GyrI: a counter-defensive strategy against proteinaceous inhibitors of DNA gyrase

DNA gyrase is the target of two plasmid-encoded toxins CcdB and microcin B17, which ensure plasmid maintenance. These proteins stabilize gyrase-DNA covalent complexes leading to double-strand breaks in the genome. In contrast, the physiological role of chromosomally encoded inhibitor of DNA gyrase (Gyrl) in Escherichia coli is unclear and its mechanism of inhibition has not been established. We demonstrate that the mode of inhibition of GyrI is distinct from all other gyrase inhibitors. It inhibits DNA gyrase prior to, or at the step of, binding of DNA by the enzyme. Gyrl reduces intrinsic as well as toxin-stabilized gyrase-DNA covalent complexes. Furthermore, Gyri reduces microcin B17-mediated double-strand breaks in vivo, imparting protection to the cells against the toxin, substantiating the in vitro results. Thus, Gyrl is an antidote to DNA gyrase-specific proteinaceous poisons encoded by plasmid addiction systems.

Phase diagram for the system Nd-Mn-O and thermodynamic properties of NdMnO3 and NdMn2O5

Studies on the phase relations in the system Nd-Mn-O at 1223 K showed two stable ternary compounds, NdMnO3 and NdMn2O5. An isothermal section of the ternary phase diagram for the system Nd-Mn-O was constructed based on phase analysis of samples quenched after equilibration using XRPD and EDS. An advanced version of the solid-state cell incorporating a buffer electrode was used to determine the Gibbs energies of decomposition of NdMnO3 and NdMn2O5 in the temperature range from 925 to 1400 K. Pure oxygen gas at 0.1 MPa was used as the reference electrode, and yttria-stabilized zirconia as the solid electrolyte. The buffer electrode was designed to prevent polarization of the three-phase electrode and ensure accurate data. The measured oxygen potential corresponding to the reaction,2 Nd2O3 + 4 MnO + O-2 --> 4 NdMnO3 can be represented by the equation,Amu(o2) / J.mol(-1) (+/-580) = -523 960 + 170.96 (T/K)Similarly, for the formation of NdMn2O5 according to the reaction,3 NdMnO3 + Mn3O4 + O-2 --> 3 NdMn2O5 Amu(o2) / J.mol(-1) (+/-660) = - 269 390 + 181.74 (T/K) (C) 2002 Elsevier Science Ltd. All rights reserved.

Phase diagram of a two-species lattice model with a linear instability

We discuss the properties of a one-dimensional lattice model of a driven system with two species of particles in which the mobility of one species depends on the density of the other. This model was introduced by Lahiri and Ramaswamy (Phys. Rev. Lett., 79, 1150 (1997)) in the context of sedimenting colloidal crystals, and its continuum version was shown to exhibit an instability arising from linear gradient couplings. In this paper we review recent progress in understanding the full phase diagram of the model. There are three phases. In the first, the steady state can be determined exactly along a representative locus using the condition of detailed balance. The system shows phase separation of an exceptionally robust sort, termed strong phase separation, which survives at all temperatures. The second phase arises in the threshold case where the first species evolves independently of the second, but the fluctuations of the first influence the evolution of the second, as in the passive scalar problem. The second species then shows phase separation of a delicate sort, in which long-range order coexists with fluctuations which do not damp down in the large-size limit. This fluctuation-dominated phase ordering is associated with power law decays in cluster size distributions and a breakdown of the Porod law. The third phase is one with a uniform overall density, and along a representative locus the steady state is shown to have product measure form. Density fluctuations are transported by two kinematic waves, each involving both species and coupled at the nonlinear level. Their dissipation properties are governed by the symmetries of these couplings, which depend on the overall densities. In the most interesting case,, the dissipation of the two modes is characterized by different critical exponents, despite the nonlinear coupling.

Matching sender and receiver: poikilothermy and frequency tuning in a tree cricket

Animals communicate in non-ideal and noisy conditions. The primary method they use to improve communication efficiency is sender-receiver matching: the receiver's sensory mechanism filters the impinging signal based on the expected signal. In the context of acoustic communication in crickets, such a match is made in the frequency domain. The males broadcast a mate attraction signal, the calling song, in a narrow frequency band centred on the carrier frequency (CF), and the females are most sensitive to sound close to this frequency. In tree crickets, however, the CF changes with temperature. The mechanisms used by female tree crickets to accommodate this change in CF were investigated at the behavioural and biomechanical level. At the behavioural level, female tree crickets were broadly tuned and responded equally to CFs produced within the naturally occurring range of temperatures (18 to 27 degrees C). To allow such a broad response, however, the transduction mechanisms that convert sound into mechanical and then neural signals must also have a broad response. The tympana of the female tree crickets exhibited a frequency response that was even broader than suggested by the behaviour. Their tympana vibrate with equal amplitude to frequencies spanning nearly an order of magnitude. Such a flat frequency response is unusual in biological systems and cannot be modelled as a simple mechanical system. This feature of the tree cricket auditory system not only has interesting implications for mate choice and species isolation but may also prove exciting for bio-mimetic applications such as the design of miniature low frequency microphones.

PL due to Discrete Gap Levels in Some Chalcogenide Glasses- A Configurational Coordinate Diagram Illustration

Photoluminescence (PL) studies were carried out on a-Se and a few Ge20Se80−xBix and Ge20Se70−xBixTe10 bulk glassy semiconductors at 4.2 K with Ar+ laser as excitation source. While a-Se and samples with lesser at% of Bi show fine structured PL with a large Stokes shift, samples with higher at% of Bi did not show any detectable PL. The investigations show at least three radiative recombination transitions. Features extracted by deconvoluting the experimental spectra show that the discrete gap levels associated with the inherent coordination defects are involved in the PL transitions. Absence of PL in samples with higher Bi at% are explained on the basis of nonradiative transition mechanisms. Overall PL mechanism involving gap levels in chalcogenide glasses is illustrated with the help of a configurational coordinate diagram.

Efficient statistical modeling for the compression of tree structured intermediate code

We propose a scheme for the compression of tree structured intermediate code consisting of a sequence of trees specified by a regular tree grammar. The scheme is based on arithmetic coding, and the model that works in conjunction with the coder is automatically generated from the syntactical specification of the tree language. Experiments on data sets consisting of intermediate code trees yield compression ratios ranging from 2.5 to 8, for file sizes ranging from 167 bytes to 1 megabyte.

Tree structure for efficient data mining using rough sets

In data mining, an important goal is to generate an abstraction of the data. Such an abstraction helps in reducing the space and search time requirements of the overall decision making process. Further, it is important that the abstraction is generated from the data with a small number of disk scans. We propose a novel data structure, pattern count tree (PC-tree), that can be built by scanning the database only once. PC-tree is a minimal size complete representation of the data and it can be used to represent dynamic databases with the help of knowledge that is either static or changing. We show that further compactness can be achieved by constructing the PC-tree on segmented patterns. We exploit the flexibility offered by rough sets to realize a rough PC-tree and use it for efficient and effective rough classification. To be consistent with the sizes of the branches of the PC-tree, we use upper and lower approximations of feature sets in a manner different from the conventional rough set theory. We conducted experiments using the proposed classification scheme on a large-scale hand-written digit data set. We use the experimental results to establish the efficacy of the proposed approach. (C) 2002 Elsevier Science B.V. All rights reserved.

Counter-free input-determined timed automata

We identify a class of timed automata, which we call counter-free input-determined automata, which characterize the class of timed languages definable by several timed temporal logics in the literature, including MTL. We make use of this characterization to show that MTL+Past satisfies an “ultimate stability” property with respect to periodic sequences of timed words. Our results hold for both the pointwise and continuous semantics. Along the way we generalize the result of McNaughton-Papert to show a counter-free automata characterization of FO-definable finitely varying functions.

An O(mn) Gomory-Hu Tree Construction Algorithm for Unweighted Graphs

We present a fast algorithm for computing a Gomory-Hu tree or cut tree for an unweighted undirected graph G = (V,E). The expected running time of our algorithm is Õ(mc) where |E| = m and c is the maximum u-vedge connectivity, where u,v ∈ V. When the input graph is also simple (i.e., it has no parallel edges), then the u-v edge connectivity for each pair of vertices u and v is at most n-1; so the expected running time of our algorithm for simple unweighted graphs is Õ(mn).All the algorithms currently known for constructing a Gomory-Hu tree [8,9] use n-1 minimum s-t cut (i.e., max flow) subroutines. This in conjunction with the current fastest Õ(n20/9) max flow algorithm due to Karger and Levine [11] yields the current best running time of Õ(n20/9n) for Gomory-Hu tree construction on simpleunweighted graphs with m edges and n vertices. Thus we present the first Õ(mn) algorithm for constructing a Gomory-Hu tree for simple unweighted graphs.We do not use a max flow subroutine here; we present an efficient tree packing algorithm for computing Steiner edge connectivity and use this algorithm as our main subroutine. The advantage in using a tree packing algorithm for constructing a Gomory-Hu tree is that the work done in computing a minimum Steiner cut for a Steiner set S ⊆ V can be reused for computing a minimum Steiner cut for certain Steiner sets S' ⊆ S.

Impact of Sulphate counter ion in the migration of sodium ion through soils

Laboratory advection-diffusion tests are performed on two regional soils-Brown Earth and Red Earth-in order to assess their capacity to control contaminant migration with synthetic contaminant solution of sodium sulphate with sodium concentration of 1000 mg/L. The test was designed to study the transport/attenuation behaviour of sodium in the presence of sulphate. Effective diffusion coefficient (De) that takes into consideration of attenuation processes is used. Cation exchange capacity is an important factor for the attenuation of cationic species. Monovalent sodium ion cannot usually replace other cations and the retention of sodium ion is very less. This is particularly true when chloride is anion is solution. However, sulphate is likely to play a role in the attenuation of sodium. Cation exchange capacity and type of exchangeable ions of soils are likely to play an important role. The effect of sulphate ions on the effective diffusion coefficient of sodium, in two different types of soils, of different cation exchange capacity has been studied. The effective diffusion coefficients of sodium ion for both the soils were calculated using Ogata Bank’s equation. It was shown that effective diffusion coefficient of sodium in the presence of sulphate is lower for Brown Earth than for Red Earth due to exchange of sodium with calcium ions from the exchangeable complex of clay. The soil with the higher cation exchange retained more sodium. Consequently, the breakthrough times and the number of pore volumes of sodium ion increase with the cation exchange capacity of soil.

Dye sensitized solar cell based on platinum decorated multiwall carbon nanotubes as catalytic layer on the counter electrode

In this study we have employed multiwall carbon nanotubes (MWCNT), decorated with platinum as catalytic layer for the reduction of tri-iodide ions in dye sensitized solar cell (DSSC). MWCNTs have been prepared by a simple one step pyrolysis method using ferrocene as the catalyst and xylene as the carbon source. Platinum decorated MWCNTs have been prepared by chemical reduction method. The as prepared MWCNTs and Pt/MWCNTs have been characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). In combination with a dye adsorbed TiO(2) photoanode and an organic liquid electrolyte, Pt/MWCNT composite showed an enhanced short circuit current density of 16.12 mA/cm(2) leading to a cell efficiency of 6.50% which is comparable to that of Platinum. (C) 2011 Elsevier Ltd. All rights reserved.

The Co Cr S ternary diagram at 1223 K and applications to corrosion

Ternary phase relations in the Co-Cr-S system at 1223 K were determined using microprobe analysis of quenched samples. The results are consistent with the data available on the binary systems. A complete solid solution exists between cobalt monosulfide and chromium monosulfide. The CoCr2S4 thiospinel is the only ternary compound formed. A sulfur potential diagram was constructed for the region involving equilibrium between alloy and monosulfide based on thermodynamic data on the Co-Cr, Co-S, and Cr-S binary systems and the ternary information obtained in this study. The sulfidation behavior of Co-Cr alloys reported in the literature is discussed in light of the sulfur potential diagram.

A new matched thermochemical diagram for vacuum refining of nickel and cupronickel alloys

Sulfur and oxygen dissolved in nickel and cupronickel melts can be remwed as gaseous oxides of sulfur by a vacuum treatment. Presented in this paper is a new matched thermcxhemical disgran~ that permit.. direct evaluation of the equilibrium partial pressure of SO, as a function of temperature wer an alloy of specified compition. The matched thermochemical diagram consists of a central plot which shows the integral Gibbs' energy of mixing for the binary system SO, at different temperatures. The central plot is flanked on either side by terminal plots of the chemical potentials of oxygen and sulfur, as functions of temperature, for different alloy compositions. By projecting the chemical wtentials of oxygen and sulfur from the terminal lots on to the central diagram, ihe equilibrium partial pressure of S0,can be directly ;cad on the nomograms on the central plot at different temperatures. The matched therrnochemical diagrams are useful in assuring the efficiency of vacuum refining.