Identification of biomolecule mass transport and binding rate parameters in living cells by inverse modeling

BACKGROUND: Quantification of in-vivo biomolecule mass transport and reaction rate parameters from experimental data obtained by Fluorescence Recovery after Photobleaching (FRAP) is becoming more important. METHODS AND RESULTS: The Osborne-Moré extended version of the Levenberg-Marquardt optimization algorithm was coupled with the experimental data obtained by the Fluorescence Recovery after Photobleaching (FRAP) protocol, and the numerical solution of a set of two partial differential equations governing macromolecule mass transport and reaction in living cells, to inversely estimate optimized values of the molecular diffusion coefficient and binding rate parameters of GFP-tagged glucocorticoid receptor. The results indicate that the FRAP protocol provides enough information to estimate one parameter uniquely using a nonlinear optimization technique. Coupling FRAP experimental data with the inverse modeling strategy, one can also uniquely estimate the individual values of the binding rate coefficients if the molecular diffusion coefficient is known. One can also simultaneously estimate the dissociation rate parameter and molecular diffusion coefficient given the pseudo-association rate parameter is known. However, the protocol provides insufficient information for unique simultaneous estimation of three parameters (diffusion coefficient and binding rate parameters) owing to the high intercorrelation between the molecular diffusion coefficient and pseudo-association rate parameter. Attempts to estimate macromolecule mass transport and binding rate parameters simultaneously from FRAP data result in misleading conclusions regarding concentrations of free macromolecule and bound complex inside the cell, average binding time per vacant site, average time for diffusion of macromolecules from one site to the next, and slow or rapid mobility of biomolecules in cells. CONCLUSION: To obtain unique values for molecular diffusion coefficient and binding rate parameters from FRAP data, we propose conducting two FRAP experiments on the same class of macromolecule and cell. One experiment should be used to measure the molecular diffusion coefficient independently of binding in an effective diffusion regime and the other should be conducted in a reaction dominant or reaction-diffusion regime to quantify binding rate parameters. The method described in this paper is likely to be widely used to estimate in-vivo biomolecule mass transport and binding rate parameters

Disease-Toxicant Interactions in Manganese Exposed Huntington Disease Mice: Early Changes in Striatal Neuron Morphology and Dopamine Metabolism

YAC128 Huntington's disease (HD) transgenic mice accumulate less manganese (Mn) in the striatum relative to wild-type (WT) littermates. We hypothesized that Mn and mutant Huntingtin (HTT) would exhibit gene-environment interactions at the level of neurochemistry and neuronal morphology. Twelve-week-old WT and YAC128 mice were exposed to MnCl2-4H2O (50 mg/kg) on days 0, 3 and 6. Striatal medium spiny neuron (MSN) morphology, as well as levels of dopamine (DA) and its metabolites (which are known to be sensitive to Mn-exposure), were analyzed at 13 weeks (7 days from initial exposure) and 16 weeks (28 days from initial exposure). No genotype-dependent differences in MSN morphology were apparent at 13 weeks. But at 16 weeks, a genotype effect was observed in YAC128 mice, manifested by an absence of the wild-type age-dependent increase in dendritic length and branching complexity. In addition, genotype-exposure interaction effects were observed for dendritic complexity measures as a function of distance from the soma, where only YAC128 mice were sensitive to Mn exposure. Furthermore, striatal DA levels were unaltered at 13 weeks by genotype or Mn exposure, but at 16 weeks, both Mn exposure and the HD genotype were associated with quantitatively similar reductions in DA and its metabolites. Interestingly, Mn exposure of YAC128 mice did not further decrease DA or its metabolites versus YAC128 vehicle exposed or Mn exposed WT mice. Taken together, these results demonstrate Mn-HD disease-toxicant interactions at the onset of striatal dendritic neuropathology in YAC128 mice. Our results identify the earliest pathological change in striatum of YAC128 mice as being between 13 to 16 weeks. Finally, we show that mutant HTT suppresses some Mn-dependent changes, such as decreased DA levels, while it exacerbates others, such as dendritic pathology

Comparison of the Left Main Coronary Bifurcating Angle among Patients with Normal, Non-significantly and Significantly Stenosed Left Coronary Arteries

[[abstract]]We evaluated the correlation of the left main coronary bifurcating angle (LCBA) with the severity of coronary atherosclerosis, risk factors of coronary artery disease (CAD) and the feasibility of measuring the LBCA using the axial plane. Coronary Computed tomography angiographies (CTAs) of 313 patients between Nov. 2006 and Oct. 2013 were reviewed and separated into three groups. Group I (211 patients) had significant stenosis (≥50%) of the left anterior descending coronary artery (LAD) and/or left circumflex coronary artery (LCX). Group II (62 subjects) had atherosclerosis without significant stenosis. Group III (40 subjects) had unremarkable coronary CTAs. Both Group I and II patients received conventional catheter angiography to confirm the severities of coronary stenoses. Significant differences were found among the groups with respect to risk factors, such as male gender, hypertension and body mass index. Axial plane measurement was feasible in most patients (82.1%), without significant differences among the groups. The mean LCBA was 84.7° among all patients, and significantly differed among groups I, II and III (87.34°, 81.16° and 75.53°, P < 0.001). The LCBA of group I was significantly higher than group III (P < 0.001) in univariate analysis, but insignificant in multivariate analysis (P = 0.064)

Population size estimation for capture - recapture models with applications to epidemiological data

[[abstract]]The capture-recapture method is applied to estimate the population size of a target population based on ascertainment data in epidemiological applications. We generalize the three-list case of Chao & Tsay (1998) to situations where more than three lists are available. An estimation procedure is presented using the concept of sample coverage, which can be interpreted as a measure of overlap information among multiple list records. When there is enough overlap, an estimator of the total population size is proposed. The bootstrap method is used to construct a variance estimator and confidence interval. If the overlap rate is relatively low, then the population size cannot be precisely estimated and thus only a lower (upper) bound is proposed for positively (negatively) dependent lists. The proposed method is applied to two data sets, one with a high and one with a low overlap rate.[[fileno]]2010409010034[[department]]統計