Biochemical characterization of C4 protein of cotton leaf curl Kokhran virus-Dabawali

Background: Cotton leaf curl Kokhran Virus-Dabawali (CLCuKV-Dab) is a monopartite begomovirus encoding two proteins V1 and V2 in the virion sense and four proteins Cl, C2, C3 and C4 in the complementary sense. The C4 protein of monopartite begomoviruses has been implicated to play a role in symptom determination and virus movement. The present work aims at the biochemical characterization of this protein. Methods: The C4 protein of CLCuKV-Dab was purified in fusion with GST and tested for the ability to hydrolyze ATP and other phosphate containing compounds. ATPase activity was assayed by using radiolabeled gamma-32P]-ATP and separating the product of reaction by thin layer chromatography. The hydrolysis of other compounds was monitored by the formation of a blue colored phosphomolybdate complex which was estimated by measuring the absorbance at 655 nm. Results: The purified GST-C4 protein exhibited metal ion dependent ATPase and inorganic pyrophosphatase activities. Deletion of a sequence resembling the catalytic motif present in phosphotyrosine phosphatases resulted in 70% reduction in both the activities. Mutational analysis suggested arginine 13 to be catalytically important for the ATPase and cysteine 8 for the pyrophosphatase activity of GST-C4. Interaction of V2 with GST-C4 resulted in an increase in both the enzymatic activities of GST-C4. Conclusions: The residues important for the enzymatic activities of GST-C4 are present in a motif different from the classical Walker motifs and the non-classical ATP binding motifs reported so far. General significance: The C4 protein of CLCuKV-Dab, a putative natively unfolded protein, exhibits enzymatic activities.

Quantum entropic ambiguities: Ethylene

In a quantum system, there may be many density matrices associated with a state on an algebra of observables. For each density matrix, one can compute its entropy. These are, in general, different. Therefore, one reaches the remarkable possibility that there may be many entropies for a given state R. Sorkin (private communication)]. This ambiguity in entropy can often be traced to a gauge symmetry emergent from the nontrivial topological character of the configuration space of the underlying system. It can also happen in finite-dimensional matrix models. In the present work, we discuss this entropy ambiguity and its consequences for an ethylene molecule. This is a very simple and well-known system, where these notions can be put to tests. Of particular interest in this discussion is the fact that the change of the density matrix with the corresponding entropy increase drives the system towards the maximally disordered state with maximum entropy, where Boltzman's formula applies. Besides its intrinsic conceptual interest, the simplicity of this model can serve as an introduction to a similar discussion of systems such as colored monopoles and the breaking of color symmetry.

Two new atom centered fragment descriptors and scoring function enhance classification of antibacterial activity

Classification of pharmacologic activity of a chemical compound is an essential step in any drug discovery process. We develop two new atom-centered fragment descriptors (vertex indices) - one based solely on topological considerations without discriminating atomor bond types, and another based on topological and electronic features. We also assess their usefulness by devising a method to rank and classify molecules with regard to their antibacterial activity. Classification performances of our method are found to be superior compared to two previous studies on large heterogeneous data sets for hit finding and hit-to-lead studies even though we use much fewer parameters. It is found that for hit finding studies topological features (simple graph) alone provide significant discriminating power, and for hit-to-lead process small but consistent improvement can be made by additionally including electronic features (colored graph). Our approach is simple, interpretable, and suitable for design of molecules as we do not use any physicochemical properties. The singular use of vertex index as descriptor, novel range based feature extraction, and rigorous statistical validation are the key elements of this study.

Local structural distortions and their role in superconductivity in SmFeAsO1-xFx superconductors

EXAFS studies at the As K edge as a function of temperature were carried out in SmFeAsO1-xFx (x = 0 and 0.2) compounds to understand the role of local structural distortions in superconductivity observed in F-doped compounds. A significant correlation between the thermal variation of local structural parameters such as anion height and superconducting onset is found in the fluorinated compounds. Such a variation in anion height is absent in the non-superconducting compound. An increase in the Fe-As bond distance just below the superconducting onset temperature indicates a similarity between the distortions observed in the high-T-C cuprates and these Fe-based superconductors.

Rainbow Connection Number of Graph Power and Graph Products

Rainbow connection number, rc(G), of a connected graph G is the minimum number of colors needed to color its edges so that every pair of vertices is connected by at least one path in which no two edges are colored the same (note that the coloring need not be proper). In this paper we study the rainbow connection number with respect to three important graph product operations (namely the Cartesian product, the lexicographic product and the strong product) and the operation of taking the power of a graph. In this direction, we show that if G is a graph obtained by applying any of the operations mentioned above on non-trivial graphs, then rc(G) a parts per thousand currency sign 2r(G) + c, where r(G) denotes the radius of G and . In general the rainbow connection number of a bridgeless graph can be as high as the square of its radius 1]. This is an attempt to identify some graph classes which have rainbow connection number very close to the obvious lower bound of diameter (and thus the radius). The bounds reported are tight up to additive constants. The proofs are constructive and hence yield polynomial time -factor approximation algorithms.

A matrix model for QCD: QCD color is mixed

We use general arguments to show that colored QCD states when restricted to gauge invariant local observables are mixed. This result has important implications for confinement: a pure colorless state can never evolve into two colored states by unitary evolution. Furthermore, the mean energy in such a mixed colored state is infinite. Our arguments are confirmed in a matrix model for QCD that we have developed using the work of Narasimhan and Ramadas(3) and Singer.(2) This model, a (0 + 1)-dimensional quantum mechanical model for gluons free of divergences and capturing important topological aspects of QCD, is adapted to analytical and numerical work. It is also suitable to work on large N QCD. As applications, we show that the gluon spectrum is gapped and also estimate some low-lying levels for N = 2 and 3 (colors). Incidentally the considerations here are generic and apply to any non-Abelian gauge theory.

A matrix model for QCD

Gribov's observation that global gauge fixing is impossible has led to suggestions that there may be a deep connection between gauge fixing and confinement. We find an unexpected relation between the topological nontriviality of the gauge bundle and colored states in SU(N) Yang-Mills theory, and show that such states are necessarily impure. We approximate QCD by a rectangular matrix model that captures the essential topological features of the gauge bundle, and demonstrate the impure nature of colored states explicitly. Our matrix model also allows the inclusion of the QCD theta-term, as well as to perform explicit computations of low-lying glueball masses. This mass spectrum is gapped. Since an impure state cannot evolve to a pure one by a unitary transformation, our result shows that the solution to the confinement problem in pure QCD is fundamentally quantum information-theoretic.

A simplified model for dark matter interacting primarily with gluons

We consider a simple renormalizable model providing a UV completion for dark matter whose interactions with the Standard Model are primarily via the gluons. The model consists of scalar dark matter interacting with scalar colored mediator particles. A novel feature is the fact that (in contrast to more typical models containing dark matter whose interactions are mediated via colored scalars) the colored scalars typically decay into multi-quark final states, with no associated missing energy. We construct this class of models and examine associated phenomena related to dark matter annihilation, scattering with nuclei, and production at colliders.

Looking for BSM physics using top-quark polarization and decay-lepton kinematic asymmetries

We explore beyond-standard-model (BSM) physics signatures in the l + jets channel of the t (t) over bar pair production process at the Tevatron and the LHC. We study the effects of BSM physics scenarios on the top-quark polarization and on the kinematics of the decay leptons. To this end, we construct asymmetries using the lepton energy and angular distributions. Further, we find their correlations with the top polarization, net charge asymmetry and top forward-backward asymmetry. We show that when used together, these observables can help discriminate effectively between SM and different BSM scenarios, which can lead to varying degrees of top polarization at the Tevatron as well as the LHC. We use two types of colored mediator models to demonstrate the effectiveness of proposed observables, an s-channel axigluon and a u-channel diquark.

Two-Dimensional Noise-Predictive Maximum Likelihood Method for Magnetic Recording Channels

Noise-predictive maximum likelihood (NPML) is a well known signal detection technique used in partial response maximum likelihood (PRML) scheme in 1D magnetic recording channels. The noise samples colored by the partial response (PR) equalizer are predicted/ whitened during the signal detection using a Viterbi detector. In this paper, we propose an extension of the NPML technique for signal detection in 2D ISI channels. The impact of noise prediction during signal detection is studied in PRML scheme for a particular choice of 2D ISI channel and PR targets.

Shape effects on the yield stress and deformation of silicon nanowires: A molecular dynamics simulation

The tension and compression of single-crystalline silicon nanowires (SiNWs) with different cross-sectional shapes are studied systematically using molecular dynamics simulation. The shape effects on the yield stresses are characterized. For the same surface to volume ratio, the circular cross-sectional SiNWs are stronger than the square cross-sectional ones under tensile loading, but reverse happens in compressive loading. With the atoms colored by least-squares atomic local shear strain, the deformation processes reveal that the failure modes of incipient yielding are dependent on the loading directions. The SiNWs under tensile loading slip in {111} surfaces, while the compressive loading leads the SiNWs to slip in the {110} surfaces. The present results are expected to contribute to the design of the silicon devices in nanosystems.

High-conversion-efficiency and broadband tunable femtosecond noncollinear optical parametric amplifier

We build a compact high-conversion-efficiency and broadband tunable noncollinear optical parametric amplifier (OPA) in the infra-red (IR) pumped by a femtosecond Ti:sapphire CPA laser. The OPA consists of an internal seed of white-light continuum generator (WLG) and two noncollinear optical parametric amplifiers. The tunable wavelength range is from 1.2 mu m to 2.4 mu m for both signal and idle pulses. The total OPA efficiency in the last OPA stage reaches about 40% in a wider tunable spectral range (from 1.3 mu m to 1.7 mu m for signal pulse, from 1.5 mu m to 2.0 mu m for idle pulse respectively).

Conical emission of Ti : sapphire femtosecond laser pulses propagating in water

Conical emission is investigated for Ti:sapphire femtosecond laser pulses propagating in water. The colored rings can be observed in the forward direction due to the constructive and destructive interference of transverse wavevector, which are induced by the spatio-temporal gradient of the free-electron density. With increasing input laser energy, due to filamentation and pulse splitting induced by the plasma created by multiphoton excitation of electrons from the valence band to the conduction band, the on-axis spectrum of the conical emission is widely broadened and strongly modulated with respect to input laser spectrum, and finally remains fairly constant at higher laser energy due to intensity clamping in the filaments.

The development of an asymmetric palladium-catalyzed conjugate addition and its application toward the total syntheses of taiwaniaquinoid natural products

The asymmetric synthesis of quaternary stereocenters remains a challenging problem in organic synthesis. Past work from the Stoltz laboratory has resulted in methodology to install quaternary stereocenters α- or γ- to carbonyl compounds. Thus, the asymmetric synthesis of β-quaternary stereocenters was a desirable objective, and was accomplished by engineering the palladium-catalyzed addition of arylmetal organometallic reagents to α,β-unsaturated conjugate acceptors.

Herein, we described the rational design of a palladium-catalyzed conjugate addition reactions utilizing a catalyst derived from palladium(II) trifluoroacetate and pyridinooxazole ligands. This reaction is highly tolerant of protic solvents and oxygen atmosphere, making it a practical and operationally simple reaction. The mild conditions facilitate a remarkably high functional group tolerance, including carbonyls, halogens, and fluorinated functional groups. Furthermore, the reaction catalyzed conjugate additions with high enantioselectivity with conjugate acceptors of 5-, 6-, and 7-membered ring sizes. Extension of the methodology toward the asymmetric synthesis of flavanone products is presented, as well.

A computational and experimental investigation into the reaction mechanism provided a stereochemical model for enantioinduction, whereby the α-methylene protons adjacent the enone carbonyl clashes with the tert-butyl groups of the chiral ligand. Additionally, it was found that the addition of water and ammonium hexafluorophosphate significantly increases the reaction rate without sacrificing enantioselectivity. The synergistic effects of these additives allowed for the reaction to proceed at a lower temperature, and thus facilitated expansion of the substrate scope to sensitive functional groups such as protic amides and aryl bromides. Investigations into a scale-up synthesis of the chiral ligand (S)-tert-butylPyOx are also presented. This three-step synthetic route allowed for synthesis of the target compound of greater than 10 g scale.

Finally, the application of the newly developed conjugate addition reaction toward the synthesis of the taiwaniaquinoid class of terpenoid natural products is discussed. The conjugate addition reaction formed the key benzylic quaternary stereocenter in high enantioselectivity, joining together the majority of the carbons in the taiwaniaquinoid scaffold. Efforts toward the synthesis of the B-ring are presented.

Eggs, Larvae and Young of The Striped Bass, Roccus saxatilis

Detailed descriptions of the early development of the striped bass, Roccus saxitilis (Walbaum), with emphasis on variation in size and morphology, sequence of fin formation, changes in body form, and attainment of the full complement of maristic numbers, are presented and illustrated for the first time. The egg is spherical, transparent, non-adhesive and relatively large. It is pelagic and buoyant, although it sinks in quiet fresh water. When unfertilized, it averages 1.3 mm, in diameter, but is 3.4 mm. when fertilized and water-hardened. The granular yolk sac, green when alive and whitish-yellow when preserved, averages 1.2 mm., and the single amber-colored oil globule is about 0.6 mm. in diameter. Newly hatched striped bass prolarvae, which range from 2.9-3.7 mm. in total length, are relatively undeveloped and nearly transparent, with no mouth opening, unpigmented eyes, and a greatly enlarged yolk sac with the large oil globule projecting beyond the head. When 5-6 mm. long the yolk sac and oil globule are assimilated and the postlarvae I show advanced development of the internal anatomy. Although the fish is still transparent, scattered melanophores are found on the head and body and chromatophores in the eyes and the ventro-posterior edge of the body. Postlarvae transform to young between 7 and 10 mm. in length when the finfolds are lost except in the dorsal, anal and caudal regions. The largest fish in this group possess a well-formed skeleton with a full complement of 25 vertebrae. Between 10 and 20 mm. in length all fish are fully transformed, muscular tissue renders most of the internal structure obscure, and the myotomes, which generally correspond in number with the vertebrae, are no longer visible. At fish lengths of 20-30 mm. scales are found on all specimens, and with the exception of the pectoral fin-rays, a full complement of meristic structures is present in all other fins. At this stage the body is pigmented uniformly with small spots. Linear regressions between several dependent variables and the , independent variable of standard length indicate that the rate of development of head, eye. and snout to anus lengths is proportional to the length of the larvae and young. Body depth and standard length are non-linear among newly-hatched larvae. Hatchery-reared striped bass demonstrated a slow rate of growth, and were regarded as "stunted," when compared to growth rates observed in another study and field collections. Observations were also made on abnormal eggs and teratological larvae and young. Blue-sac disease is tentatively identified and described for the first time in larvae and pugnosed larvae and young are also described for the first time in striped bass.