Binding of two DNA molecules by type II topoisomerases for decatenation

Topoisomerases (topos) maintain DNA topology and influence DNA transaction processes by catalysing relaxation, supercoiling and decatenation reactions. In the cellular milieu, division of labour between different topos ensures topological homeostasis and control of central processes. In Escherichia coli, DNA gyrase is the principal enzyme that carries out negative supercoiling, while topo IV catalyses decatenation, relaxation and unknotting. DNA gyrase apparently has the daunting task of undertaking both the enzyme functions in mycobacteria, where topo IV is absent. We have shown previously that mycobacterial DNA gyrase is an efficient decatenase. Here, we demonstrate that the strong decatenation property of the enzyme is due to its ability to capture two DNA segments in trans. Topo IV, a strong dedicated decatenase of E. coli, also captures two distinct DNA molecules in a similar manner. In contrast, E. coli DNA gyrase, which is a poor decatenase, does not appear to be able to hold two different DNA molecules in a stable complex. The binding of a second DNA molecule to GyrB/ParE is inhibited by ATP and the non-hydrolysable analogue, AMPPNP, and by the substitution of a prominent positively charged residue in the GyrB N-terminal cavity, suggesting that this binding represents a potential T-segment positioned in the cavity. Thus, after the GyrA/ParC mediated initial DNA capture, GyrB/ParE would bind efficiently to a second DNA in trans to form a T-segment prior to nucleotide binding and closure of the gate during decatenation.

Resolution of Singularities for a Class of Hilbert Modules

Let M be the completion of the polynomial ring C(z) under bar] with respect to some inner product, and for any ideal I subset of C (z) under bar], let I] be the closure of I in M. For a homogeneous ideal I, the joint kernel of the submodule I] subset of M is shown, after imposing some mild conditions on M, to be the linear span of the set of vectors {p(i)(partial derivative/partial derivative(w) over bar (1),...,partial derivative/partial derivative(w) over bar (m)) K-I] (., w)vertical bar(w=0), 1 <= i <= t}, where K-I] is the reproducing kernel for the submodule 2] and p(1),..., p(t) is some minimal ``canonical set of generators'' for the ideal I. The proof includes an algorithm for constructing this canonical set of generators, which is determined uniquely modulo linear relations, for homogeneous ideals. A short proof of the ``Rigidity Theorem'' using the sheaf model for Hilbert modules over polynomial rings is given. We describe, via the monoidal transformation, the construction of a Hermitian holomorphic line bundle for a large class of Hilbert modules of the form I]. We show that the curvature, or even its restriction to the exceptional set, of this line bundle is an invariant for the unitary equivalence class of I]. Several examples are given to illustrate the explicit computation of these invariants.

Revenue management in remanufacturing: perspectives, review of current literature and research directions

The pace of development in the world has increased over the years and with it, the use of hi-tech gadgets, consumer durables, automobiles, etc. has also gone up. In this context, as resources become more and more scarce, there are multiple challenges that emerge both from a sustainable development perspective, and from the perspective of meeting profitability objectives of a firm. Remanufacturing has come up in a big way as an answer to these challenges, but firms are struggling with respect to revenue management of this nascent area. We assess the current literature and distil the key factors that firms need to consider as they assimilate remanufacturing in their operations and revenue management strategy. We provide an assessment of white spaces in research in this area and also outline the directions for future research.

Retrogressed eclogite (20 kbar, 1020 °C) from the Neoproterozoic Palghat–Cauvery suture zone, southern India

The Palghat–Cauvery suture zone in southern India separates Archaean crustal blocks to the north and the Proterozoic Madurai block to the south. Here we present the first detailed study of a partially retrogressed eclogite (from within the Sittampundi anorthositic complex in the suture zone) that occurs as a 20-cm wide layer in a garnet gabbro layer in anorthosite. The eclogite largely consists of an assemblage of coexisting porphyroblasts of almandine–pyrope garnet and augitic clinopyroxene. However, a few garnets contain inclusions of omphacite. Rims and symplectites composed of Na–Ca amphibole and plagioclase form a retrograde assemblage. Petrographic analysis and calculated phase equilibria indicate that garnet–omphacite–rutile–melt was the peak metamorphic assemblage and that it formed at ca. 20 kbar and above 1000 °C. The eclogite was exhumed on a very tight hairpin-type, anticlockwise P–T path, which we relate to subduction and exhumation in the Palghat–Cauvery suture zone. The REE composition of the minerals suggests a basaltic oceanic crustal protolith metamorphosed in a subduction regime. Geological–structural relations combined with geophysical data from the Palghat–Cauvery suture zone suggest that the eclogite facies metamorphism was related to formation of the suture zone. Closure of the Mozambique Ocean led to development of the suture zone and to its western extension in the Betsimisaraka suture of Madagascar.

The heat kernel on AdS(3) and its applications

We derive the heat kernel for arbitrary tensor fields on S-3 and (Euclidean) AdS(3) using a group theoretic approach. We use these results to also obtain the heat kernel on certain quotients of these spaces. In particular, we give a simple, explicit expression for the one loop determinant for a field of arbitrary spin s in thermal AdS(3). We apply this to the calculation of the one loop partition function of N = 1 supergravity on AdS(3). We find that the answer factorizes into left- and right-moving super Virasoro characters built on the SL(2, C) invariant vacuum, as argued by Maloney and Witten on general grounds.

Biochemical, histopathological and ultrastructural changes in rat liver induced by r-( + )-pulegone, a monoterpene ketone

Biochemical, histopathological and ultrastructural changes occurring at different time points after intraperitoneal administration of a single dose of pulegone (300 mg/kg) were studied. Significant decreases in the level of liver microsomal cytochrome P-450 (67%), heme (37%), aminopyrine N-demethylase (60%) and glucose-6-phosphatase (58%), were noticed 24 hr after pulegone treatment. Alanine amino transferase (ALT) levels increased in a time dependent manner, following exposure of rats to pulegone. Light microscopic studies of liver tissues showed dilation of central veins and distention of sinusoidal spaces 6 hr after pulegone treatment. Initial centrilobular necrosis was noticed at 12 hr. Centrilobular necrosis became severe at 18 hr and nuclear changes included karyorrhexis and karyolysis. Midzonal and periportal degenerative changes in addition to centrilobular necrosis was observed 24 hr after pulegone administration. Electron microscopic changes showed severe degeneration of endoplasmic reticulum, swelling of mitochondria and nuclear changes, 24 hr after administration of pulegone. The time course profile of the hepatocytes after treatment with pulegone indicates that endoplasmic reticulum is the organelle most affected, following which other degenerative changes occur ultimately leading to cell death.

On shock dynamics

This is in continuation of our paper On the propagation of a multi-dimensional shock of arbitrary strength’ published earlier in this journal (Srinivasan and Prasad [9]). We had shown in our paper that Whitham’s shock dynamics, based on intuitive arguments, cannot be relied on for flows other than those involving weak shocks and that too with uniform flow behind the shock. Whitham [12] refers to this as misinterpretation of his approximation and claims that his theory is not only correct but also provides a natural closure of the open system of the equations of Maslov [3]. The main aim of this note is to refute Whitham’s claim with the help of an example and a numerical integration of a problem in gasdynamics.

Explicit filtering LES for turbulent non-premixed combustion

Two models for large eddy simulation of turbulent reacting flow in homogeneous turbulence were studied. The sub-grid stress arising out of non-linearities of the Navier-Stokes equations were modeled using an explicit filtering approach. A filtered mass density function (FMDF) approach was used for closure of the sub-grid scalar fluctuations. A posteriori calculations, when compared with the results from the direct numerical simulation, indicate that the explicit filtering is adequate in representing the effect of sub-grid stress on the filtered velocity field in the absence of reaction. Discrepancies arise when reactions occur, but the FMDF approach suffices to account for sub-grid scale fluctuations of the reacting scalars, accurately.

Spectral analysis on SL(2, R)

Let G be the group . For this group we prove a version of Schwartz's theorem on spectral analysis for the group G. We find the sharp range of Lebesgue spaces L (p) (G) for which a smooth function is not mean periodic unless it is a cusp form. Failure of the Schwartz-like theorem is also proved when C (a)(G) is replaced by L (p) (G) with suitable p. We show that the last result is linked with the failure of the Wiener-tauberian theorem for G.

FUZZY CONIFOLD Y-F(6) AND MONOPOLES ON S-F(2) x S-F(2)

In this paper, we construct the fuzzy (finite-dimensional) analogs of the conifold Y-6 and its base X-5. We show that fuzzy X-5 is (the analog of) a principal U(1) bundle over fuzzy spheres S-F(2) x S-F(2) and explicitly construct the associated monopole bundles. In particular, our construction provides an explicit discretization of the spaces T-k,T-k and T-k,T-0.

Ideas generated in conceptual design and their effects on creativity

Search of design spaces to generate solutions affects the design outcomes during conceptual design. This research aims to understand the different types of search that occurs during conceptual design and their effect on the design outcomes. Additionally, we study the effect of other factors, such as creativity, problem-solving style, and experience of designers, on the design outcomes. Two sets of design experiments, with experienced and novice designers, are used in this study. We find that designers employ twelve different types of searches during conceptual design for problem understanding, solution generation, and solution evaluation activities. Results also suggest that creativity is influenced positively by the type and amount of searches, duration of designing, and experience of designers.

Structural plasticity in Mycobacterium tuberculosis uracil-DNA glycosylase (MtUng) and its functional implications

17 independent crystal structures of family I uracil-DNA glycosylase from Mycobacterium tuberculosis (MtUng) and its complexes with uracil and its derivatives, distributed among five distinct crystal forms, have been determined. Thermodynamic parameters of binding in the complexes have been measured using isothermal titration calorimetry. The two-domain protein exhibits open and closed conformations, suggesting that the closure of the domain on DNA binding involves conformational selection. Segmental mobility in the enzyme molecule is confined to a 32-residue stretch which plays a major role in DNA binding. Uracil and its derivatives can bind to the protein in two possible orientations. Only one of them is possible when there is a bulky substituent at the 50 position. The crystal structures of the complexes provide a reasonable rationale for the observed thermodynamic parameters. In addition to providing fresh insights into the structure, plasticity and interactions of the protein molecule, the results of the present investigation provide a platform for structure-based inhibitor design.

A note on tetrablock contractions

A commuting triple of operators (A, B, P) on a Hilbert space H is called a tetrablock contraction if the closure of the set E = {(a(11),a(22),detA) : A = GRAPHICS] with parallel to A parallel to <1} is a spectral set. In this paper, we construct a functional model and produce a set of complete unitary invariants for a pure tetrablock contraction. In this construction, the fundamental operators, which are the unique solutions of the operator equations A - B* P = DPX1DP and B - A* P = DPX2DP where X-1, X-2 is an element of B(D-P) play a pivotal role. As a result of the functional model, we show that every pure tetrablock isometry (A, B, P) on an abstract Hilbert space H is unitarily equivalent to the tetrablock contraction (MG1*+G2z, MG2*+G1z, M-z) on H-DP*(2). (D), where G(1) and G(2) are the fundamental operators of (A*, B*, P*). We prove a Beurling Lax Halmos type theorem for a triple of operators (MF1*+F2z, MF2*+F1z, M-z), where epsilon is a Hilbert space and F-1, F-2 is an element of B(epsilon). We also deal with a natural example of tetrablock contraction on a functions space to find out its fundamental operators.