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Results for “Models, Structural”

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PubMed1999

A simple structured model for maintenance, biomass formation, and ajmalicine production by nondividing Catharanthus roseus cells.

The stoichiometry of maintenance and carbohydrate storage as well as ajmalicine production kinetics of non-dividing Catharanthus roseus cells in the second stage of a two-stage batch process were investigated. For the mathematical description of these processes, a simple structured model with 5 parameters is proposed. In the model the biomass is divided in two compartments: active biomass and storage carbohydrates. In induction medium (standard medium without phosphate, nitrogen and hormones), biomass formation, glucose consumption, and CO(2) production appeared to be constant in time. Therefore, it is assumed that the active biomass level is constant. The maintenance coefficient m(S), and the yield of storage carbohydrates on glucose Y(SC) were optimized by fitting the model on experimental data: 0.003 C-mol/C-mol/h and 0.82 C-mol/C-mol, respectively. Production kinetics were incorporated in this model and related to the active biomass fraction. The maximum specific ajmalicine production rate q(p)(max) was fitted on the data: 7.5 micromol/C-mol/h. The model was tested at several different experimental conditions, and proved to describe the experimental results adequately. An independent experiment at a very high cell density in order to obtain maximum product formation was used to validate the model. It provided a satisfactory description of the results, but the final ajmalicine concentration (198 micromol/L after 18 days) was lower than the calculated maximum, due to accumulation of inhibiting gaseous metabolites.

Biomass↗

PubMed1999

Body image, social comparison, and eating disturbance: a covariance structure modeling investigation.

OBJECTIVE: To evaluate the role of appearance-based social comparison processes as a possible mediational link between developmental factors (negative social feedback, i.e., teasing about appearance; biological status, i.e., early physical maturation) and levels of body dissatisfaction, eating disturbance, and global psychological functioning. METHOD: In this study of 173 female undergraduates, covariance structure modeling (CSM) was used to examine direct and mediational relationships among these variables. RESULTS: Appearance-based social comparison mediated the effect of appearance-related teasing on body image and eating disturbance; body image mediated the effect of teasing on eating disturbance; eating disturbance had a direct effect on overall psychological functioning. DISCUSSION: Implications for devising and testing other theoretical models are discussed.

Adolescent↗

PubMed2001

Estimation of the heritability of latent variables which are included in a structural model for metabolic syndrome.

In a study looking for risk factors of atherosclerosis in families with combined hyperlipidemia and hypertension, clinical and biochemical data of 1,149 persons were analyzed to develop two hypothetical multivariate scores concerning the degree to which a patient is affected by the metabolic syndrome. The scores are based on a structural model for low-density cholesterol (LDL) and high-density cholesterol (HDL), triglycerides, uric acid, creatinine, glucose, insulin, systolic blood pressure and waist-to-hip ratio. Age, gender and body mass index were used for adjusting all variables. In segregation analyses of 42 pedigrees without using genotype information, estimations of the heritabilities and environmentally caused variance and covariance components were computed for the individual score values of the two latent factors. The first score shows a heritability of 42%; the environment component disappeared. The score mainly reflects the HDL, LDL and triglyceride levels. The second score shows a heritability of 16% with an environment component of 7%. It includes mainly insulin, uric acid and creatinine. In the search for genetic causes, both scores could be a basis for further phenotypic classification of the metabolic syndrome.

Arteriosclerosis↗

PubMed1994

Spectroscopic characterization of tyrosine-Z in histidine 190 mutants of the D1 protein in photosystem II (PSII) in Chlamydomonas reinhardtii. Implications for the structural model of the donor side of PSII.

EPR spectra attributed to the redox active tyrosine residues on the oxidizing side of photosystem II (TyrZ and TyrD) have almost identical line shapes, although the tyrosyl radicals differ in stability and redox characteristics. Strongly modified spectra of oxidized TyrD in site-directed mutants in a histidine residue, H189 on the D2 reaction center protein in the cyanobacterium Synechocystis 6803, support a structural model where H189 interacts closely, probably via a hydrogen bond, to TyrD (Tommos, C., Davidsson, L., Svensson, B., Madsen, C., Vermass, W., and Styring, S. (1993) Biochemistry 32, 5436-5441). To determine whether TyrZ and the corresponding histidine on the D1 protein (D1-H190) interacts similarly, we have generated His-Phe (H190F) and His-Tyr (H190Y) mutations in the C2 symmetry related H190 residue on the D1 reaction center protein by site-directed mutagenesis in Chlamydomonas reinhardtii. The H190F and H190Y mutants assemble photosystem II reaction centers capable of primary photochemistry but unable to oxidize water. We have obtained kinetic spectra of a flash-induced transient EPR signal that we assign to oxidized TyrZ in the D1-H190 mutants. The spectra are identical in line width (18-20 G) and hyperfine structure to the wild-type spectrum from oxidized TyrZ and exhibit decay kinetics (t 1/2 approximately 500 ms) typical for the TyrZ radical in managenese-depleted photosystem II membranes. However, both TyrZ and TyrD were oxidized with reduced (10-15%) quantum yield in these mutants, indicating that the kinetics of electron donation to P+680 were significantly modified as a result of the mutation. Thus, the altered kinetics of TyrZ in the mutants suggest that there is an interaction between TyrZ and His-190 on the D1 protein. However, unlike the situation on the D2 side, the presence of a hydrogen bond between TyrZ and H190 on the D1 protein is improbable.

Amino Acid Sequence↗

PubMed1988

Structural models of the evolutionarily conservative central domain of silk-moth chorion proteins.

Silk-moth chorion proteins belong to a small number of families: A, B, C, Hc-A and Hc-B. The central domain is an evolutionarily conservative region in each family, of variable length and composition between families. This domain shows clear 6-fold periodicities for various amino acid residues, e.g. glycine. The periodicities, together with the well-documented prevalence of beta-sheet and beta-turn secondary structure of chorion proteins, strongly support a structural model in which four-residue beta-strands alternate with beta-turns, forming a compact antiparallel, probably twisted beta-sheet. Conformational analysis, aided by interactive graphics refinement and recent experimental findings, further suggest that this structure consists of beta-strands, alternating with I' and II' beta-turns, and apparently forms the basis for the molecular and supramolecular assembly of chorion.

Amino Acid Sequence↗

PubMed1994

Network interactions among limbic cortices, basal forebrain, and cerebellum differentiate a tone conditioned as a Pavlovian excitor or inhibitor: fluorodeoxyglucose mapping and covariance structural modeling.

1. The objective was to examine how opposite learned behavioral responses to the same physical tone were differentiated by the pattern of interactions between extraauditory neural regions. This was pursued using a new approach combining behavior, neuroimaging, and network analysis to integrate information about differences in regional activity with differences in the covariance relationships between brain areas. 2. A tone was used as either a Pavlovian conditioned excitor or inhibitor. Rats were conditioned with reinforced trials of a conditioned excitor (A+) intermixed with nonreinforced trials of a tone-light compound (AX-). The tone was the excitor (A+) for the tone-excitor group and was the inhibitor (X-) for the tone-inhibitor group. After conditioning, all rats were injected with [14C(U)]2-fluoro-2-deoxyglucose (FDG) and presented with the same tone. 3. FDG autoradiography was used to measure regional activity and to generate interregional correlations of activity resulting from the presentation of the tone. A stepwise discriminant analysis was used to select brain regions that differentiated the excitor from the inhibitor effects. 4. Network analysis consisted of constructing an anatomic model of the brain regions, selected by the discriminant analysis, linking the regions with their known anatomical connections. Then, functional models for the tone-excitor and -inhibitor groups were constructed using structural equation modeling. Correlations of activity between regions were decomposed to calculate numerical weights, or path coefficients, for each anatomic path. These path coefficients were used to compare the interactions for the tone-excitor and -inhibitor models. 5. Regional differences in FDG uptake were found in the sulcal frontal cortex (SFC), lateral septum (LS), medial septum/diagonal band (MS/DB), retrosplenial cortex (RS), and dentate-interpositus nuclei of the cerebellum (DEN). Discriminant analysis selected three other regions that significantly discriminated the tone-excitor and -inhibitor groups: perirhinal cortex (PRh), nucleus accumbens (ACB), and the anteroventral nucleus of the thalamus (AVN). 6. Structural equation modeling identified two functional circuits that differentiated the groups. One involved the basal forebrain regions (LS, MS/DB, ACB) and the other limbic thalamocortical structures (SFC, RS, PRh, AVN). Differences in the interactions within these circuits were mainly in sign of the covariance relationships between regions, from positive for the tone-excitor model to negative path coefficients for the tone-inhibitor model. The path coefficient between the basal forebrain circuit and the limbic thalamocortical circuit showed the largest magnitude difference. This quantitative difference was mediated by a path from the MS/DB to PRh.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1983

An extended secondary structure model for the TMV assembly origin, and its correlation with protection studies and an assembly defective mutant.

Recognition of the unique internal assembly origin on tobacco mosaic virus (TMV) RNA by the disk aggregate of the viral coat protein probably involves an extended region of the RNA (larger than that coated by a single disk) folded into a specific conformation. A secondary structure model is proposed for the RNA preferentially coated by limiting amounts of coat protein disks on the basis of partial nuclease digestion data. Part of this sequence can form three symmetrically spaced hairpins with marginally stable base paired sequences at the tips of the stems. The pattern of progressive protection of the RNA from nuclease attack during assembly suggests that these three hairpins are successively coated by the first three disks to add. The spacing of these hairpins is identical to that of three hairpins in the pseudo assembly origin (part of the coat protein gene homologous to the assembly origin). In Ni 2519, a TMV mutant whose assembly is defective at high temperature because it can no longer discriminate between the true and pseudo assembly origins, a point mutation has occurred near the tip of the third metastably base paired stem of the true assembly origin which would disrupt its structure and alter one copy of a repeated heptanucleotide. This suggests an important role for the ordered and cooperative recognition of successive loops in determining the specificity of assembly.

Journal Article↗

PubMed2004

Comparison of a multi-layer structural model for arterial walls with a fung-type model, and issues of material stability.

The goals of this paper are (i) to re-examine the constitutive law for the description of the (passive) highly nonlinear and anisotropic response of healthy elastic arteries introduced recently by the authors, (ii) to show how the mechanical response of a carotid artery under inflation and extension predicted by the structural model compares with that for a three-dimensional form of Fung-type strain-energy function, (iii) to provide a new set of material parameters that can be used in a finite element program, and (iv) to show that the model has certain mathematical features that are important from the point of view of material and numerical stability.

Animals↗

PubMedDate not supplied

Determinants of perceived health in patients with left ventricular dysfunction: a structural modeling analysis.

OBJECTIVE: Few studies have evaluated the determinants of perceived health in patients with chronic illness. The present study was designed to evaluate the role of biomedical, demographic, and psychosocial influences on global subjective health by means of a structural equation modeling approach. METHOD: A conceptual model of perceived health was tested in a subsample of patients (N = 146) from the multicenter Studies of Left Ventricular Dysfunction (SOLVD) trial. Domain-specific quality of life constructs (emotional status, social support, and physical functioning), were assessed by means of multiple indicators. These latent (mediating) variables, along with six single-indicator biomedical and background variables, were modeled as predictors of a composite index of perceived health. RESULTS: A satisfactory fit was obtained for the proposed model, with practical fit indices ranging from .89 to .95. High levels of perceived health were associated with low levels of emotional distress and high levels of physical functioning. Social support was positively correlated with physical functioning and negatively associated with emotional distress. Among the background variables, no direct associations were observed between any of the single-indicator variables and perceived health. Several background variables (eg, age, income, walk-test scores) had indirect effects via associations with the latent variables of physical functioning and emotional distress. CONCLUSIONS: These findings support the use of a structural modeling approach in assessing determinants of perceived health in patients with congestive heart failure. Further research is needed to evaluate the utility of the model in other patient populations.

Activities of Daily Living↗

PubMed2005

Marginal structural models for estimating the effect of highly active antiretroviral therapy initiation on CD4 cell count.

The effect of highly active antiretroviral therapy (HAART) on the evolution of CD4-positive T-lymphocyte (CD4 cell) count among human immunodeficiency virus (HIV)-positive participants was estimated using inverse probability-of-treatment-and-censoring (IPTC)-weighted estimation of a marginal structural model. Of 1,763 eligible participants from two US cohort studies followed between 1996 and 2002, 60 percent initiated HAART. The IPTC-weighted estimate of the difference in mean CD4 cell count at 1 year among participants continuously treated versus those never treated was 71 cells/mm3 (95% confidence interval: 47.5, 94.6), which agrees with the reported results of randomized experiments. The corresponding estimate from a standard generalized estimating equations regression model that included baseline and most recent CD4 cell count and HIV type 1 RNA viral load as regressors was 26 cells/mm3 (95% confidence interval: 17.7, 34.3). These results indicate that nonrandomized studies of HIV treatment need to be analyzed with methods (e.g., IPTC-weighted estimation) that, in contrast to standard methods, appropriately adjust for time-varying covariates that are simultaneously confounders and intermediate variables. The 1-year estimate of 71 cells/mm3 was followed by an estimated continued increase of 29 cells/mm3 per year (estimated effect at 6 years: 216 cells/mm3), providing evidence that the large short-term effect found in randomized experiments persists and continues to improve over 6 years.

Acquired Immunodeficiency Syndrome↗

PubMed1994

Covariance structure models of expectancy.

Antecedent variables under the broad categories of genetic, environmental and cultural influences have been linked to the risk for alcohol abuse. Such risk factors have not been shown to result in high correlations with alcohol consumption and leave unclear an understanding of the mechanism by which these variables lead to increased risk. This study employed covariance structure modeling to examine the mediational influence of stored information in memory about alcohol, alcohol expectancies in relation to two biologically and environmentally driven antecedent variables, family history of alcohol abuse and a sensation-seeking temperament in a college population. We also examined the effect of criterion contamination on the relationship between sensation-seeking and alcohol consumption. Results indicated that alcohol expectancy acts as a significant, partial mediator of the relationship between sensation-seeking and consumption, that family history of alcohol abuse is not related to drinking outcome and that overlap in items on sensation-seeking and alcohol consumption measures may falsely inflate their relationship.

Adaptation, Psychological↗

PubMed2006

Predicting intentions for long-term anabolic-androgenic steroid use among men: a covariance structure model.

Long-term use of anabolic-androgenic steroids (AASs) is associated with both positive and negative effects. The authors examined possible mechanisms by which these effects contribute to AAS satisfaction and predict intentions for future AAS use. Five hundred male AAS users completed an interactive Web-based instrument assessing the psychological and physical effects of AAS use. Covariance structure modeling was used to evaluate both direct and indirect effects of AAS consequences on satisfaction with AASs and intentions for future AAS use. Results suggest that gain in muscle mass and psychological benefits from AAS use uniquely contributed to both AAS satisfaction and intentions for future use. Side effects from AAS use also uniquely contributed to AAS satisfaction, but ancillary drug use was found to partially mediate this relationship, suggesting that the satisfaction of experienced AAS users is enhanced by their mastery of side effects through the use of ancillary drugs. The final model explained 29% of the variance in intentions for future AAS use. Mechanisms for sustained AAS use and implications for intervention and prevention strategies are discussed.

Adolescent↗

PubMed2005

Progress and challenges in high-resolution refinement of protein structure models.

Achieving atomic level accuracy in de novo structure prediction presents a formidable challenge even in the context of protein models with correct topologies. High-resolution refinement is a fundamental test of force field accuracy and sampling methodology, and its limited success in both comparative modeling and de novo prediction contexts highlights the limitations of current approaches. We constructed four tests to identify bottlenecks in our current approach and to guide progress in this challenging area. The first three tests showed that idealized native structures are stable under our refinement simulation conditions and that the refinement protocol can significantly decrease the root mean square deviation (RMSD) of perturbed native structures. In the fourth test we applied the refinement protocol to de novo models and showed that accurate models could be identified based on their energies, and in several cases many of the buried side chains adopted native-like conformations. We also showed that the differences in backbone and side-chain conformations between the refined de novo models and the native structures are largely localized to loop regions and regions where the native structure has unusual features such as rare rotamers or atypical hydrogen bonding between beta-strands. The refined de novo models typically have higher energies than refined idealized native structures, indicating that sampling of local backbone conformations and side-chain packing arrangements in a condensed state is a primary obstacle.

Computer Simulation↗

PubMed1981

Monosaccharide composition of human monoclonal (18) and normal (8) IGM immunoglobulins: proposed structural models for their glycan chains.

The carbohydrate composition of 18 monoclonal IgM (Waldenström macroglobulinemia) was determined by gas-liquid chromatography. Two populations occurred with mean sugar contents of 7.3% (12 IgM and 10% (6 IgM). A value of 7.2% was obtained for 8 IgM prepared from 8 normal sera. On the basis of mean molar ratios established for each monosaccharide residue, structural models for oligosaccharide units are proposed. The number of complex glycan chains (N-acetyllactosaminic type) is higher in the 10% population, which would correspond to IgM with a mean sedimentation constant of 18.3So20, W. On the other hand, the 7.3% population has a lower content of "mature" chains and its sedimentation constant would be inferior: 17S)20, W.

Antibodies, Monoclonal↗

PubMed2001

Structural model for the cooperative assembly of HIV-1 Rev multimers on the RRE as deduced from analysis of assembly-defective mutants.

The functional efficacy of the HIV-1 Rev protein is highly dependent on its ability to assemble onto its HIV-1 RNA target (the RRE) as a multimeric complex. To elucidate the mechanism of multimeric assembly, we have devised two rapid and broadly applicable strategies for examining cooperative interactions between proteins bound to RNA, one based on cooperative translational repression of a two-site reporter and the other on gel shift analysis with crude E. coli extracts. Using these strategies, we have identified two distinct surfaces of Rev (head and tail) that are critical for different steps in multimeric assembly. Our data indicate that Rev assembles cooperatively on the RRE via a series of symmetrical tail-to-tail and head-to-head protein-protein interactions. The insights into molecular architecture suggested by these findings have enabled us to derive a structural model for Rev and its multimerization on the RRE.

Allosteric Site↗

PubMed1983

A structural model for the interaction of haem with unsaturated fatty acids explaining its quasi-lipoxygenase activity. Quantum chemical calculations.

The quasi-lipoxygenase activity of haemoglobin differs in many respects from the well-known haemin-catalyzed lipid peroxidation (1-4), especially in its high substrate specificity for unsaturated fatty acids containing one 1,4-pentadiene system (dienoic fatty acids). In this report a structural model for the fatty acid haem interaction based on quantum-chemical calculations is presented which show that only dienoic fatty acids are bound to the haem in such a way that the initial hydrogen abstraction that is necessary for the over-all reaction, is favoured sterically and energetically.

Animals↗

PubMedDate not supplied

A proposed structural model of endothelin.

We have assessed the hydropathic nature, secondary structure, and flexibility of endothelin and report a testable model for the structure of this 21-amino acid vasoconstrictor peptide. The proposed model consists of a rigid (disulfide bonded), hydrophilic amino-terminal half of the molecule with two turns, and an extended hydrophobic sheet structure comprising the C-terminal half of the molecule. The extended structure may be stabilized by intermolecular hydrogen bonding, leading to dimers or higher order aggregates, and is hydrophobic enough to partition into an organic solvent such as ether, as long as the molecule can keep its hydrophilic amino terminus in an aqueous phase. To test this model, partitioning measurements were made on bioactive synthetic endothelin. It was found to partition at the interface of an ether/water system in a concentration- and surface area-dependent manner. A further indication as to the amphipathic nature of the molecule is that microcrystals of synthetic endothelin tend to grow at an organic-aqueous interface in a two-phase system.

Amino Acid Sequence↗

PubMed1991

A tree-structure model for analyzing laboratory test costs.

A method of costing clinical laboratory tests is described in which total laboratory costs are apportioned into 3 components: an 'organizational overhead cost' to describe the cost of running an organization; a 'cost per episode' to describe the costs incurred per request; and a 'cost per test' to describe the actual analytical costs of tests performed. A tree-like structural model is described which allows for distribution of this 'cost per test' component to the contributing tests and the calculation of the true 'cost per test'. The implementation of this model on a computer spreadsheet has been achieved. When combined with the other cost components, the true total costs of laboratory testing can be determined for any particular test. The model also allows calculation of the incremental and marginal costs of a test and permits optimization of laboratory test frequencies and work-load to minimize laboratory analytical costs.

Algorithms↗