgeraniol suppressed the effects. Furthermore, pamidronate, alendronate, and risedronate inhibited protein prenylation in Caco-2 cells, as determined by analysis of the processing of Rap1A, a prenylated small GTPase. These studies suggest that the effects of nitrogen-containing bisphosphonates observed in the GI tract may be due to inhibition of proliferation or apoptosis of gut epithelial cells, following loss of prenylated proteins and sterols.

Apoptosis↗
PubMed2003

Minocycline inhibits caspase-independent and -dependent mitochondrial cell death pathways in models of Huntington's disease.

Minocycline is broadly protective in neurologic disease models featuring cell death and is being evaluated in clinical trials. We previously demonstrated that minocycline-mediated protection against caspase-dependent cell death related to its ability to prevent mitochondrial cytochrome c release. These results do not explain whether or how minocycline protects against caspase-independent cell death. Furthermore, there is no information on whether Smac/Diablo or apoptosis-inducing factor might play a role in chronic neurodegeneration. In a striatal cell model of Huntington's disease and in R6/2 mice, we demonstrate the association of cell death/disease progression with the recruitment of mitochondrial caspase-independent (apoptosis-inducing factor) and caspase-dependent (Smac/Diablo and cytochrome c) triggers. We show that minocycline is a drug that directly inhibits both caspase-independent and -dependent mitochondrial cell death pathways. Furthermore, this report demonstrates recruitment of Smac/Diablo and apoptosis-inducing factor in chronic neurodegeneration. Our results further delineate the mechanism by which minocycline mediates its remarkably broad neuroprotective effects.

Animals↗
PubMed1995

Dermal metabolism of topically applied drugs: pathways and models reconsidered.

The study of skin metabolism is of prime importance not only in the field of transdermal drug delivery but also for the safe and efficient local skin treatment with topically applied substances. Since it has become clear that even peptides may be delivered across the permeation barrier of the stratum corneum, e.g. by means of iontophoresis, phonophoresis or electroporation, the enzymatic barrier of the epidermis deserves more attention as another important limiting factor for the dermal delivery of drugs. The purpose of this review is to give a survey of the major aspects concerning the assessment of the metabolism of xenobiotics in the skin. First, this review will focus on the localization of enzyme activity within the skin. Further, important aspects to be considered for the planning and evaluation of skin metabolism studies will be discussed: differences among species and requirements of skin quality. Among the various metabolic pathways within the skin broad interest will be concentrated on the metabolism of peptide drugs. Therefore, exopeptidases in the skin are the subject of an additional section. Also models for skin metabolism studies will be especially considered including the development of suitable cell culture models. Finally, major gap areas in the investigation of skin metabolism will be identified and summarized, namely; classes of xenobiotics, proteolytic enzyme activity in the skin, validity of experimental models, localization of enzyme activity and physical model development.

Administration, Cutaneous↗
PubMed2004

Ca2+ and ionic strength dependencies of S1-ADP binding to actin-tropomyosin-troponin: regulatory implications.

Skeletal and cardiac muscle contraction are inhibited by the actin-associated complex of tropomyosin-troponin. Binding of Ca(2+) to troponin or binding of ATP-free myosin to actin reverses this inhibition. Ca(2+) and ATP-free myosin stabilize different tropomyosin-actin structural arrangements. The position of tropomyosin on actin affects the binding of ATP-free myosin to actin but does not greatly affect myosin-ATP binding. Ca(2+) and ATP-free myosin alter both the affinity of ATP-free myosin for actin and the kinetics of that binding. A parallel pathway model of regulation simulated the effects of Ca(2+) and ATP-free myosin binding on both equilibrium binding of myosin-nucleotide complexes to actin and the general features of ATPase activity. That model was recently shown to simulate the kinetics of myosin-S1 binding but the analysis was limited to a single condition because of the limited data available. We have now measured equilibrium binding and binding kinetics of myosin-S1-ADP to actin at a series of ionic strengths and free Ca(2+) concentrations. The parallel pathway model of regulation is consistent with those data. In that model the interaction between adjacent regulatory complexes fully saturated with Ca(2+) was destabilized and the inactive state of actin was stabilized at high ionic strength. These changes explain the previously observed change in binding kinetics with increasing ionic strength.

Actins↗
PubMed2005

Inflammatory aetiology of human myometrial activation tested using directed graphs.

There are three main hypotheses for the activation of the human uterus at labour: functional progesterone withdrawal, inflammatory stimulation, and oxytocin receptor activation. To test these alternatives we have taken information and data from the literature to develop causal pathway models for the activation of human myometrium. The data provided quantitative RT-PCR results on key genes from samples taken before and during labour. Principal component analysis showed that pre-labour samples form a homogenous group compared to those during labour. We therefore modelled the alternative causal pathways in non-laboring samples using directed graphs and statistically compared the likelihood of the different models using structural equations and D-separation approaches. Using the computer program LISREL, inflammatory activation as a primary event was highly consistent with the data (p = 0.925), progesterone withdrawal, as a primary event, is plausible (p = 0.499), yet comparatively unlikely, oxytocin receptor mediated initiation is less compatible with the data (p = 0.091). DGraph, a software program that creates directed graphs, produced similar results (p= 0.684, p= 0.280, and p = 0.04, respectively). This outcome supports an inflammatory aetiology for human labour. Our results demonstrate the value of directed graphs in determining the likelihood of causal relationships in biology in situations where experiments are not possible.

Journal Article↗
PubMed1999

The feasibility of pharmacological volume control of sickle cells is dependent on the quantization of the transport pathways. A model study.

Normal erythrocytes are under physiological conditions characterized by low cation and high anion conductance. However, in the case of sickle cell anemia the erythrocytes contain a modified haemoglobin, HbS, which under low oxygen tension gives rise to sickling. This condition is preceded by an increase in cation conductance, especially due to the Ca2+-activated K+-channels, leading to net-efflux of KCI and thereby decreased cellular volume, which is part of the pathological condition.A possible symptomatic treatment could be application of conductance blockers, targeting the Ca2+-activated K+-channel or the anion conductance in order to minimize the passive transport of ions and solvent. It has been argued, that due to the high anion conductance, solute loss depended at moderately increased cation conductances on the cation only. Consequently the Ca2+-activated K+-conductance should be the target for attempts to modify solute loss.It is shown that: knowledge of mean conductances (time averages) for pathways showing fluctuations are insufficient to predict the quantitative effect of conductance inhibitors, since inhibition is strongly dependent on the kinetics of the mechanisms mediating the translocation and a block of the high conductance anion pathway can be as effective as inhibition of the Ca+-activated K+-conductance with regard to net salt loss.

Anemia, Sickle Cell↗
PubMed2003

Intravascular tissue factor pathway--a model for rapid initiation of coagulation within the blood vessel.

The loss of blood through vessel wall ruptures is initially prevented by the rapid adhesion of platelets to the subendothelium, and the formation of a thrombus consisting of platelets and different types of leukocytes. Concomitantly, the coagulation process is thought to be activated by vascular wall tissue factor (TF). Here, a new model for the initiation of coagulation is presented, based on unexpected findings on the presence and functional activation of TF within the blood itself. TF was recently found to be stored in the alpha-granules of resting platelets under physiological conditions. Activation by collagen exposes TF on the platelet cell membrane and on platelet derived microvesicles. Adhesive interactions of the TF bearing platelets and microvesicles to neutrophils and monocytes support the functional activation of the blood based TF. The intravascular TF pathway is proposed to play a significant role during hemostasis by enabling the generation of fibrin at the site of the developing thrombus.

Blood Coagulation↗
PubMed1997

Asymmetric affective evaluation of words and faces.

In two experiments the relationship between direct and indirect forms of affective evaluation was investigated within the framework of a dual-pathway model (LeDoux, 1986, 1989). Emotionally valenced faces were hypothesized to be more directly evaluated affectively than valenced words. A Stroop-like asymmetry was expected, with faces interfering more with word evaluation than vice versa. Similar to experiments investigating affective influences of words on words (Greenwald, Klinger & Liu, 1989), a backward dichoptic pattern-masking technique was used in both experiments, with lateralized presentations of targets and masked primes in a short and a long presentation condition. In Expt 1, priming of emotionally negative, neutral and positive faces on the affective evaluation of emotionally negative, neutral and positive words was investigated in a two-alternative forced-choice task. In Expt 2, primes and targets were reversed. A clear asymmetry occurred in both subliminal and supraliminal conditions, but completely opposite to the one expected. Implications for a dual-pathway model are discussed.

Affect↗
PubMed1992

Site-specific parameter values for the Nuclear Regulatory Commission's food pathway dose model.

Routine operations at the Savannah River Site (SRS) in Western South Carolina result in radionuclide releases to the atmosphere and to the Savannah River. The resulting radiation doses to the off-site maximum individual and the off-site population within 80 km of the SRS are estimated on a yearly basis. These estimates are currently generated using dose models prescribed for the commercial nuclear power industry by the Nuclear Regulatory Commission (NRC). The NRC provides default values for dose-model parameters for facilities without resources to develop site-specific values. A survey of land- and water-use characteristics for the Savannah River area has been conducted to determine site-specific values for water recreation, consumption, and agricultural parameters used in the NRC Regulatory Guide 1.109 (1977) dosimetric models. These site parameters include local characteristics of meat, milk, and vegetable production; recreational and commercial activities on the Savannah River; and meat, milk, vegetable, and seafood consumption rates. This paper describes how parameter data were obtained at the Savannah River Site and the impacts of such data on off-site dose. Dose estimates using site-specific parameter values are compared to estimates using the NRC default values.

Food Contamination, Radioactive↗
PubMed2005

How batrachotoxin modifies the sodium channel permeation pathway: computer modeling and site-directed mutagenesis.

A structural model of the rNav1.4 Na+ channel with batrachotoxin (BTX) bound within the inner cavity suggested that the BTX pyrrole moiety is located between a lysine residue at the DEKA selectivity filter (Lys1237) and an adjacent phenylalanine residue (Phe1236). We tested this pyrrole-binding model by site-directed mutagenesis of Phe1236 at D3/P-loop with 11 amino acids. Mutants F1236D and F1236E expressed poorly, whereas nine other mutants either expressed robust Na+ currents, like the wild-type (F1236Y/Q/K), or somewhat reduced current (F1236G/A/C/N/W/R). Gating properties were altered modestly in most mutant channels, with F1236G displaying the greatest shift in activation and steady-state fast inactivation (-10.1 and -7.5 mV, respectively). Mutants F1236K and F1236R were severely resistant to BTX after 1000 repetitive pulses (+50 mV/20 ms at 2 Hz), whereas seven other mutants were sensitive but with reduced magnitudes compared with the wild type. It is noteworthy that rNav1.4-F1236K mutant Na+ channels remained highly sensitive to block by the local anesthetic bupivacaine, unlike several other BTX-resistant mutant channels. Our data thus support a model in which BTX, when bound within the inner cavity, interacts with the D3/P-loop directly. Such a direct interaction provides clues on how BTX alters the Na+ channel selectivity and conductance.

Amino Acid Sequence↗
PubMed2006

The epidermal growth factor receptor pathway: a model for targeted therapy.

The epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase receptor that is frequently expressed in epithelial tumors. The EGFR was the first receptor to be proposed as a target for cancer therapy, and after 2 decades of intensive research, there are several anti-EGFR agents available in the clinic. Recent advances in our understanding in the mechanisms of receptor activation and function, discovery of primary and secondary EGFR somatic mutations, as well as a new generation of anti-EGFR agents provide new leads on the clinical targeting of this receptor and may serve as a model for strategies aimed at targeting other receptors.

ErbB Receptors↗
PubMed1999

Attention-deficit/hyperactivity disorder and scholastic achievement: a model of dual developmental pathways.

A conceptual model has recently been hypothesized in which parallel but correlated developmental pathways exist for attention deficit behaviors and conduct problems. An important component of this model suggests that attention deficit behaviors are related to later scholastic underachievement, whereas conduct problems are unrelated to scholastic underachievement except by their common correlation with attention deficit and intelligence. The present study replicated the general model using a cross-sectional sample of 325 children, and examined whether hypothesized dual pathways (behavioral and cognitive) better account for the relationship between attention deficit, intelligence, and later scholastic achievement. Results of the structural equation modeling analysis were consistent with the hypothesized dual pathway model and suggest that school behavior and select cognitive abilities serve as important mediators between attention deficit, intelligence, and later scholastic achievement. Implications of these results for understanding the developmental trajectory of children with attention deficit and general theoretical models of ADHD are discussed.

Achievement↗
PubMed2006

Developing Itô stochastic differential equation models for neuronal signal transduction pathways.

Mathematical modeling and simulation of dynamic biochemical systems are receiving considerable attention due to the increasing availability of experimental knowledge of complex intracellular functions. In addition to deterministic approaches, several stochastic approaches have been developed for simulating the time-series behavior of biochemical systems. The problem with stochastic approaches, however, is the larger computational time compared to deterministic approaches. It is therefore necessary to study alternative ways to incorporate stochasticity and to seek approaches that reduce the computational time needed for simulations, yet preserve the characteristic behavior of the system in question. In this work, we develop a computational framework based on the Itô stochastic differential equations for neuronal signal transduction networks. There are several different ways to incorporate stochasticity into deterministic differential equation models and to obtain Itô stochastic differential equations. Two of the developed models are found most suitable for stochastic modeling of neuronal signal transduction. The best models give stable responses which means that the variances of the responses with time are not increasing and negative concentrations are avoided. We also make a comparative analysis of different kinds of stochastic approaches, that is the Itô stochastic differential equations, the chemical Langevin equation, and the Gillespie stochastic simulation algorithm. Different kinds of stochastic approaches can be used to produce similar responses for the neuronal protein kinase C signal transduction pathway. The fine details of the responses vary slightly, depending on the approach and the parameter values. However, when simulating great numbers of chemical species, the Gillespie algorithm is computationally several orders of magnitude slower than the Itô stochastic differential equations and the chemical Langevin equation. Furthermore, the chemical Langevin equation produces negative concentrations. The Itô stochastic differential equations developed in this work are shown to overcome the problem of obtaining negative values.

Computer Simulation↗