Non-Arrhenius kinetics for the loop closure of a DNA hairpin

Intramolecular chain diffusion is an elementary process in the conformational fluctuations of the DNA hairpin-loop. We have studied the temperature and viscosity dependence of a model DNA hairpin-loop by FRET (fluorescence resonance energy transfer) fluctuation spectroscopy (FRETfs). Apparent thermodynamic parameters were obtained by analyzing the correlation amplitude through a two-state model and are consistent with steady-state fluorescence measurements. The kinetics of closing the loop show non-Arrhenius behavior, in agreement with theoretical prediction and other experimental measurements on peptide folding. The fluctuation rates show a fractional power dependence (β = 0.83) on the solution viscosity. A much slower intrachain diffusion coefficient in comparison to that of polypeptides was derived based on the first passage time theory of SSS [Szabo, A., Schulten, K. & Schulten, Z. (1980) J. Chem. Phys. 72, 4350–4357], suggesting that intrachain interactions, especially stacking interaction in the loop, might increase the roughness of the free energy surface of the DNA hairpin-loop.

Quantitative ER ↔ Golgi Transport Kinetics and Protein Separation upon Golgi Exit Revealed by Vesicular Integral Membrane Protein 36 Dynamics in Live CellsV⃞

To quantitatively investigate the trafficking of the transmembrane lectin VIP36 and its relation to cargo-containing transport carriers (TCs), we analyzed a C-terminal fluorescent-protein (FP) fusion, VIP36-SP-FP. When expressed at moderate levels, VIP36-SP-FP localized to the endoplasmic reticulum, Golgi apparatus, and intermediate transport structures, and colocalized with epitope-tagged VIP36. Temperature shift and pharmacological experiments indicated VIP36-SP-FP recycled in the early secretory pathway, exhibiting trafficking representative of a class of transmembrane cargo receptors, including the closely related lectin ERGIC53. VIP36-SP-FP trafficking structures comprised tubules and globular elements, which translocated in a saltatory manner. Simultaneous visualization of anterograde secretory cargo and VIP36-SP-FP indicated that the globular structures were pre-Golgi carriers, and that VIP36-SP-FP segregated from cargo within the Golgi and was not included in post-Golgi TCs. Organelle-specific bleach experiments directly measured the exchange of VIP36-SP-FP between the Golgi and endoplasmic reticulum (ER). Fitting a two-compartment model to the recovery data predicted first order rate constants of 1.22 ± 0.44%/min for ER → Golgi, and 7.68 ± 1.94%/min for Golgi → ER transport, revealing a half-time of 113 ± 70 min for leaving the ER and 1.67 ± 0.45 min for leaving the Golgi, and accounting for the measured steady-state distribution of VIP36-SP-FP (13% Golgi/87% ER). Perturbing transport with AlF4− treatment altered VIP36-SP-GFP distribution and changed the rate constants. The parameters of the model suggest that relatively small differences in the first order rate constants, perhaps manifested in subtle differences in the tendency to enter distinct TCs, result in large differences in the steady-state localization of secretory components.

Rapid activation of Na+/H+ exchange by aldosterone in renal epithelial cells requires Ca2+ and stimulation of a plasma membrane proton conductance.

There is increasing evidence for an additional acute, nongenomic action of the mineralocorticoid hormone aldosterone on renal epithelial cells, leading to a two-step model of mineralocorticoid action on electrolyte excretion. We investigated the acute effect of aldosterone on intracellular free Ca2+ and on intracellular pH in an aldosterone-sensitive Madin-Darby canine kidney cell clone. Within seconds of application of aldosterone, but not of the glucocorticoid hydrocortisone, there was a 3-fold sustained increase of intracellular Ca2+ at a half-maximal concentration of 10(-10) mol/liter. Omission of extracellular Ca2+ prevented this hormone response. In the presence of extracellular Ca2+ aldosterone led to intracellular alkalinization. The Na+/H+ exchange inhibitor ethyl-isopropanol-amiloride (EIPA) prevented the aldosterone-induced alkalinization but not the aldosterone-induced increase of intracellular Ca2+. Omission of extracellular Ca2+ also prevented aldosterone-induced alkalinization. Instead, aldosterone led to a Zn(2+)-dependent intracellular acidification in the presence of EIPA, indicative of an increase of plasma membrane proton conductance. Under control conditions, Zn2+ prevented the aldosterone-induced alkalinization completely. We conclude that aldosterone stimulated net-entry of Ca2+ from the extracellular compartment and a plasma membrane H+ conductance as prerequisites for the stimulation of plasma membrane Na+/H+ exchange which in turn modulates K+ channel acitivity. It is probable that the aldosterone-sensitive H+ conductance maintains Na+/H+ exchange activity by providing an acidic environment in the vicinity of the exchanger. Thus, genomic action of aldosterone determines cellular transport equipment, whereas the nongenomic action regulates transporter activity that requires responses within seconds or minutes, which explains the rapid effects on electrolyte excretion.

Microsatellite variability and genetic distances.

We analyze the within- and between-population dynamics of the distribution of the number of repeats at multiple microsatellite DNA loci subject to stepwise mutation. Analytical expressions for moments up to the fourth order within a locus and the variance of between-locus variance at mutation-drift equilibrium have been obtained. These statistics may be used to test the appropriateness of the one-step mutation model and to detect between-locus variation in the mutation rate. Published data are compatible with the one-step mutation model, although they do not reject the two-step model. Using both multinomial sampling and diffusion approximations for the analysis of the genetic distance introduced by Goldstein et al. [Goldstein, D. B., Linares, A. R., Cavalli-Sforza, L. L. & Feldman, M. W. (1995) Proc. Natl. Acad. Sci. USA 92, 6723-6727], we show that this distance follows a chi 2 distribution with degrees of freedom equal to the number of loci when there is no variation in mutation rates among the loci. In the presence of such variation, the variance of the distance is obtained. We conclude that the number of microsatellite loci required for the construction of phylogenetic trees with reliable branch lengths may be several hundred. Also, mutations that change repeat scores by several units, even though extremely rare, may dramatically influence estimates of population parameters.

Modelo tridimensional em elementos finitos para a análise de cabo umbilical STU submetido ao carregamento de crushing.

Este trabalho desenvolve e apresenta um modelo tridimensional em elementos finitos de um cabo umbilical do tipo STU (Steel Tube Umbilical) utilizado na extração offshore de petróleo. Tal modelo é utilizado para estudar o carregamento de crushing, que é imposto ao cabo umbilical pelas sapatas do tensionador durante o seu lançamento, de modo a obter de forma detalhada a distribuição de tensões nos componentes do núcleo, com foco nos tubos de aço utilizados para o transporte de fluidos. A metodologia empregada no desenvolvimento do modelo é descrita detalhadamente ao longo do trabalho, de forma que possa vir a ser utilizada no estudo de outras configurações de cabos umbilicais. O modelo elaborado é utilizado (i) como paradigma para a validação de um modelo bidimensional, que visa analisar o mesmo problema de forma mais simples e rápida, e (ii) para o estudo do comportamento das tensões nos tubos de aço na região de transição de entrada/saída da sapata. Na comparação entre os modelos bi e tridimensional, o trabalho conclui pela validade do modelo bidimensional na avaliação das tensões nos tubos de aço resultantes do carregamento de crushing, na região central do cabo. O estudo realizado na região de transição de entrada/saída da sapata permitiu verificar que ocorre um aumento dos níveis de tensão nos tubos de aço nessas regiões de transição, com redistribuição do campo de tensões após plastificação.

Equações de quarta ordem na modelagem de oscilações de pontes

Equações diferenciais de quarta ordem aparecem naturalmente na modelagem de oscilações de estruturas elásticas, como aquelas observadas em pontes pênseis. São considerados dois modelos que descrevem as oscilações no tabuleiro de uma ponte. No modelo unidimensional estudamos blow up em espaço finito de soluções de uma classe de equações diferenciais de quarta ordem. Os resultados apresentados solucionam uma conjectura apresentada em [F. Gazzola and R. Pavani. Wide oscillation finite time blow up for solutions to nonlinear fourth order differential equations. Arch. Ration. Mech. Anal., 207(2):717752, 2013] e implicam a não existência de ondas viajantes com baixa velocidade de propagação em uma viga. No modelo bidimensional analisamos uma equação não local para uma placa longa e fina, suportada nas extremidades menores, livre nas demais e sujeita a protensão. Provamos existência e unicidade de solução fraca e estudamos o seu comportamento assintótico sob amortecimento viscoso. Estudamos ainda a estabilidade de modos simples de oscilação, os quais são classificados como longitudinais ou torcionais.

Role of potassium orbitals in the metallic behavior of K3picene

Detailed electronic structure calculations of picene clusters doped by potassium modeling the crystalline K3picene structure show that while two electrons are completely transferred from potassium atoms to the lowest-energy unoccupied molecular orbital of pristine picene, the third one remains closely attached to both material components. Multiconfigurational analysis is necessary to show that many structures of almost degenerate total energies compete to define the cluster ground state. Our results prove that the 4s orbital of potassium should be included in any interaction model describing the material. We propose a quarter-filled two-orbital model as the most simple model capable of describing the electronic structure of K-intercalated picene. Precise solutions obtained by a development of the Lanczos method show low-energy electronic excitations involving orbitals located at different positions. Consequently, metallic transport is possible in spite of the clear dominance of interaction over hopping.

Ambient ozone pollution and daily mortality in three megacities in China

Thesis (Master's)--University of Washington, 2016-06

Population pharmacokinetic analysis of mycophenolic acid in renal transplant recipients following oral administration of mycophenolate mofetil

Aim To develop a population pharmacokinetic model for mycophenolic acid in adult kidney transplant recipients, quantifying average population pharmacokinetic parameter values, and between- and within-subject variability and to evaluate the influence of covariates on the pharmacokinetic variability. Methods Pharmacokinetic data for mycophenolic acid and covariate information were previously available from 22 patients who underwent kidney transplantation at the Princess Alexandra Hospital. All patients received mycophenolate mofetil 1 g orally twice daily. A total of 557 concentration-time points were available. Data were analysed using the first-order method in NONMEM (version 5 level 1.1) using the G77 FORTRAN compiler. Results The best base model was a two-compartment model with a lag time (apparent oral clearance was 271 h(-1), and apparent volume of the central compartment 981). There was visual evidence of complex absorption and time-dependent clearance processes, but they could not be successfully modelled in this study. Weight was investigated as a covariate, but no significant relationship was determined. Conclusions The complexity in determining the pharmacokinetics of mycophenolic acid is currently underestimated. More complex pharmacokinetic models, though not supported by the limited data collected for this study, may prove useful in the future. The large between-subject and between-occasion variability and the possibility of nonlinear processes associated with the pharmacokinetics of mycophenolic acid raise questions about the value of the use of therapeutic monitoring and limited sampling strategies.

Segregation distortion for seed testa color in mungbean (Vigna radiata L. Wilcek)

Genetic segregation experiments with plant species are commonly used for understanding the inheritance of traits. A basic assumption in these experiments is that each gamete developed from megasporogenesis has an equal chance of fusing with a gamete developed from microsporogenesis, and every zygote formed has an equal chance of survival. If gametic and/or zygotic selection occurs whereby certain gametes or zygotic combinations have a reduced chance of survival, progeny distributions are skewed and are said to exhibit segregation distortion. In this study, inheritance data are presented for the trait seed testa color segregating in large populations (more than 200 individuals) derived from closely related mungbean (Vigna radiata L. Wilcek) taxa. Segregation ratios suggested complex inheritance, including dominant and recessive epistasis. However, this genetic model was rejected in favor of a single-gene model based on evidence of segregation distortion provided by molecular marker data. The segregation distortion occurred after each generation of self-pollination from F-1 thru F-7 resulting in F-7 phenotypic frequencies of 151:56 instead of the expected 103.5:103.5. This study highlights the value of molecular markers for understanding the inheritance of a simply inherited trait influenced by segregation distortion.

Characterizing the physical and chemical properties of a vermicompost filter bed

Vermicompost filtration is a new on-site waste treatment system. Consequently, little is known about the filter medium properties. The aim of this preliminary study was to quantify physical and compositional properties of vermicompost filter beds that had been used to treat domestic solid organic waste and wastewater. This paper presents the trials performed on pilot-scale reactors filled with vermicompost from a full-scale vermicompost filtration system. Household solid organic waste and raw wastewater at the rate of 130 L/m(2)/d was applied to the reactor bed surface over a four-month period. It was found that fresh casts laid on the bed surface had a BOD of 1290 mg/g VS while casts buried to a depth of 10 cm had a BOD of 605 mg/g VS. Below this depth there was little further biodegradation of earthworm casts despite cast ages of up to five years. Solid material in the reactor accounted for only 7-10% of the reactor volume. The total voidage comprised of large free-draining pores, which accounted for 15-20% of the reactor volume and 60-70% micropores, able to hold up water against gravity. It was shown that water could flow through the medium micropores and macropores following a wastewater application. The wastewater flow characteristics were modeled by a two-region model based on the Richards Equation, an equation used to describe porous spatially heterogeneous materials.

Analysis of population pharmacokinetic data using NONMEM and WinBUGS

The aim of this report is to describe the use of WinBUGS for two datasets that arise from typical population pharmacokinetic studies. The first dataset relates to gentamicin concentration-time data that arose as part of routine clinical care of 55 neonates. The second dataset incorporated data from 96 patients receiving enoxaparin. Both datasets were originally analyzed by using NONMEM. In the first instance, although NONMEM provided reasonable estimates of the fixed effects parameters it was unable to provide satisfactory estimates of the between-subject variance. In the second instance, the use of NONMEM resulted in the development of a successful model, albeit with limited available information on the between-subject variability of the pharmacokinetic parameters. WinBUGS was used to develop a model for both of these datasets. Model comparison for the enoxaparin dataset was performed by using the posterior distribution of the log-likelihood and a posterior predictive check. The use of WinBUGS supported the same structural models tried in NONMEM. For the gentamicin dataset a one-compartment model with intravenous infusion was developed, and the population parameters including the full between-subject variance-covariance matrix were available. Analysis of the enoxaparin dataset supported a two compartment model as superior to the one-compartment model, based on the posterior predictive check. Again, the full between-subject variance-covariance matrix parameters were available. Fully Bayesian approaches using MCMC methods, via WinBUGS, can offer added value for analysis of population pharmacokinetic data.

Aeration for plant root respiration in a tidal marsh

This paper investigates the tidal effects on aeration conditions for plant root respiration in a tidal marsh. We extend the work of Ursino et al. ( 2004) by using a two-phase model for air and water flows in the marsh. Simulations have been conducted to examine directly the link between the airflow dynamics and the aeration condition in the marsh soil. The results show that the effects of entrapped air on water movement in the vadose zone are significant in certain circumstances. Single-phase models based on Richards' equation, which neglect such effects, may not be adequate for quantifying the aeration condition in tidal marsh. The optimal aeration condition, represented by the maximum of the integral magnitude of tidally advected air mass ( TAAM) flux, is found to occur near the tidal creek for the four soil textures simulated. This may explain the observation that some salt marsh plant species grow better near tidal creeks than in the inner marsh areas. Our analyses, based on the two-phase model and predicted TAAM flux magnitude, provide further insight into the positive feedback'' mechanism proposed by Ursino et al. ( 2004). That is, pioneer plants may grow successfully near the creek where the root aeration condition is optimal. The roots of the pioneer plants can soften and loosen the rhizosphere soil, which increases the evapotranspiration rate, the soil porosity, and absolute permeability and weakens the capillary effects. These, in turn, improve further the root aeration conditions and may lead to colonization by plants less resistant to anaerobic conditions.

Thermal strain in the mushy zone related to hot tearing

A volume-averaged two-phase model addressing the main transport phenomena associated with hot tearing in an isotropic mushy zone during solidification of metallic alloys has recently been presented elsewhere along with a new hot tearing criterion addressing both inadequate melt feeding and excessive deformation at relatively high solid fractions. The viscoplastic deformation in the mushy zone is addressed by a model in which the coherent mush is considered as a porous medium saturated with liquid. The thermal straining of the mush is accounted for by a recently developed model taking into account that there is no thermal strain in the mushy zone at low solid fractions because the dendrites then are free to move in the liquid, and that the thermal strain in the mushy zone tends toward the thermal strain in the fully solidified material when the solid fraction tends toward one. In the present work, the authors determined how variations in the parameters of the constitutive equation for thermal strain influence the hot tearing susceptibility calculated by the criterion. It turns out that varying the parameters in this equation has a significant effect on both liquid pressure drop and viscoplastic strain, which are key parameters in the hot tearing criterion. However, changing the parameters in this constitutive equation will result in changes in the viscoplastic strain and the liquid pressure drop that have opposite effects on the hot tearing susceptibility. The net effect on the hot tearing susceptibility is thus small.

Bayesian population pharmacokinetic analysis of sirolimus

Objective: It is usual that data collected from routine clinical care is sparse and unable to support the more complex pharmacokinetic (PK) models that may have been reported in previous rich data studies. Informative priors may be a pre-requisite for model development. The aim of this study was to estimate the population PK parameters of sirolimus using a fully Bayesian approach with informative priors. Methods: Informative priors including prior mean and precision of the prior mean were elicited from previous published studies using a meta-analytic technique. Precision of between-subject variability was determined by simulations from a Wishart distribution using MATLAB (version 6.5). Concentration-time data of sirolimus retrospectively collected from kidney transplant patients were analysed using WinBUGS (version 1.3). The candidate models were either one- or two-compartment with first order absorption and first order elimination. Model discrimination was based on computation of the posterior odds supporting the model. Results: A total of 315 concentration-time points were obtained from 25 patients. Most data were clustered at trough concentrations with range of 1.6 to 77 hours post-dose. Using informative priors, either a one- or two-compartment model could be used to describe the data. When a one-compartment model was applied, information was gained from the data for the value of apparent clearance (CL/F = 18.5 L/h), and apparent volume of distribution (V/F = 1406 L) but no information was gained about the absorption rate constant (ka). When a two-compartment model was fitted to the data, the data were informative about CL/F, apparent inter-compartmental clearance, and apparent volume of distribution of the peripheral compartment (13.2 L/h, 20.8 L/h, and 579 L, respectively). The posterior distribution of the volume distribution of central compartment and ka were the same as priors. The posterior odds for the two-compartment model was 8.1, indicating the data supported the two-compartment model. Conclusion: The use of informative priors supported the choice of a more complex and informative model that would otherwise have not been supported by the sparse data.