Synergistic effects of UdgB and Ung in mutation prevention and protection against commonly encountered DNA damaging agents in Mycobacterium smegmatis

The incorporation of dUMP during replication or the deamination of cytosine in DNA results in the occurrence of uracils in genomes. To maintain genomic integrity, uracil DNA glycosylases (UDGs) excise uracil from DNA and initiate the base-excision repair pathway. Here, we cloned, purified and biochemically characterized a family 5 UDG, UdgB, from Mycobacterium smegmatis to allow us to use it as a model organism to investigate the physiological significance of the novel enzyme. Studies with knockout strains showed that compared with the wild-type parent, the mutation rate of the udgB(-) strain was approximately twofold higher, whereas the mutation rate of a strain deficient in the family 1 UDG (ung(-)) was found to be similar to 8.4-fold higher. Interestingly, the mutation rate of the double-knockout (ung(-)ludgB(-)) strain was remarkably high, at similar to 19.6-fold. While CG to TA mutations predominated in the ung(-) and ung(-)/udgb(-) strains, AT to GC mutations were enhanced in the udgB(-) strain. The ung(-)/udgB(-) strain was notably more sensitive to acidified nitrite and hydrogen peroxide stresses compared with the single knockouts (ung(-) or udgB(-)). These observations reveal a synergistic effect of UdgB and Ung in DNA repair, and could have implications for the generation of attenuated strains of Mycobacterium tuberculosis.

Nonaxisymmetric unsteady motion over a rotating disk in the presence of free convection and magnetic field

The nonaxisymmetric unsteady motion produced by a buoyancy-induced cross-flow of an electrically conducting fluid over an infinite rotating disk in a vertical plane and in the presence of an applied magnetic field normal to the disk has been studied. Both constant wall and constant heat flux conditions have been considered. It has been found that if the angular velocity of the disk and the applied magnetic field squared vary inversely as a linear function of time (i.e. as (1??t*)?1, the governing Navier-Stokes equation and the energy equation admit a locally self-similar solution. The resulting set of ordinary differential equations has been solved using a shooting method with a generalized Newton's correction procedure for guessed boundary conditions. It is observed that in a certain region near the disk the buoyancy induced cross-flow dominates the primary von Karman flow. The shear stresses induced by the cross-flow are found to be more than these of the primary flow and they increase with magnetic parameter or the parameter ? characterizing the unsteadiness. The velocity profiles in the x- and y-directions for the primary flow at any two values of the unsteady parameter ? cross each other towards the edge of the boundary layer. The heat transfer increases with the Prandtl number but reduces with the magnetic parameter.

Role of free valences and spin densities on the migrating atom in location of saddle points in radical-exchange reactions

The principle of the conservation of bond orders during radical-exchange reactions is examined using Mayer's definition of bond orders. This simple intuitive approximation is not valid in a quantitative sense. Ab initio results reveal that free valences (or spin densities) develop on the migrating atom during reactions. For several examples of hydrogen-transfer reactions, the sum of the reaction coordinate bond orders in the transition state was found to be 0.92 +/- 0.04 instead of the theoretical 1.00 because free valences (or spin densities) develop on the migrating atom during reactions. It is shown that free valence is almost equal to the square of the spin density on the migrating hydrogen atom and the maxima in the free valence (or spin density) profiles coincide (or nearly coincide) with the saddle points in the corresponding energy profiles.

Some results on the reconstruction problems. p-claw-free, chordal, and p4-reducible graphs

A claw is an induced subgraph isomorphic to K-1,K-3. The claw-point is the point of degree 3 in a claw. A graph is called p-claw-free when no p-cycle has a claw-point on it. It is proved that for p greater than or equal to 4, p-claw-free graphs containing at least one chordless p-cycle are edge reconstructible. It is also proved that chordal graphs are edge reconstructible. These two results together imply the edge reconstructibility of claw-free graphs. A simple proof of vertex reconstructibility of P-4-reducible graphs is also presented. (C) 1995 John Wiley and Sons, Inc.

Digital Dead Time Logic and Protection Circuitry for PWM Voltage Source Converters

Power semiconductor devices have finite turn on and turn off delays that may not be perfectly matched. In a leg of a voltage source converter, the simultaneous turn on of one device and the turn off of the complementary device will cause a DC bus shoot through, if the turn off delay is larger than the turn on delay time. To avoid this situation it is common practice to blank the two complementary devices in a leg for a small duration of time while switching, which is called dead time. This paper proposes a logic circuit for digital implementation required to control the complementary devices of a leg independently and at the same time preventing cross conduction of devices in a leg, and while providing accurate and stable dead time. This implementation is based on the concept of finite state machines. This circuit can also block improper PWM pulses to semiconductor switches and filters small pulses notches below a threshold time width as the narrow pulses do not provide any significant contribution to average pole voltage, but leads to increased switching loss. This proposed dead time logic has been implemented in a CPLD and is implemented in a protection and delay card for 3- power converters.

Path-integral formulation for Levy flights: Evaluation of the propagator for free, linear, and harmonic potentials in the over- and underdamped limits

Levy flights can be described using a Fokker-Planck equation, which involves a fractional derivative operator in the position coordinate. Such an operator has its natural expression in the Fourier domain. Starting with this, we show that the solution of the equation can be written as a Hamiltonian path integral. Though this has been realized in the literature, the method has not found applications as the path integral appears difficult to evaluate. We show that a method in which one integrates over the position coordinates first, after which integration is performed over the momentum coordinates, can be used to evaluate several path integrals that are of interest. Using this, we evaluate the propagators for (a) free particle, (b) particle subjected to a linear potential, and (c) harmonic potential. In all the three cases, we have obtained results for both overdamped and underdamped cases. DOI: 10.1103/PhysRevE.86.061105

The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Establishing functional relationships between multi-domain protein sequences is a non-trivial task. Traditionally, delineating functional assignment and relationships of proteins requires domain assignments as a prerequisite. This process is sensitive to alignment quality and domain definitions. In multi-domain proteins due to multiple reasons, the quality of alignments is poor. We report the correspondence between the classification of proteins represented as full-length gene products and their functions. Our approach differs fundamentally from traditional methods in not performing the classification at the level of domains. Our method is based on an alignment free local matching scores (LMS) computation at the amino-acid sequence level followed by hierarchical clustering. As there are no gold standards for full-length protein sequence classification, we resorted to Gene Ontology and domain-architecture based similarity measures to assess our classification. The final clusters obtained using LMS show high functional and domain architectural similarities. Comparison of the current method with alignment based approaches at both domain and full-length protein showed superiority of the LMS scores. Using this method we have recreated objective relationships among different protein kinase sub-families and also classified immunoglobulin containing proteins where sub-family definitions do not exist currently. This method can be applied to any set of protein sequences and hence will be instrumental in analysis of large numbers of full-length protein sequences.

Background paper on the international seafood trade and poverty

(121 p.)

The African slave trade and its remedy

Esta edição é revista e aumentada, com mais do dobro de páginas da edição primitiva, de 1839, que continha 240 páginas. Buxton, presidente da Sociedade para a Extinção do Tráfico de Escravos, apresenta um detalhadíssimo estudo do comércio de negros, desde a África Central e ambas as costas do Continente, até o Brasil, os Estados Unidos, Cuba, etc. Há estimativas de mortalidade em todos os estágios do cativeiro. A maior parte das referências são sobre Cuba e o Brasil. É um clássico pioneiro dos estudos sobre escravidão.

Relating thermodynamics to information theory : the equality of free energy and mutual information

In this thesis we uncover a new relation which links thermodynamics and information theory. We consider time as a channel and the detailed state of a physical system as a message. As the system evolves with time, ever present noise insures that the "message" is corrupted. Thermodynamic free energy measures the approach of the system toward equilibrium. Information theoretical mutual information measures the loss of memory of initial state. We regard the free energy and the mutual information as operators which map probability distributions over state space to real numbers. In the limit of long times, we show how the free energy operator and the mutual information operator asymptotically attain a very simple relationship to one another. This relationship is founded on the common appearance of entropy in the two operators and on an identity between internal energy and conditional entropy. The use of conditional entropy is what distinguishes our approach from previous efforts to relate thermodynamics and information theory.