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At least 1,081 records · Page 60Linked to original sources
PubMed2006

SPARC, an upstream regulator of connective tissue growth factor in response to transforming growth factor beta stimulation.

OBJECTIVE: To differentiate the effects of inhibition of specific small interfering RNA (siRNA) of SPARC (secreted protein, acidic and rich in cysteine) and siRNA of connective tissue growth factor (CTGF) in cultured human fibroblasts, and to identify potential interrelationships between SPARC and CTGF. METHODS: Fibroblasts from skin biopsy specimens of 2 normal individuals were transfected with siRNA of SPARC and siRNA of CTGF. The fibroblasts were stimulated with or without transforming growth factor beta1 (TGFbeta1) and examined by real-time quantitative reverse transcription-polymerase chain reaction to determine the transcription levels of several extracellular matrix genes. RESULTS: After exogenous TGFbeta1 stimulation, both SPARC siRNA and CTGF siRNA showed a protective role against overexpression of collagen genes. Following TGFbeta1 stimulation, SPARC siRNA-transfected fibroblasts showed a greater reduction in expression of the collagen genes compared with CTGF siRNA-transfected fibroblasts, as well as a significantly decreased expression of CTGF (P < 0.05). Using linear structure equations to quantitatively model a genetic network based on expression levels of each gene, a positive regulatory role of SPARC on CTGF, COL1A2, COL3A1, COL11A1, and TIMP3 was observed. However, the regulatory role of CTGF on SPARC appeared to be negative and very small, while the positive regulatory effects of CTGF on COL1A2, COL3A1, COL11A1, and TIMP3 were less than those of SPARC. CONCLUSION: The results of this quantitative comparison support the hypothesis that in these cultured fibroblasts, the regulatory effects of SPARC on some major extracellular matrix structural components are greater than those of CTGF. In addition, SPARC appears to regulate CTGF in a predominantly positive manner, while CTGF may act as a negative feedback control on SPARC following TGFbeta stimulation.

Cells, Cultured↗
PubMed2006

A general bilinear model to describe growth or decline time profiles.

Linear models are widely used because of their unrivaled simplicity, but they cannot be applied for data that have a turning-or rate-change-point, even if the data show good linearity sufficiently far from this point. To describe such bilinear-type data, a completely generalized version of a linearized biexponential model (LinBiExp) is proposed here to make possible smooth and fully parametrizable transitions between two linear segments while still maintaining a clear connection with the linear models. Applications and brief conclusions are presented for various time profiles of biological and medical interest including growth profiles, such as those of human stature, agricultural crops and fruits, multicellular tumor spheroids, single fission yeast cells, or even labor productivity, and decline profiles, such as age-effects on cognition in patients who develop dementia and lactation yields in dairy cattle. In all these cases, quantitative model selection criteria such as the Akaike and the Schwartz Bayesian information criteria indicated the superiority of the bilinear model compared to adequate less parametrized alternatives such as linear, parabolic, exponential, or classical growth (e.g., logistic, Gompertz, Weibull, and Richards) models. LinBiExp provides a versatile and useful five-parameter bilinear functional form that is convenient to implement, is suitable for full optimization, and uses intuitive and easily interpretable parameters.

Adolescent↗
PubMed2004

Linear and nonlinear relationships between neuronal activity, oxygen metabolism, and hemodynamic responses.

We investigated the relationship between neuronal activity, oxygen metabolism, and hemodynamic responses in rat somatosensory cortex with simultaneous optical intrinsic signal imaging and spectroscopy, laser Doppler flowmetry, and local field potential recordings. Changes in cerebral oxygen consumption increased linearly with synaptic activity but with a threshold effect consistent with the existence of a tissue oxygen buffer. Modeling analysis demonstrated that the coupling between neuronal activity and hemodynamic response magnitude may appear linear over a narrow range but incorporates nonlinear effects that are better described by a threshold or power law relationship. These results indicate that caution is required in the interpretation of perfusion-based indicators of brain activity, such as functional magnetic resonance imaging (fMRI), and may help to refine quantitative models of neurovascular coupling.

Animals↗
PubMed2006

Computational analysis of the membrane association of group IIA secreted phospholipases A2: a differential role for electrostatics.

Secreted phospholipases A2 (sPLA2's) are enzymes that hydrolyze glycerophospholipids at the sn-2 position, which leads to the production of lipid mediators of many cellular processes. These interfacial enzymes are regulated by their lipid specificity at two levels: membrane binding and substrate recognition. Different sPLA2's utilize different combinations of electrostatic and hydrophobic interactions to adsorb to membrane surfaces, which results in the wide range of membrane binding behaviors observed. Here, the finite difference Poisson Boltzmann (FDPB) method is used to quantitatively analyze the contribution of electrostatic interactions to the membrane association of two highly basic group II sPLA2's: Agkistrodon piscivorus piscivorus (AppD49) sPLA2 and nonpancreatic human group IIA (hGIIA) sPLA2. The calculations predict how membrane binding is affected by ionic strength, membrane composition, substitutions of residues in the enzymes, and the presence of calcium in the active site. In addition, the results provide molecular models for the membrane-associated forms of the enzymes. Furthermore, these models account for (1) changes in orientation and protonation state of both the native and charge reversal forms of the enzymes at the membrane surface and (2) the effect of protein/vesicle aggregation, as observed for hGIIA sPLA2. Importantly, the modeling quantitatively describes the complex membrane binding behaviors of these interfacial enzymes in terms of simple physical forces and provides structural information that is difficult to obtain experimentally. The computational analysis shows that nonspecific electrostatic interactions not only play a major role in recruiting these enzymes to membrane surfaces but also orient the enzymes for productive catalysis at the membrane interface.

Agkistrodon↗
PubMed1984

Theory and experiment for the effect of vascular microstructure on surface tissue heat transfer--Part I: Anatomical foundation and model conceptualization.

A new theoretical model supported by ultrastructural studies and high-spatial resolution temperature measurements is presented for surface tissue heat transfer in a two-part study. In this first paper, vascular casts of the rabbit thigh prepared by the tissue clearance method were serially sectioned parallel to the skin surface to determine the detailed variation of the vascular geometry as a function of tissue depth. Simple quantitative models of the basic vascular structures observed were then analyzed in terms of their characteristic thermal relaxation lengths and a new three-layer conceptual model proposed for surface tissue heat transfer. Fine wire temperature measurements with an 80-micron average diameter thermocouple junction and spatial increments of 20 micrometers between measurement sites have shown for the first time the detailed temperature fluctuations in the microvasculature and have confirmed the fundamental assumptions of the proposed three-layer model for the deep tissue, skeletal muscle and cutaneous layers.

Animals↗
PubMed2006

Modeling the effects of a Staphylococcal Enterotoxin B (SEB) on the apoptosis pathway.

BACKGROUND: The lack of detailed understanding of the mechanism of action of many biowarfare agents poses an immediate challenge to biodefense efforts. Many potential bioweapons have been shown to affect the cellular pathways controlling apoptosis 1234. For example, pathogen-produced exotoxins such as Staphylococcal Enterotoxin B (SEB) and Anthrax Lethal Factor (LF) have been shown to disrupt the Fas-mediated apoptotic pathway 24. To evaluate how these agents affect these pathways it is first necessary to understand the dynamics of a normally functioning apoptosis network. This can then serve as a baseline against which a pathogen perturbed system can be compared. Such comparisons can expose both the proteins most susceptible to alteration by the agent as well as the most critical reaction rates to better instill control on a biological network. RESULTS: We explore this through the modeling and simulation of the Fas-mediated apoptotic pathway under normal and SEB influenced conditions. We stimulated human Jurkat cells with an anti-Fas antibody in the presence and absence of SEB and determined the relative levels of seven proteins involved in the core pathway at five time points following exposure. These levels were used to impute relative rate constants and build a quantitative model consisting of a series of ordinary differential equations (ODEs) that simulate the network under both normal and pathogen-influenced conditions. Experimental results show that cells exposed to SEB exhibit an increase in the rate of executioner caspase expression (and subsequently apoptosis) of 1 hour 43 minutes (+/- 14 minutes), as compared to cells undergoing normal cell death. CONCLUSION: Our model accurately reflects these results and reveals intervention points that can be altered to restore SEB-influenced system dynamics back to levels within the range of normal conditions.

Antibodies, Monoclonal↗
PubMed2006

[The PLS calibration model optimization and determination of rice protein content by near-infrared reflectance spectroscopy].

A hundred and ninety one representative brown rice samples from the Chinese Rice Genebank and the DH population derived from the cross of japonica upland rice IRAT109 with paddy rice Yuefu were selected for this study. Their protein content range was 5.90%-14.50%. Near-infrared diffusive spectroscopy (NIDRS) and partial least square (PLS) were used to determine protein content with different wavelength ranges and data preprocessing methods for regression and information extraction. The object function [R/(1+RMSECV)] of quantitative model was defined, and the samples of calibration and validation tests were classified by projective distribution of PLS loadings. These methods were applied to the optimization of the calibration model. It is demonstrated that the calibration model developed by the spectral data pretreatment of the first derivative + standard vector normalization with the same spectral region (5 000-9 000 cm(-1) resulted in the best determination of protein content in brown rice when the maximum values of the object function were reached. The maximum values of the object functions of calibration and validation sets were 0.701 and 0.687, respectively. Projective distributions of PLS loadings were used to validate the models, and the result was the same as that of validating model by object function [R/(1+RMSECV)].

Least-Squares Analysis↗
PubMed1986

Additive variation maintained under stabilizing selection: a two-locus model of pleiotropy for two quantitative characters.

A model with two diallelic loci controlling two additive quantitative characters is suggested. One of the loci has a similar effect on both characters, whereas the second locus has an antagonistic effect on two characters. Both characters experience direct stabilizing selection. The model yields a stable polymorphic state, with both characters maintaining genetic variation. The genetic correlation between the characters at the equilibrium is zero, in spite of the pleiotropic effects of the loci controlling them.

Alleles↗
PubMed2002

Characterization of crude oils using fluorescence lifetime data.

The average fluorescence lifetimes of nine North Sea crude oils with API gravities of between 20 and 51 were measured using a modular, filter based, instrument developed in-house. Two pulsed light emitting diode (LED) excitation sources (460 and 510 nm) were used to excite fluorescence, the lifetime of which was measured at a range of emission wavelengths. Fluorescence lifetimes were found to vary from 1.8 to 8.2 ns with confidence intervals of +/- 0.11 ns. The average lifetimes at all emission wavelengths were linearly correlated with API gravity and with aromatic concentration with the best results being obtained with the 460 nm excitation source. Predictive models with an accuracy of +/- 7.6 API degrees were generated using partial least-squares methods from average fluorescence lifetimes measured at an emission wavelength of 500 nm using 460 nm excitation. A better correlation was found between the aromatic concentration of the oils and the ratio of the average fluorescence lifetimes at measured at 550 and 650 nm using 460 nm excitation. This led to a quantitative model with an accuracy of +/- 5.4% for aromatic concentration.

Biophysical Phenomena↗
PubMed1985

Light microscope based analysis of three-dimensional structure: applications to the study of Drosophila salivary gland nuclei. II. Algorithms for model analysis.

In Drosophila melanogaster there are significant differences in the way the polytene chromosomes are arranged in different nuclei from the same salivary gland (Mathog et al., 1984). Visual inspection of the models of these nuclei was inadequate to delineate all of the features conserved in their structures. In order to bypass this limitation, models of these nuclei were constructed in a format compatible with computational manipulation (Mathog et al., 1985). By applying some simple algorithms to these models, quantitative comparisons were made which revealed otherwise cryptic features common to many nuclei. Given here are the details of several algorithms for describing and comparing the arrangement of the chromosomes within the nuclei.

Animals↗
PubMed1999

Adaptive control: a strategy to treat autoimmunity.

Anti-idiotype of (natural) autoantibodies participate in the regulation of autoantibodies, their idiotypes. Focusing on an idiotype/anti-idiotype pair embedded in an environment such as the central immune system, we start with the experimental fact that the level of anti-idiotypes is low in autoimmune patients but high in healthy individuals, and present a quantitative model. This is then used to develop an adaptive control strategy that induces a transition back to the tolerant, healthy, state and thus offers a vista of treating autoimmune diseases caused by the failure of idiotypic control of autoreactive B cells. The idea is to introduce an antigen or anti-idiotype that binds to the autoantibodies with high affinity, and to determine whether or not a fixed dose is to be injected depending on the autoantibody titer exceeding or not exceeding a threshold. Quantitative criteria are provided. The procedure is the more adaptive in that monitoring the autoantibody titer need only happen every x-th day where x can greatly exceed one. Adaptive control turns out to be robust. The arguments presented here also give a quantitative explanation of why the antigen-autoantibody interaction has to be specific so as to induce a backward transition and why an IVIg treatment therefore does not lead to a permanent improvement.

Antibodies, Anti-Idiotypic↗
PubMed1991

DNA bending by Fos and Jun: the flexible hinge model.

DNA bending is essential for the assembly of multiprotein complexes that contact several DNA sequence elements. An approach based on phasing analysis was developed that allows determination of both the directed DNA bend angle and the orientation of DNA bending. This technique has been applied to the analysis of DNA bending by the transcription regulatory proteins Fos and Jun. Complexes that contained different combinations of full-length and truncated Fos and Jun induced DNA bends of different magnitudes and orientations. The DNA bends induced by the individual proteins were determined on the basis of a quantitative model for DNA bending by dimeric complexes. This information was used to visualize the consequences of DNA bending by Fos and Jun for the structures of Fos-Jun-DNA and Jun-DNA complexes.

Computer Graphics↗
PubMed2005

A simple model for the cooperative stabilisation of actin filaments by phalloidin and jasplakinolide.

The stabilisation of magnesium actin filaments by phalloidin and jasplakinolide was studied using the method of differential scanning calorimetry. The results showed that actin could adapt three conformations in the presence of drugs. One conformation was adapted in direct interaction with the drug, while another conformation was identical to that observed in the absence of drugs. A third conformation was induced through allosteric inter-protomer interactions. The effect of both drugs propagated cooperatively along the actin filaments. The number of the cooperative units determined by using a quantitative model was larger for jasplakinolide (15 actin protomers) than for phalloidin (7 protomers).

Actin Cytoskeleton↗
PubMed2004

Critical conditions for pattern formation and in vitro tubulogenesis driven by cellular traction fields.

In vitro angiogenesis assays have shown that tubulogenesis of endothelial cells within biogels, like collagen or fibrin gels, only appears for a critical range of experimental parameter values. These experiments have enabled us to develop and validate a theoretical model in which mechanical interactions of endothelial cells with extracellular matrix influence both active cell migration--haptotaxis--and cellular traction forces. Depending on the number of cells, cell motility and biogel rheological properties, various 2D endothelial patterns can be generated, from non-connected stripe patterns to fully connected networks, which mimic the spatial organization of capillary structures. The model quantitatively and qualitatively reproduces the range of critical values of cell densities and fibrin concentrations for which these cell networks are experimentally observed. We illustrate how cell motility is associated to the self-enhancement of the local traction fields exerted within the biogel in order to produce a pre-patterning of this matrix and subsequent formation of tubular structures, above critical thresholds corresponding to bifurcation points of the mathematical model. The dynamics of this morphogenetic process is discussed in the light of videomicroscopy time lapse sequences of endothelial cells (EAhy926 line) in fibrin gels. Our modeling approach also explains how the progressive appearance and morphology of the cellular networks are modified by gradients of extracellular matrix thickness.

Biomechanical Phenomena↗
PubMed2006

Food webs: experts consuming families of experts.

Food webs of habitats as diverse as lakes or desert valleys are known to exhibit common "food-web patterns", but the detailed mechanisms generating these structures have remained unclear. By employing a stochastic, dynamical model, we show that many aspects of the structure of predatory food webs can be understood as the traces of an evolutionary history where newly evolving species avoid direct competition with their relatives. The tendency to avoid sharing natural enemies (apparent competition) with related species is considerably weaker. Thus, "experts consuming families of experts" can be identified as the main underlying food-web pattern. We report the results of a systematic, quantitative model validation showing that the model is surprisingly accurate.

Animals↗
PubMed2004

Synergistic interactions of lipids and myelin basic protein.

This report describes force measurements and atomic force microscope imaging of lipid-protein interactions that determine the structure of a model membrane system that closely mimics the myelin sheath. Our results suggest that noncovalent, mainly electrostatic and hydrophobic, interactions are responsible for the multilamellar structure and stability of myelin. We find that myelin basic protein acts as a lipid coupler between two apposed bilayers and as a lipid "hole-filler," effectively preventing defect holes from developing. From our protein-mediated-adhesion and force-distance measurements, we develop a simple quantitative model that gives a reasonably accurate picture of the molecular mechanism and adhesion of bilayer-bridging proteins by means of noncovalent interactions. The results and model indicate that optimum myelin adhesion and stability depend on the difference between, rather than the product of, the opposite charges on the lipid bilayers and myelin basic protein, as well as on the repulsive forces associated with membrane fluidity, and that small changes in any of these parameters away from the synergistically optimum values can lead to large changes in the adhesion or even its total elimination. Our results also show that the often-asked question of which membrane species, the lipids or the proteins, are the "important ones" may be misplaced. Both components work synergistically to provide the adhesion and overall structure. A better appreciation of the mechanism of this synergy may allow for a better understanding of stacked and especially myelin membrane structures and may lead to better treatments for demyelinating diseases such as multiple sclerosis.

Hydrophobic and Hydrophilic Interactions↗
PubMed1996

Efficiency of DNA replication in the polymerase chain reaction.

A detailed quantitative kinetic model for the polymerase chain reaction (PCR) is developed, which allows us to predict the probability of replication of a DNA molecule in terms of the physical parameters involved in the system. The important issue of the determination of the number of PCR cycles during which this probability can be considered to be a constant is solved within the framework of the model. New phenomena of multimodality and scaling behavior in the distribution of the number of molecules after a given number of PCR cycles are presented. The relevance of the model for quantitative PCR is discussed, and a novel quantitative PCR technique is proposed.

DNA Replication↗
PubMed2002

Polarized angular dependent spectroscopy of epithelial cells and epithelial cell nuclei to determine the size scale of scattering structures.

An understanding of the relationship between tissue structures and light scattering from tissue will help facilitate the development and acceptance of noninvasive optical diagnostics including elastic scattering spectroscopy, diffuse reflectance, and optical coherence tomography. For example, a quantitative model of the structures that scatter light in epithelial cells would allow determination of what structures control the characteristics of in vivo light transport measurements and subsequently could provide a detailed relationship between cellular structures and optical measurements. We have determined the size distribution of refractive index structure variations in epithelial cells as well as in nuclei isolated from epithelial cells from measurements of the angular dependence of polarized light scattering. The quantitative size distributions we obtained for both whole cells and isolated nuclei include particles with effective radii of 2 microm to 10 nm or less and contain orders of magnitude more small particles than large particles. These results demonstrate that not only are biological cells very heterogeneous, but so are the nuclei within them. Light scattering is likely sensitive to structures smaller than those commonly investigated by standard pathology methods.

Animals↗