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At least 361 records · Page 20Linked to original sources
PubMed1990

A model system for studying the adsorption of a hydrophobic mutagen to dietary fibre.

The adsorption of 1,8-dinitropyrene (DNP) to alpha-cellulose has been studied as a model system for examining the adsorption of a hydrophobic mutagen to dietary fiber. Most of the DNP rapidly disappeared from an aqueous solution and partitioned between the glass wall of the test tube and the alpha-cellulose. Factors affecting DNP distribution included (i) the time of incubation, (ii) the final concentration of the solvent, dimethyl sulphoxide, in which the DNP has been dissolved, and (iii) the relative concentrations of DNP and alpha-cellulose. We suggest that this model system could be applied to other mutagens, and that alpha-cellulose would provide a useful standard fiber to permit inter-laboratory comparisons.

Adsorption↗
PubMed2006

Modeling ozone and aerosol formation and transport in the pacific northwest with the community Multi-Scale Air Quality (CMAQ) modeling system.

The Community Multi-Scale Air Quality (CMAQ) modeling system was used to investigate ozone and aerosol concentrations in the Pacific Northwest (PNW) during hot summertime conditions during July 1-15, 1996. Two emission inventories (El) were developed: emissions for the first El were based upon the National Emission Trend 1996 (NET96) database and the BEIS2 biogenic emission model, and emissions for the second El were developed through a "bottom up" approach that included biogenic emissions obtained from the GLOBEIS model. The two simulations showed that elevated PM2.5 concentrations occurred near and downwind of the Interstate-5 corridor along the foothills of the Cascade Mountains and in forested areas of central Idaho. The relative contributions of organic and inorganic aerosols varied by region, but generally organic aerosols constituted the largest fraction of PM2.5. In wilderness areas near the 1-5 corridor, organic carbon from anthropogenic sources contributed approximately 50% of the total organic carbon with the remainder from biogenic precursors, while in wilderness areas in Idaho, biogenic organic carbon accounted for 80% of the total organic aerosol. Regional analysis of the secondary organic aerosol formation in the Columbia River Gorge, Central Idaho, and the Olympics/Puget Sound showed that the production rate of secondary organic carbon depends on local terpene concentrations and the local oxidizing capacity of the atmosphere, which was strongly influenced by anthropogenic emissions. Comparison with observations from 12 IMPROVE sites and 21 ozone monitoring sites showed that results from the two El simulations generally bracketed the average observed PM parameters and that errors calculated for the model results were within acceptable bounds. Analysis across all statistical parameters indicated that the NW-AIRQUEST El solution performed better at predicting PM2.5, PM1, and beta(ext) even though organic carbon PM was over-predicted, and the NET96 El solution performed better with regard to the inorganic aerosols. For the NW-AIRQUEST El solution, the normalized bias was 30% and the normalized absolute error was 49% for PM2.5 mass. The NW-AIRQUEST solution slightly overestimated peak hourly ozone downwind of urban areas, while the NET96 solution slightly underestimated peak values, and both solutions over-predicted average 03 concentrations across the domain by approximately 6 ppb.

Aerosols↗
PubMed1996

A novel in vitro model system for studying the action of ara-C.

The antimetabolite 1-beta-D-arabinofuranosyl-cytosine (ara-C) has proven to be one of the most effective agents available for the treatment of acute leukemia. While ara-C has been implicated as a potent inhibitor of mammalian cell DNA replication, the specific mechanism by which ara-C kills cells is not known. In this report we describe the development of an in vitro model system to study the molecular mechanism of ara-CMP incorporation into DNA. This model system makes use of a recently described human cell multiprotein DNA replication complex (MRC) that is competent to replicate DNA in vitro. The MRC can successfully incorporate ara-CMP into replicating DNA at internucleotide positions. These results are similar to those described for studies using intact cells. This MRC-driven in vitro replication system may therefore serve as a powerful model for the study of anticancer agents that directly affect human cell DNA synthesis.

Antimetabolites, Antineoplastic↗
PubMed2003

NMR analysis of methyl groups at 100-500 kDa: model systems and Arp2/3 complex.

Large macromolecular machines are among the most important and challenging targets for structural and mechanistic analyses. Consequently, there is great interest in development of NMR methods for the study of multicomponent systems in the 50-500 kDa range. Biochemical methods also must be developed in concert to produce such systems in selectively labeled form. Here, we present (1)H/(13)C-HSQC spectra of protonated methyl groups in a model system that mimics molecular weights up to approximately 560 kDa. Signals from side chain methyl groups of Ile, Leu, and Val residues are clearly detectable at correlation times up to approximately 330 ns. We have also developed a biochemical procedure to produce the 240 kDa, heteroheptameric Arp2/3 actin nucleation complex selectively labeled at one subunit and obtained (1)H/(13)C-HSQC spectra of this assembly. Sensitivity in spectra of both the Arp2/3 complex and the model system indicate that methyl groups will be useful sources of information in nonsymmetric systems with molecular weights greater than 600 kDa at concentrations less than 100 microM. Methyl analyses will complement TROSY and CRINEPT analyses of amides in NMR studies of structure and molecular interactions of extremely large macromolecules and assemblies.

Actin-Related Protein 2↗
PubMed1989

[The action of inhibitors of sugar transport phlorizin, phloretin and cytochalasin B in model systems].

Phlorizin, phloretin and cytochalasin B are known to be specific sugar transport inhibitors. A study was made of their effects on the carbohydrate-protein interaction in solution as a model system for examining the initial steps of sugar membrane transport. Glycogen precipitation by concanavalin A is inhibited only by alpha-methylmannoside, whereas both phlorizin and phloretin inhibit interactions between hexokinase and glucose, and between glucose-6-phosphate dehydrogenase and glucose-6-phosphate. Cytochalasin B was found to exert no effect on both the concanavalin A--glycogen interaction and the enzyme reactions investigated. The data obtained in the model system examination may suggest that the sites of glucose and cytochalasin binding are, respectively, spatially uncoupled.

Biological Transport↗
PubMed1983

A patient classification system based on the Behavioral System Model of Nursing: Part 1.

This article has described the development of a patient classification system based on the Behavioral System Model of Nursing. Although the system was specifically developed for the psychiatric setting, the framework of the model permits application to all clinical settings. A primary advantage of utilizing a model is that it provides an objective framework for organizing observations of patient behavior, thereby increasing consistency and continuity of care provided by all nursing staff. Part 2 will appear in the next issue of JONA and will discuss the clinical application of the patient classification system.

Humans↗
PubMedDate not supplied

Mcg light chain dimer as a model system for ligand design: a docking study.

Mcg light chain dimer has been extensively studied by crystallography and peptide binding studies to investigate its peptide cross-reactivity as well as to use it as a model system for designing space filling peptide ligands. Here we extend these investigations by utilizing automated docking. Mcg light chain dimer is an ideal model system for such study due to the availability of experimental data for both the native structure and the 14 complexes with various peptide ligands. We show the ability of the docking approach to reproduce the experimental structures and discuss the limitations associated with such outcomes. We demonstrate the usefulness of the docking approach in generating structural information otherwise not available from the experiment.

Binding Sites, Antibody↗
PubMed1997

Structural basis of receptor/G protein coupling selectivity studied with muscarinic receptors as model systems.

Different muscarinic acetylcholine receptor subtypes were used as model systems to study the structural basis of receptor/G protein coupling selectivity. Extensive mutagenesis studies have previously led to the identification of single amino acids on the m3 muscarinic receptor protein (located in the second intracellular loop (i2) and at the N- and C-terminus of the third intracellular loop (i3)) that dictate selective recognition of Gq/11 proteins by this receptor subtype. Based on these results, we proposed a model of the intracellular m3 receptor surface in which the functionally critical residues project into the interior of the transmembrane receptor core. To identify specific regions on the G protein(s) that are contacted by these different, functionally critical receptor sites, we recently employed a novel experimental strategy involving the coexpression of hybrid m2/m3 muscarinic receptors with hybrid G alpha-subunits. Using this approach, we could demonstrate that the C-terminus of G protein alpha i/o-subunits is recognized by a short sequence element in the m2 muscarinic receptor ("VTIL") that is located at the junction between the sixth transmembrane domain (TM VI) and the i3 loop. We could show that this interaction is critically involved in determining coupling selectivity and triggering G protein activation. By using a similar strategy (coexpression of mutant muscarinic receptors with hybrid G alpha-subunits), other major receptor/G protein contact sites are currently being identified. These studies, complemented by biochemical and biophysical approaches, should eventually lead to a detailed structural model of the ligand-receptor-G protein complex.

Animals↗
PubMed1991

Application of continuous relaxation time distributions to the fitting of data from model systems and excised tissue.

Biological systems exhibit heterogeneity at many different levels, leading to the expectation of multiple relaxation time components for water protons in tissue samples. Traditional methods which fit the relaxation data to an a priori number of discrete components are open to observer bias in their interpretation of this data, and moreover, are intuitively less realistic for heterogeneous systems than methods which produce continuous relaxation time distributions. Previous validations of continuous distribution techniques have been made on simulated data assuming uniform Gaussian noise. In the current work we have investigated the ability of one particular linear inverse theory technique to reproduce known relaxation time distributions from the data on a controllable model system. Furthermore, using the experience gained on the model system, we have applied this same technique to the analysis of in vitro relaxation time measurements on excised brain tissue and found for water protons in white matter, four reproducible components for the transverse relaxation, whereas gray matter gave rise to only two. The longitudinal relaxation displayed only one component in either white matter or gray matter.

Algorithms↗
PubMed1988

The design and application of a model system to investigate physical factors affecting container leakage.

A model system was designed and constructed to investigate the mechanisms of food container leakage. Factors which were found to affect the leakage of microorganisms into the container, included the presence of a vacuum, the size and shape of the leakage channel and the volume of liquid passing through the channel. Differences were observed among the test organisms used.

Equipment Design↗
PubMed1994

De novo design and structural characterization of an alpha-helical hairpin peptide: a model system for the study of protein folding intermediates.

The de novo design and structural characterization of an alpha-helical hairpin peptide (alpha-helix/turn/alpha-helix, alpha t alpha) are reported. The peptide is intended to provide a model system for the study of the interactions of secondary structural elements during protein folding. Both the diffusion-collision and framework models of protein folding envision that the earliest intermediates in protein folding are transient secondary structures or microdomains which interact and become mutually stabilizing. Design principles for the alpha t alpha peptide were drawn from the large body of work on the structure of peptides in solution. Computer modeling was not used in the design process. Study of alpha t alpha by circular dichroism and two-dimensional nuclear magnetic resonance indicates that the designed peptide is monomeric, helical, and stable in aqueous solution at room temperature. Analysis of two-dimensional nuclear magnetic resonance experiments indicates that the two helices and the turn form in the intended positions and that the helices associate in the designed orientation. Development of alpha t alpha represents an advance in protein design in that both the secondary structural elements and designed tertiary interactions have been realized and can be detected in solution by nuclear magnetic resonance. The resulting model system resembles a protein folding intermediate and will allow the study of interacting helices in a context that approximates an early stage in protein folding.

Amino Acid Sequence↗
PubMed2004

An in vitro model system that can differentiate the stages of DNA replication affected by anticancer agents.

We have previously reported on the potential use of a novel in vitro human cell-derived model system to investigate the mechanism of action of anticancer agents that directly affect the process of DNA replication. Our cell-free system uses a multiprotein DNA replication complex (designated the DNA synthesome) that has been isolated, characterized, and extensively purified from a wide variety of mammalian cells and tissues. The DNA synthesome is competent to orchestrate simian virus 40 (SV40) origin-specific and large T antigen-dependent DNA replication in vitro. In this study, the synthesome-based cell-free system was tested to evaluate the mechanism of action of 1-beta-d-arabinofuranosylcytosine (ara-C), camptothecin (CPT), and doxorubicin (DOX). Using a novel synthesome-based in vitro kinetic assay, we demonstrated that DNA replication mediated by the synthesome is initiated within the SV40 replication origin and proceeds bidirectionally in a manner analogous to that occurring within the cell. Ara-CTP, CPT, and DOX have been found to affect different stages of the in vitro DNA replication process mediated by the complex. Ara-CTP inhibited both the initiation and elongation stages, whereas CPT produced most of its effects by inhibiting the elongation phase of DNA replication. DOX inhibited the termination stage of DNA synthesis mediated by the synthesome. The data presented here support our contention that the DNA synthesome represents a highly effective in vitro model system for investigating the mechanism by which some anticancer agents can directly affect the process of DNA replication.

Antineoplastic Agents↗
PubMed1990

A systems model of chronic musculo-skeletal pain.

A comprehensive systems model of chronic musculo-skeletal pain is presented. Physical and mechanical events may impinge directly upon the organism to produce pain. In addition life experience, as interpreted by each individual, may result in unpleasant affect which may lead through three psychosomatic pathways to musculo-skeletal pain. The suggested pathways are conversion, dysponesis and neurotransmitter disturbance. It is suggested that the construing of the self as being "ill", "an invalid" or a "pain person" is a crucial step in the development of the chronic pain syndrome and that therapies which fail to change this self-construct are unlikely to meet with long-term success.

Chronic Disease↗
PubMed1999

SUM-159PT cells: a novel estrogen independent human breast cancer model system.

Breast cancer remains one of the most common malignant diseases in women in North America and Western Europe, yet therapies for the more aggressive estrogen independent tumors are limited and few model systems are available for the study of this type of breast cancer. In these studies, we characterized a novel estrogen independent breast cancer cell line, SUM-159PT. SUM-159PT cells are epithelial in origin, demonstrated by expression of cytokeratin 18. SUM-159PT cells are estrogen independent, demonstrated by lack of estrogen receptor (ER) protein and ER ligand binding studies. Furthermore, SUM-159PT cells injected subcutaneously or orthotopically are tumorigenic in ovariectomized athymic nude mice in the absence of estradiol supplementation. SUM-159PT cells are capable of invading through an 8 microm Matrigel membrane and display a stellate morphology in Matrigel, indicative of a metastatic phenotype. Correlating with this phenotype, we have detected secondary tumors upon inoculation of SUM-159PT cells into the mammary fat pad. To further investigate the metastatic potential of the SUM-159PT cells, we examined the expression of two proteins, vimentin and E-cadherin, implicated in the transition of carcinoma cells to a metastatic phenotype. Western blot and immunohistochemical analysis demonstrated that both SUM-159PT cells and xenografts express vimentin. No expression of E-cadherin was detected in SUM-159PT cells. Our data indicate that despite estrogen independence, SUM-159PT cells are growth inhibited in vitro by compounds such as 1,25(OH)2D3, transforming growth factor beta (TGF-beta), and the phorbol ester TPA. These studies indicate that SUM-159PT cells represent a good model system for the study of late stage estrogen independent, invasive breast cancer.

Animals↗
PubMed1992

Cefclidin (E1040), a novel cephalosporin: lack of selection of beta-lactamase overproducing mutants in an in vitro pharmacokinetic model system.

The bactericidal activity of cefclidin (E1040), a new cephalosporin, against a clinical strain of Citrobacter freundii was compared with that of ceftazidime in a two-compartment in vitro pharmacokinetic model system designed to simulate plasma concentrations in humans for 12 hours after intravenous administration of a 1 g dose. Both cefclidin and ceftazidime showed rapid bactericidal activity against C. freundii. However, during the simulation of ceftazidime treatment, regrowth was observed after two hours and a subpopulation emerged which was resistant to ceftazidime. Neither regrowth nor the emergence of resistant mutants was observed with cefclidin during the 12-hour simulation. The ceftazidime-resistant mutants constitutively overproduced beta-lactamase at levels which were about 500-fold higher than that of the parent wild-type strain. Against this beta-lactamase overproducing mutant, no bactericidal activity of ceftazidime was observed in the in vitro model system, whereas the bactericidal activity of cefclidin was observed during the 12-hour period. The emergence of Enterobacter cloacae mutants derepressed for beta-lactamase production was also observed with ceftazidime but not cefclidin. The affinity of cefclidin for the beta-lactamase isolated from these mutants was lower than that of ceftazidime, and the kinetic parameters of enzymatic hydrolysis showed that cefclidin was hydrolyzed more slowly at a low concentration (0.2 microM) than was ceftazidime. It is suggested that the high activity of cefclidin against strains derepressed for beta-lactamase plays a major role in the absence of emergence of resistant mutants.

Bacteria↗
PubMed2006

Protection of adult mouse progenitor cells and human glioma cells by de novo decorin expression in an oxygen- and glucose-deprived cell culture model system.

We employed an in vitro hypoxia cell culture model system and gene transfer technology to examine the effect of the decorin gene on cell survival against oxygen and glucose deprivation (OGD). Ectopic expression of decorin in subventricular zone (SVZ) cells from adult male mouse brain and human glioblastoma U-87 cells kept the cells viable against 24 h of OGD. Fewer than 1% of decorin-synthesizing cells were apoptotic after 12 h of OGD. In contrast, 100% of the control cells were apoptotic even after 4 h of OGD. De novo decorin synthesis in SVZ and U-87 cells induced expression of p21, p27 and Ras, AKT (acutely transforming retrovirus AKT8 in rodent T-cell lymphoma), and phosphorylated AKT. Blocking of phosphoinositide 3-kinase (PI-3K), Ras, and the epidermal growth factor receptor with specific inhibitors had no effect on induction of Ras, p21, and p27 at the messenger RNA level in decorin-synthesizing SVZ and U-87 cells. PI-3K inhibitors significantly increased apoptosis in decorin-expressing cells. Our data indicate that induction of p21, p27, Ras, AKT, and phosphorylated AKT by decorin inhibits apoptosis and protects U-87 and SVZ cells against OGD. Therefore, our data suggest that decorin is a potent trophic factor that protects neuronal progenitor cells and glioma cells from OGD.

Aging↗
PubMed1983

Functions of the 5'-phosphoryl group of pyridoxal 5'-phosphate in phosphorylase: a study using pyridoxal-reconstituted enzyme as a model system.

Pyridoxal-reconstituted phosphorylase was used as a model system to study the possible functions of the 5'-phosphoryl group of pyridoxal 5'-phosphate (PLP) in rabbit muscle glycogen phosphorylase. Kinetic study was conducted by using competitive inhibitors of phosphite, an activator, and alpha-D-glucopyranose 1-phosphate (glucose-1-P) to study the relationship between the PLP phosphate and the binding of glucose-1-P to phosphorylase. Fluorine-19 nuclear magnetic resonance (19F NMR) spectroscopy of fluorophosphate bound to pyridoxal phosphorylase showed that its ionization state did not change during enzymatic catalysis. Evaluation of the apparent kinetic parameters for the activation of pyridoxal phosphorylase with different analogues having varied pKa2 values demonstrated a dependency of KM on pKa2. Molybdate, capable of binding as chelates in a trigonal-bipyramidal configuration, was tested for its inhibitory property with pyridoxal phosphorylase. On the basis of the results in this study, several conclusions may be drawn: (1) The bound phosphite in pyridoxal phosphorylase and, possibly, the 5'-phosphoryl group of PLP in native phosphorylase do not effect the glucose-1-P binding. (2) One likely function of the 5'-phosphoryl group of PLP in native phosphorylase is acting as an anchoring point to hold the PLP molecule and/or various amino acid side chains in a proper orientation for effective catalysis. (3) The force between the PLP phosphate and its binding site in phosphorylase is mainly electrostatic; a change of ionization state during catalysis is unlikely. (4) Properties of the central atoms of different anions are important for their effects as either activators or inhibitors of pyridoxal phosphorylase.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗