An integrated mechanistic model for transcription-coupled nucleotide excision repair.

Preferential repair of the transcribed strand of active genes is usually attributed to a coupling protein that dislodges RNA polymerase stalled at a damage site and recruits repair enzymes. Experimental observations of the effect of transcription on preferential repair in Escherichia coli are contradictory and inexplicable by this model. In this study, it is argued that the multiple conformations displayed by a stalled RNA polymerase result in two sub-pathways for repair: Mfd coupled and direct. Together with the fact that RNA polymerase recruits the repair enzymes in a promoter dependent manner, an integrated mechanistic model is proposed that is capable of explaining the effect of transcription on preferential repair reported in literature. The quantitative behavior of the model is illustrated by describing the various reactions using a biochemical network. The implications of the model on the mechanism for transcription-coupled repair in higher organisms are briefly discussed.

RecA mediated initial alignment of homologous DNA molecules displays apparent first order kinetics with little effect of heterology.

The mechanism and determinants of RecA mediated initial alignment of homologous DNA molecules were studied by performing Monte Carlo simulations of the dynamics of DNA molecules. The simulation procedure was used to assess the effect of heterologous DNA and dilution on the rate of formation and yield of homologous alignments. The results show that the apparent first order kinetic behavior and the impact of heterologous DNA, reported in literature [J. Biol. Chem. 261 (1986) 1025], can be observed even if the conversion of the initially aligned molecules into a stable joint is not rate-determining. The present study is the first step towards developing rigorous computational models to describe the process of homologous recombination, and theoretical frameworks to retrieve biophysical parameters of strand pairing and exchange proteins from in vitro assays of joint molecule formation.

Evaluation of the resistance of membrane and erythrocytes to oxygen transport in pulmonary capillaries.

The conductance of the diffusion pathway for oxygen in pulmonary capillaries is usually described in terms of two lumped components; the membrane and erythrocyte diffusing capacities. In this study the relative importance of these two components was investigated theoretically over a wide range of alveolar oxygen partial pressures. It was found that the membrane diffusing capacity is largely independent of the alveolar oxygen partial pressure and the erythrocyte diffusing capacity increases steeply with a decrease in alveolar oxygen partial pressure. The ratio of the resistance of the membrane to that of the erythrocytes to oxygen transport is a strong function of the alveolar oxygen partial pressure [1.5 (PAO2 = 30 mmHg); 1.0 (PAO2 = 100 mmHg); 0.5 (PAO2 = 700 mmHg)].

Mathematical analysis of solid-liquid mass transfer in a batch reactor for the enzymatic transformation of testosterone to 4AD.

A previous mathematical analysis of mass transfer in a two-phase (solid-liquid) batch reactor for enzymatic transformation of testosterone to 4AD (Pereira et al., 1987) is extended to incorporate the effect of convective mixing. The results of the analysis showed that for a given enzyme loading, the mass transfer resistance in the solid (a function of the bead size) and the intensity of convective mixing (as embodied in the mass transfer coefficient) are two parameters that can be varied such that the overall mass transfer rate from the solid to the liquid phase ensures optimal reactor performance.

Impact of microscope numerical aperture on microspectrophotometric measurements of hemoglobin in microvessels.

In the microspectrophotometric method to measure hemoglobin concentration and oxygen saturation in microvessels it is recommended that a low numerical aperture (NA) condenser be employed to ensure that the recorded image is a true projection of the object. However, this tenet has never been rigorously justified. In this study, the microspectrophotometric method is evaluated using the theory of three-dimensional image formation by a light microscope for a wide range of NA. The results of the calculations show that for measurements for hemoglobin concentration, the recorded image is close to the true projection only when the size of the microvessel is large compared to the degree of smearing ( proportional, variant 1/NA) but small compared to the degree of defocus ( proportional, variant NA(2)). These opposing tendencies lead to an optimum NA for which the errors are minimum. This optimum NA is a function of the size of the microvessel and the manner in which the hemoglobin concentration is distributed within the lumen. For measurements of oxygen saturation, the recorded image is the true projection as long as the measurements are made in regions near the microvessel centerline. For measurements made in regions away from the centerline, good agreement was obtained only when the distribution of oxygen saturation was uniform. Reconstruction of the axisymmetric profiles from the recorded projections showed that the errors in the projections cause the recovered profiles to deviate from the true profiles. These deviations are directly related to the extent by which the recorded projections deviate from the true projection.