A Generalized Theory of DNA Looping and Cyclization

We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise boundary conditions on DNA, which necessitates a treatment beyond the Shimada-Yamakawa model for ring cyclization. Our model allows for DNA to be treated as a heteropolymer with sequence-dependent intrinsic curvature and stiffness. In this framework, we independently compute enthlapic and entropic contributions to the $J$ factor and show that even at small length scales $(\sim \ell_{p})$ entropic effects are significant. We propose a simple analytic formula to describe our numerical results for a homogenous DNA in planar loops, which can be used to predict experimental cyclization and loop formation rates as a function of loop size and binding geometry. We also introduce an effective torsional persistence length that describes the coupling between twist and bending of DNA when looped.Comment: 6 pages, 4 figures, submitted to EP

A hybrid CA-PDE Model of chlamydia trachomatis infection in the female genital tract

Chlamydia trachomatis is amongst the most common sexually transmitted diseases in the world and when left untreated, may lead to serious sequelae particularly in women such as pelvic inflammatory disease, ectopic pregnancy and infertility. Currently, most mathematical modelling in the literature regarding Chlamydia is based on time dependent differential equations. The serious pathology associated with C. trachomatis occurs when the chlamydial infection ascends to the upper genital tract. But no modelling study has investigated the important spatial aspects of the disease. In this work, we include spatiotemporal considerations of the progression of chlamydial infection in the genital tract. This novel direction is achieved using cellular automata modelling with probabilistic decision processes. In this presentation, the modelling strategy will be described, as well as its relationship with existing models and the advances in understanding that are achieved with such a model. Such an approach provides valuable insights into disease progression and will lead to experimentally testable predictions and a basis for further investigation in this area

THE ADOPTION AND DIFFUSION OF LEVEL FIELDS AND BASINS

Strategic investments in agriculture often are lumpy and irreversible, with significant impacts on operating and fixed costs. Leveling cotton fields to zero slope in central Arizona is a strategic decision made by relatively younger farmers who are farming fine-textured soils in irrigation districts with higher expected water costs. The diffusion of the technology across the region between 1968-89 appears to be both a function of institutional changes (e.g., the Groundwater Management Act of 1980, the Central Arizona Project) and the long-run expected price changes induced by these new policies.Crop Production/Industries,

Reconstruction of Cluster Masses using Particle Based Lensing I: Application to Weak Lensing

We present Particle-Based Lensing (PBL), a new technique for gravitational lensing mass reconstructions of galaxy clusters. Traditionally, most methods have employed either a finite inversion or gridding to turn observational lensed galaxy ellipticities into an estimate of the surface mass density of a galaxy cluster. We approach the problem from a different perspective, motivated by the success of multi-scale analysis in smoothed particle hydrodynamics. In PBL, we treat each of the lensed galaxies as a particle and then reconstruct the potential by smoothing over a local kernel with variable smoothing scale. In this way, we can tune a reconstruction to produce constant signal-noise throughout, and maximally exploit regions of high information density. PBL is designed to include all lensing observables, including multiple image positions and fluxes from strong lensing, as well as weak lensing signals including shear and flexion. In this paper, however, we describe a shear-only reconstruction, and apply the method to several test cases, including simulated lensing clusters, as well as the well-studied ``Bullet Cluster'' (1E0657-56). In the former cases, we show that PBL is better able to identify cusps and substructures than are grid-based reconstructions, and in the latter case, we show that PBL is able to identify substructure in the Bullet Cluster without even exploiting strong lensing measurements. We also make our codes publicly available.Comment: Accepted for publication in ApJ; Codes available at http://www.physics.drexel.edu/~deb/PBL.htm ; 12 pages,9 figures, section 3 shortene

Sampling and sensitivity analyses tools (SaSAT) for computational modelling

SaSAT (Sampling and Sensitivity Analysis Tools) is a user-friendly software package for applying uncertainty and sensitivity analyses to mathematical and computational models of arbitrary complexity and context. The toolbox is built in Matlab®, a numerical mathematical software package, and utilises algorithms contained in the Matlab® Statistics Toolbox. However, Matlab® is not required to use SaSAT as the software package is provided as an executable file with all the necessary supplementary files. The SaSAT package is also designed to work seamlessly with Microsoft Excel but no functionality is forfeited if that software is not available. A comprehensive suite of tools is provided to enable the following tasks to be easily performed: efficient and equitable sampling of parameter space by various methodologies; calculation of correlation coefficients; regression analysis; factor prioritisation; and graphical output of results, including response surfaces, tornado plots, and scatterplots. Use of SaSAT is exemplified by application to a simple epidemic model. To our knowledge, a number of the methods available in SaSAT for performing sensitivity analyses have not previously been used in epidemiological modelling and their usefulness in this context is demonstrated

Renal urate excretion in patients with Wilson's disease

Renal urate excretion in patients with Wilson's disease. Because many patients with Wilson's disease have hypouricemia, a study was made of 10 patients and 10 control persons to determine the nature of the renal excretory defect. Uric acid excretion was studied before and after the administration of pyrazinamidem—an agent which is postulated to selectively block urate secretion. Urate excretion was also correlated with the quantity of various types of amino acids excreted. In the presence of pyrazinamide, total urate excretion is decreased markedly just as in normal individuals. It appears that proximal reabsorption of urate may not be impaired. There is a positive correlation between excessive urate excretion and that of serine, arginine, valine, and glutamine.Excrétion rénale des urates chez les malades atteints de maladie de Wilson. Du fait que beaucoup de malades atteints de maladie de Wilson ont une hypouricémie une étude a été réalisée chez dix malades et dix sujets témoins afin de déterminer la nature du trouble de l'excrétion des urates. L'excrétion d'acide urique a été étudiée avant et après l'administration de pyrazinamide, agent dont on suppose qu'il bloque électivement la secrétion d'urate. L'excrétion d'urate a été aussi corrélée avec la quantité de divers acides aminés excrétés. En présence de pyrazinamide l'excrétion totale d'urate est notablement diminuée, comme chez les témoins. Il apparaît que la réabsorption proximale des urates n'est probablement pas diminuée. Il existe une corrélation positive entre l'excrétion excessive d'urate et l'excrétion de sérine, d'arginine, de valine et de glutamine

Summing Up

This edition of Educational Considerations focuses on the principalship