Comparative study of parameter sensitivity analyses of the TCR-activated Erk-MAPK signalling pathway

Parameter estimation is a major challenge for mathematical modelling of biological systems. Given the uncertainties associated with model parameters, it is important to understand how sensitive the model output is to variations in parameter values. A local sensitivity analysis determines the model sensitivity to parameter variations over a localised region around the nominal parameter values, whereas a global sensitivity analysis (GSA) investigates the sensitivity over the entire parameter space. Using a T-cell receptor-activated Erk-MAPK signalling pathway model as an example, the authors present a comparative study of a variety of different sensitivity analysis techniques. These techniques include: local sensitivity analysis, existing GSA methods of partial rank correlation coefficient, Sobol's, extended Fourier amplitude sensitivity test, as well as a weighted average of local sensitivities and a new GSA method to extract global parameter sensitivities from a parameter identification routine. Results of this study revealed critical reactions in the signalling pathway and their impact on the signalling dynamics and provided insights into embedded regulatory mechanisms such as feedback loops in the pathway. From this study, a recommendation emerges for a general sensitivity analysis strategy to efficiently and reliably infer quantitative, dynamic as well as topological properties from systems biology models.     

Increased sensitivity of the fatty tissue of rats with spontaneous hypertension to the action of ACTH. The role of calcium]

The action of ACTH on the adipose tissue lypolysis was studied in rats with spontaneous and renal hypertension as well as in normotensive rats of the respective control groups. It was demonstrated that sensitivity of the adipose tissue SHR to ACTH was increased as compared to normotensive controls. The data presented indicate that the increased sensitivity is due to the state or content of intracellular calcium. The rats with renal hypertension did not show such an increased sensitivity of the adipose tissue to ACTH.     

Structural sensitivity of biological models revisited

Enhancing the predictive power of models in biology is a challenging issue. Among the major difficulties impeding model development and implementation are the sensitivity of outcomes to variations in model parameters, the problem of choosing of particular expressions for the parametrization of functional relations, and difficulties in validating models using laboratory data and/or field observations. In this paper, we revisit the phenomenon which is referred to as structural sensitivity of a model. Structural sensitivity arises as a result of the interplay between sensitivity of model outcomes to variations in parameters and sensitivity to the choice of model functions, and this can be somewhat of a bottleneck in improving the models predictive power. We provide a rigorous definition of structural sensitivity and we show how we can quantify the degree of sensitivity of a model based on the Hausdorff distance concept. We propose a simple semi-analytical test of structural sensitivity in an ODE modeling framework. Furthermore, we emphasize the importance of directly linking the variability of field/experimental data and model predictions, and we demonstrate a way of assessing the robustness of modeling predictions with respect to data sampling variability. As an insightful illustrative example, we test our sensitivity analysis methods on a chemostat predator-prey model, where we use laboratory data on the feeding of protozoa to parameterize the predator functional response.     

Predictors of Species Sensitivity to Fragmentation

We reviewed empirical data and hypotheses derived from demographic, optimal foraging, life-history, community, and biogeographic theory for predicting the sensitivity of species to habitat fragmentation. We found 12 traits or trait groups that have been suggested as predictors of species sensitivity: population size; population fluctuation and storage effect; dispersal power; reproductive potential; annual survival; sociality; body size; trophic position; ecological specialisation, microhabitat and matrix use; disturbance and competition sensitive traits; rarity; and biogeographic position. For each trait we discuss the theoretical justification for its sensitivity to fragmentation and empirical evidence for and against the suitability of the trait as a predictor of fragmentation sensitivity. Where relevant, we also discuss experimental design problems for testing the underlying hypotheses. There is good empirical support for 6 of the 12 traits as sensitivity predictors: population size; population fluctuation and storage effects; traits associated with competitive ability and disturbance sensitivity in plants; microhabitat specialisation and matrix use; rarity in the form of low abundance within a habitat; and relative biogeographic position. Few clear patterns emerge for the remaining traits from empirical studies if examined in isolation. Consequently, interactions of species traits and environmental conditions must be considered if we want to be able to predict species sensitivity to fragmentation. We develop a classification of fragmentation sensitivity based on specific trait combinations and discuss the implications of the results for ecological theory.     

Prosimian sensory capacities

This paper reviews laboratory research on sensory capacities of prosimians. Most investigations to date have concentrated on visual and auditory sensitivity with relatively little attention directed toward olfactory and gustatory sensitivity. Diurnal prosimians have at least rudimentary color vision and appear deficient to anthropoids in other visual measures such as acuity. The most striking difference between prosimian and anthropoid auditory sensitivity is the increased sensitivity of the former group to high frequencies. No psychophysical data have been published on olfactory sensitivity of prosimians, but the relatively large olfactory areas in their brains and their propensity for scent marking strongly suggest that they have acute olfactory sensitivity. Most data on gustatory thresholds in prosimians does not permit sensitivity estimation since the data are joint functions of sensitivity as well as preferences.     

The tuning of striate neurons to cross-like figures during local blockade of intracortical inhibition]

Many neurons in the cat primary visual cortex reveal sensitivity to cruciform and corner figures as well as to local orientation discontinuities. We investigated this sensitivity in 85 V1 neurons before and after the local blockade of GABA(A)ergic inhibition by microiontophoretic application of bicuculline and observed two opposite effects: a decrease or disappearance of sensitivity to crosses in about half of the neurons and its increase or appearance in about one third of the units. The results indicate substantial and drastically different contribution of intracortical inhibition to sensitivity to line-crossings in the visual cortical neurons. Some possible mechanisms of this difference are discussed.     

Limited predictive ability of surrogate indices of insulin sensitivity/resistance in Asian-Indian men

Insulin resistance is highly prevalent in Asian Indians and contributes to worldwide public health problems, including diabetes and related disorders. Surrogate measurements of insulin sensitivity/resistance are used frequently to study Asian Indians, but these are not formally validated in this population. In this study, we compared the ability of simple surrogate indices to accurately predict insulin sensitivity as determined by the reference glucose clamp method. In this cross-sectional study of Asian-Indian men (n = 70), we used a calibration model to assess the ability of simple surrogate indices for insulin sensitivity [quantitative insulin sensitivity check index (QUICKI), homeostasis model assessment (HOMA2-IR), fasting insulin-to-glucose ratio (FIGR), and fasting insulin (FI)] to predict an insulin sensitivity index derived from the reference glucose clamp method (SI(Clamp)). Predictive accuracy was assessed by both root mean squared error (RMSE) of prediction as well as leave-one-out cross-validation-type RMSE of prediction (CVPE). QUICKI, FIGR, and FI, but not HOMA2-IR, had modest linear correlations with SI(Clamp) (QUICKI: r = 0.36; FIGR: r = -0.36; FI: r = -0.27; P < 0.05). No significant differences were noted among CVPE or RMSE from any of the surrogate indices when compared with QUICKI. Surrogate measurements of insulin sensitivity/resistance such as QUICKI, FIGR, and FI are easily obtainable in large clinical studies, but these may only be useful as secondary outcome measurements in assessing insulin sensitivity/resistance in clinical studies of Asian Indians.     

OGTT-derived measures of insulin sensitivity are confounded by factors other than insulin sensitivity itself

Insulin resistance is an important risk factor for diabetes and other diseases. It has been important to estimate insulin resistance in epidemiological and genetic studies involving significant number of individuals. Complex and invasive protocols are impractical. Therefore, insulin sensitivity indices based on the oral glucose-tolerance test (OGTT) have been introduced. The aim of the present study was to assess the accuracy with which OGTT-derived indices would reflect changes in insulin sensitivity in the face of changes in other factors, such as rate of glucose absorption and/or B-cell function. A computer model was employed to predict excursions of plasma glucose and insulin after a 75-g oral glucose load. The model was then used to predict changes in these excursions, which would be observed with altered insulin resistance, with alterations in beta-cell sensitivity to glucose and/or alterations in glucose absorption rates. Published indices of insulin sensitivity could then be calculated from the predicted curves, to ask whether changes in beta-cell function or glucose absorptions rates might be misinterpreted (using the indices) as changes in insulin sensitivity. The model accurately represented OGTT data for a normal glucose tolerant subject, closely matching published data. Imposed 50% reductions or increases in insulin sensitivity alone in the model were reflected in only small changes in OGTT-derived insulin sensitivity values. More important, imposed alterations in beta-cell sensitivity and glucose absorption without simulated changes in insulin sensitivity did change insulin sensitivity indices. These results indicate that caution is required for the interpretation of differences in OGTT-derived values of insulin sensitivity, because variation in factors other than insulin sensitivity per se appear to have the greatest effects on indices calculated from the OGTT alone.     

Characterization of sensitivity and specificity of fluorescent markers of structural state and binding ability of proteins

Methods for determining the sensitivity of fluorescent probes and their classification with respect to sensitivity and specificity using human serum albumin as a reference protein and 8-anili-nonaphthalenesulfonate, K35 and pyron red as probes are proposed. The indicators of sensitivity and specificity of fluorescent probes as markers of the structural state of proteins are the activation of the probe fluorescence in excess of protein and the constant of its binding to the strong highly affine center of protein sorption. Fluorescent probes as markers of the binding ability are assessed by a protein-dependent increase in fluorescence under the conditions of excess probe and from the constant of its binding to weak secondary binding sites of the protein.     

Properties of cells determining their immunosensitivity

Three cell cultures of C3H mouse strain--L, MMT1 and embryonic fibroblasts have different sensitivity to cytolytic action of allogeneic antiserum and to immune lymphocyte action. A sensitivity to cytolytic action of antiserum for these cultures is correlated with the amount of corresponding transplantation antigens. A sensitivity to cytolytic action of immune allogeneic lymphocytes is correlated with the amount of corresponding antigens as well as cell with properties determining the level of lymphocyte sorption on them.     

The visual sensitivity of the retina of the conger eel

We measured the visual sensitivity of the conger eel retina by means of its electroretinogram (e.r.g.) and whole nerve responses. The spectral sensitivity of the retina closely corresponded to a prediction based on the density spectrum of the conger visual pigment, measured in situ. The pigment density in the conger eel retina is high, perhaps as high as 1.0. Thus, the predicted spectral sensitivity would be much broader than is observed if the absorption spectrum of the pigment governed the visual sensitivity. The reason why the visual spectral sensitivity corresponds to the density spectrum and not to the absorption spectrum is that the photoreceptors in the conger eye are arranged in tiers and only the inner tier contributes to vision.     

Patterns of anthracycline retention modulation in human tumor cells

Laser excitation of cellular doxorubicin and daunomycin content (with or without incubation in the presence of efflux blockers such as phenothiazines or verapamil) was studied in cells from leukemic peripheral blood, bone marrow aspirates, and ascites and pleural fluid of solid tumor patients. Selected examples are presented to show that heterogeneity in cellular anthracycline retention as well as sensitivity to efflux modulators is seen in human tumor cells. Several tumor subpopulations differing in their cellular retention of anthracyclines or sensitivity to modulators were seen. In serial tumor samples from patients (pre- and post-treatment with anthracycline-containing protocols), initial drug retention and sensitivity to efflux modulators was followed by lack of drug retention and insensitivity to modulators. The present study shows that in view of the variables encountered in drug-retention characteristics and sensitivity to efflux modulators, one needs to screen tumor samples before recommending use of any particular transport modulator to enhance drug retention and sensitivity of drug-resistant cells.     

The nuclease sensitivity of active genes.

Brief micrococcal nuclease digestion of chick embryonic red blood cells results in preferential excision and solubilization of monomer nucleosomes associated with beta-globin sequences and also 5'-sequences flanking the beta-globin gene. Both regions are DNAse-I sensitive in nuclei. Such salt-soluble nucleosomes are enriched in all four major HMG proteins but HMG1 and 2 are only weakly associated. These nucleosomes appear to have lost much of the DNAse-I sensitivity of active genes. The HMG14 and 17-containing salt-soluble nucleosomes separated by electrophoresis are not DNAse-I sensitive and contain inactive gene sequences as well as active sequences. Reconstitution of HMG proteins onto bulk nucleosomes or chromatin failed to reveal an HMG-dependent sensitivity of active genes as assayed by dot-blot hybridization and it was found that the DNAse-I sensitivity of ASV proviral sequences as assayed by dot-blot hybridization was not HMG-dependent. These results indicate that higher order chromatin structures might be responsible for nuclease sensitivity of active genes.     

Influence of the stage of the cycle on olfactory sensitivity in laboratory mice

Females in estrus showed maximum olfactory sensitivity as judged by their ability in locating the buried bait. The results suggest that olfactory sensitivity in females varies during the stages of the estrous cycle. The findings further indicate that gonadal steroids play an important role in the expression of olfactory sensitivity in females.     

Reduced alpha(2)-adrenergic sensitivity of subcutaneous abdominal adipocytes as a modulator of fasting and postprandial triglyceride levels in men

This study examined the postprandial lipemia of two groups of men displaying similar age, body weight, and regional fat distribution, but characterized by either low (n = 11) or high (n = 15) alpha(2)-adrenergic sensitivity of subcutaneous abdominal adipocytes. In addition to fat cell lipolysis, adipose tissue lipoprotein lipase (AT-LPL) as well as postheparin plasma LPL activities were measured in the fasting state. Fasting AT-LPL and PH-LPL activities were similar in both groups. Maximal adipose cell lipolysis induced by isoproterenol (beta-adrenergic agonist) as well as the beta-adrenergic sensitivity did not differ between both groups of men. The selective alpha(2)-adrenergic agonist UK-14304 promoted a similar antilipolytic response in subcutaneous abdominal adipocytes from both groups. However, the alpha(2)-adrenergic sensitivity, defined as the dose of UK-14304 that produced half-maximal inhibition of lipolysis (IC(50)), was significantly different between groups (P < 0.0001). Men with low versus high subcutaneous abdominal fat cell alpha(2)-adrenergic sensitivity showed higher fasting TG levels. In the whole group, a positive relationship was observed between log-transformed IC(50) UK-14304 values of subcutaneous adipocytes and fasting TG levels (r = 0.39, P < 0.05), suggesting that a low abdominal adipose cell alpha(2)-adrenergic sensitivity is associated with high TG levels. After the consumption of a high-fat meal, subjects with low subcutaneous abdominal adipose cell alpha(2)-adrenergic sensitivity showed higher TG levels in total, medium, and small triglyceride-rich lipoprotein (TRL) fractions at 0- to 6-h time points than men with high adipocyte alpha(2)-adrenergic sensitivity (P values ranging from 0.01 to 0.05). Stepwise regression analysis showed that the fasting TG concentration was the only variable retained as a significant predictor of the area under the curve of TG levels in total TRL fractions (73% of variance) among independent variables such as body weight, percent body fat, visceral and subcutaneous abdominal adipose tissue accumulation measured by CT, as well as subcutaneous abdominal fat cell alpha(2)-adrenoceptor sensitivity.Taken together, these results indicate that a reduced antilipolytic sensitivity of subcutaneous abdominal adipocytes to catecholamines may increase fasting TG levels, which in turn play a role in the etiology of an impaired postprandial TRL clearance in men.     

Genetic Variability for Density Sensitivity of Three Components of Fitness in DROSOPHILA MELANOGASTER

This study examines natural genetic variation in density sensitivity of three components of fitness in Drosophila melanogaster using the method of chromosome extraction. Different lines are differentially sensitive to density. The distribution of measures of density sensitivity of chromosomal homozygotes is different from that of random chromosomal heterozygotes for both location and dispersion. Density sensitivity of the components is about as variable as any of the fitness components themselves at fixed densities. The consequences of the exact nature of this density dependence are discussed with respect to the stage of the life cycle at which density dependence occurs, and the mathematical form that it takes. There is no evidence of trade-offs among the components or their density sensitivity.     

Sensitivity of Vibrio and Aeromonas to antibiotics]

The antibiotic sensitivity of 696 cultures belonging to the family Vibrionaceae (V. cholerae O1, V. cholerae non-O1, V. albensis, V. parahaemolyticus, V. alginolyticus and Aeromonas spp.) was studied and general regularities of the antibiotic sensitivity were shown: a high sensitivity to broad-spectrum antibiotics (tetracycline and chloramphenicol) and a low sensitivity to ++beta lactams (carbenicillin and ampicillin). The comparative examinations revealed similarity in the antibioticograms of V. cholerae O1 (el Tor++), V. cholerae non-O1 and V. albensis, especially the latter two groups, as well as the tested halophilic Vibrio cultures by the range of the MICs, Mo, Me and the nature of the antibiotic resistance. Cultures of V. cholerae and luminescent Vibrio tended to preserve a high sensitivity. High resistance levels were noted in the halophilic Vibrio and Aeromonas cultures. No significant differences in the sensitivity of the strains of various origin (from man and environmental objects) were detected. However, several more resistant strains were isolated from the environmental objects.     

Sensitivity of ex situ and in situ spectral surface plasmon resonance sensors in the analysis of protein arrays

We have investigated the sensitivity of ex situ (analysis under air condition) and in situ (analysis under liquid condition) spectral SPR sensors, which were self-constructed with fiber optic spectrometers. The sensitivity of SPR sensors was analyzed in the wavelength range of 550-780 nm by the interactions of streptavidin and biotinylated IgG, and the sensitivity was dependent on the wavelength of measurements. The sensitivity of an ex situ SPR sensor operated at the long wavelength range from 712 nm was approximately 2.6 times higher than that at the short wavelength range from 571 nm. In addition, the sensitivity of an ex situ spectral SPR sensor was about twice as high as that of an in situ spectral SPR sensor for the same resonance wavelength range. This was interpreted in that the difference in sensitivity between two SPR sensors was significantly caused by the evanescent field intensity at the metal/dielectric interface. Thus, it was suggested that ex situ spectral SPR sensors operated at the long wavelength range are sensitive biosensors for the high-throughput analysis of protein interactions on protein arrays.     

Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms.

The sensitivity and selectivity of the FASTA and the Smith-Waterman protein sequence comparison algorithms were evaluated using the superfamily classification provided in the National Biomedical Research Foundation/Protein Identification Resource (PIR) protein sequence database. Sequences from each of the 34 superfamilies in the PIR database with 20 or more members were compared against the protein sequence database. The similarity scores of the related and unrelated sequences were determined using either the FASTA program or the Smith-Waterman local similarity algorithm. These two sets of similarity scores were used to evaluate the ability of the two comparison algorithms to identify distantly related protein sequences. The FASTA program using the ktup = 2 sensitivity setting performed as well as the Smith-Waterman algorithm for 19 of the 34 superfamilies. Increasing the sensitivity by setting ktup = 1 allowed FASTA to perform as well as Smith-Waterman on an additional 7 superfamilies. The rigorous Smith-Waterman method performed better than FASTA with ktup = 1 on 8 superfamilies, including the globins, immunoglobulin variable regions, calmodulins, and plastocyanins. Several strategies for improving the sensitivity of FASTA were examined. The greatest improvement in sensitivity was achieved by optimizing a band around the best initial region found for every library sequence. For every superfamily except the globins and immunoglobulin variable regions, this strategy was as sensitive as a full Smith-Waterman. For some sequences, additional sensitivity was achieved by including conserved but nonidentical residues in the lookup table used to identify the initial region.     

Role of carbohydrates in diurnal chilling sensitivity of tomato seedlings

Tomato seedlings (Lycopersicon esculentum Mill.) chilled starting at different times during the light/dark cycle were most chilling-sensitive at the end of the dark period (AI King, MS Reid, BD Patterson 1982 Plant Physiol 70: 211-214). Low-temperature tolerance was regained with as little as 10 minutes of light exposure. Low light intensities were less effective than high light intensities in reducing sensitivity, and the length of exposure to light directly influenced sensitivity. Seedlings kept at low night temperatures prior to chilling were also less injured following chilling. Light also restored chilling tolerance to seedlings whose roots were removed. Supplying cut shoots with sucrose, glucose, or fructose reduced chilling sensitivity and largely eliminated the diurnal difference in sensitivity. Endogenous carbohydrate content was correlated with changes in chilling sensitivity; starch and sugar content fell markedly during the dark period. Increased concentrations of sugars were detected 15 minutes after the start of the light period. This evidence all suggests that changes in chilling sensitivity over the diurnal period are regulated by the light cycle. It also suggests that increased sensitivity at the end of the dark period could be due to carbohydrate depletion, and that chilling tolerance following light exposure is likely due to carbohydrate accumulation or closely related events.