Investigations on the RNA binding and phosphorylation of groundnut bud necrosis virus nucleocapsid protein

Groundnut bud necrosis virus belongs to the genus Tospovirus, infects a wide range of crop plants and causes severe losses. To understand the role of the nucleocapsid protein in the viral life cycle, the protein was overexpressed in E. coli and purified by Ni-NTA chromatography. The purified N protein was well folded and was predominantly alpha-helical. Deletion analysis revealed that the C-terminal unfolded region of the N protein was involved in RNA binding. Furthermore, the N protein could be phosphorylated in vitro by Nicotiana benthamiana plant sap and by purified recombinant kinases such as protein kinase CK2 and calcium-dependent protein kinase. This is the first report of phoshphorylation of a nucleocapsid protein in the family Bunyaviridae. The possible implications of the present findings for the viral life cycle are discussed.

Molecular Identification and Phylogeny of Bactrocera Species (Diptera: Tephritidae)

Fruit flies that belong to the genus Bactrocera (Diptera: Tephritidae) are major invasive pests of agricultural crops in Asia and Australia. Increased transboundary movement of agricultural produce has resulted in the chance introduction of many invasive species that include Bactrocera mainly as immature stages. Therefore quick and accurate species diagnosis is important at the port of entry, where morphological identification has a limited role, as it requires the presence of adult specimens and the availability of a specialist. Unfortunately when only immature stages are present, a lacunae in their taxonomy impedes accurate species diagnosis. At this juncture, molecular species diagnostics based on COX-I have become handy, because diagnosis is not limited by developmental stages. Yet another method of quick and accurate species diagnosis for Bactrocera spp. is based on the development of species-specific markers. This study evaluated the utility of COX-I for the quick and accurate species diagnosis of eggs, larvae, pupae and adults of B. zonata Saunders, B. tau Walker, and B. dorsalis Hendel. Furthermore the utility of species-specific markers in differentiating B. zonata (500bp) and B. tau (220bp) was shown. Phylogenetic relationships among five subgenera, viz., Austrodacus, Bactrocera, Daculus, Notodacus and Zeugodacus have been resolved employing the 5' region of COX-I (1490-2198); where COX-I sequences for B. dorsalis Hendel, B. tau Walker, B. correcta Bezzi and B. zonata Saunders from India were compared with other NCBI-GenBank accessions. Phylogenetic analysis employing Maximum Parsimony (MP) and Bayesian phylogenetic approach (BP) showed that the subgenus Bactrocera is monophyletic.

On the role of cloud adjustment time scale in simulating precipitation with Relaxed Arakawa-Schubert convection scheme

The precipitation by Relaxed Arakawa-Schubert cumulus parameterization in a General Circulation Model (GCM) is sensitive to the choice of relaxation parameter or specified cloud adjustment time scale. In the present study, we examine sensitivity of simulated precipitation to the choice of cloud adjustment time scale (tau(adj)) over different parts of the tropics using National Center for Environmental Prediction (NCEP) Seasonal Forecast Model (SFM) during June-September. The results show that a single specified value of tau(adj) performs best only over a particular region and different values are preferred over different parts of the world. To find a relation between tau(adj) and cloud depth (convective activity) we choose six regions over the tropics. Based on the observed relation between outgoing long-wave radiation and tau(adj), we propose a linear cloud-type dependent relaxation parameter to be used in the model. The simulations over most parts of the tropics show improved results due to this newly formulated cloud-type dependent relaxation parameter.

Quenching across quantum critical points in periodic systems: Dependence of scaling laws on periodicity

We study the quenching dynamics of a many-body system in one dimension described by a Hamiltonian that has spatial periodicity. Specifically, we consider a spin-1/2 chain with equal xx and yy couplings and subject to a periodically varying magnetic field in the (z) over cap direction or, equivalently, a tight-binding model of spinless fermions with a periodic local chemical potential, having period 2q, where q is a positive integer. For a linear quench of the strength of the magnetic field (or chemical potential) at a rate 1/tau across a quantum critical point, we find that the density of defects thereby produced scales as 1/tau(q/(q+1)), deviating from the 1/root tau scaling that is ubiquitous in a range of systems. We analyze this behavior by mapping the low-energy physics of the system to a set of fermionic two-level systems labeled by the lattice momentum k undergoing a nonlinear quench as well as by performing numerical simulations. We also show that if the magnetic field is a superposition of different periods, the power law depends only on the smallest period for very large values of tau, although it may exhibit a crossover at intermediate values of tau. Finally, for the case where a zz coupling is also present in the spin chain, or equivalently, where interactions are present in the fermionic system, we argue that the power associated with the scaling law depends on a combination of q and the interaction strength.

Percolation and connectivity in AB random geometric graphs

Given two independent Poisson point processes Phi((1)), Phi((2)) in R-d, the AB Poisson Boolean model is the graph with the points of Phi((1)) as vertices and with edges between any pair of points for which the intersection of balls of radius 2r centered at these points contains at least one point of Phi((2)). This is a generalization of the AB percolation model on discrete lattices. We show the existence of percolation for all d >= 2 and derive bounds fora critical intensity. We also provide a characterization for this critical intensity when d = 2. To study the connectivity problem, we consider independent Poisson point processes of intensities n and tau n in the unit cube. The AB random geometric graph is defined as above but with balls of radius r. We derive a weak law result for the largest nearest-neighbor distance and almost-sure asymptotic bounds for the connectivity threshold.

Biochemical characterization of a recombinant Swainsona canescens calcium-dependent protein kinase (ScCPK1)

Calcium-dependent protein kinases (CPKs) constitute a unique family of kinases involved in many physiological responses in plants. Biochemical and kinetic properties of a recombinant Swainsona canescens calcium-dependent protein kinase (ScCPK1) were examined in this study. The optimum pH and temperature for activity were pH 7.5 and 37 degrees C, respectively. Substrate phosphorylation activity of ScCPK1 was calmodulin (CaM) independent. Yet CaM antagonists, W7 N-(6-aminohexyl)-5-chloro-1-naphthalene sulphonamide] and calmidazolium inhibited the activity with IC50 values of 750 nM and 350 pM, respectively. Both serine and threonine residues were found to be phosphorylated in auto-phosphorylated ScCPK1 and in histone III-S phosphorylated by ScCPK1. The Ca2+] for half maximal activity (K-0.5) was found to be 0.4 mu M for ScCPK1 with histone III-S as substrate. Kinetic analysis showed that Km of ScCPK1 for histone III-S was 4.8 mu M. These data suggest that ScCPK1 is a functional Ser/Thr kinase, regulated by calcium, and may have a role in Ca2+-mediated signaling in S. canescens. (C) 2012 Elsevier Masson SAS. All rights reserved.

Mutations in Drosophila Myosin Rod Cause Defects in Myofibril Assembly

The roles of myosin during muscle contraction are well studied, but how different domains of this protein are involved in myofibril assembly in vivo is far less understood. The indirect flight muscles (IFMs) of Drosophila melanogaster provide a good model for understanding muscle development and function in vivo. We show that two missense mutations in the rod region of the myosin heavy-chain gene, Mhc, give rise to IFM defects and abnormal myofibrils. These defects likely result from thick filament abnormalities that manifest during early sarcomere development or later by hypercontraction. The thick filament defects are accompanied by marked reduction in accumulation of flightin, a myosin binding protein, and its phosphorylated forms, which are required to stabilise thick filaments. We investigated with purified rod fragments whether the mutations affect the coiled-coil structure, rod aggregate size or rod stability. No significant changes in these parameters were detected, except for rod thermodynamic stability in one mutation. Molecular dynamics simulations suggest that these mutations may produce localised rod instabilities. We conclude that the aberrant myofibrils are a result of thick filament defects, but that these in vivo effects cannot be detected in vitro using the biophysical techniques employed. The in vivo investigation of these mutant phenotypes in IFM development and function provides a useful platform for studying myosin rod and thick filament formation generically, with application to the aetiology of human myosin rod myopathies. (C) 2012 Elsevier Ltd. All rights reserved.

Serine/Threonine/Tyrosine Protein Kinase Phosphorylates Oleosin, a Regulator of Lipid Metabolic Functions

Plant oils are stored in oleosomes or oil bodies, which are surrounded by a monolayer of phospholipids embedded with oleosin proteins that stabilize the structure. Recently, a structural protein, Oleosin3 (OLE3), was shown to exhibit both monoacylglycerol acyltransferase and phospholipase A(2) activities. The regulation of these distinct dual activities in a single protein is unclear. Here, we report that a serine/threonine/tyrosine protein kinase phosphorylates oleosin. Using bimolecular fluorescence complementation analysis, we demonstrate that this kinase interacts with OLE3 and that the fluorescence was associated with chloroplasts. Oleosin-green fluorescent protein fusion protein was exclusively associated with the chloroplasts. Phosphorylated OLE3 exhibited reduced monoacylglycerol acyltransferase and increased phospholipase A(2) activities. Moreover, phosphatidylcholine and diacylglycerol activated oleosin phosphorylation, whereas lysophosphatidylcholine, oleic acid, and Ca2+ inhibited phosphorylation. In addition, recombinant peanut (Arachis hypogaea) kinase was determined to predominantly phosphorylate serine residues, specifically serine-18 in OLE3. Phosphorylation levels of OLE3 during seed germination were determined to be higher than in developing peanut seeds. These findings provide direct evidence for the in vivo substrate selectivity of the dual-specificity kinase and demonstrate that the bifunctional activities of oleosin are regulated by phosphorylation.

Large mass splittings for fourth generation fermions allowed by LHC Higgs boson exclusion

In the context of the standard model with a fourth generation, we explore the allowed mass spectra in the fourth-generation quark and lepton sectors as functions of the Higgs mass. Using the constraints from unitarity and oblique parameters, we show that a heavy Higgs allows large mass splittings in these sectors, opening up new decay channels involving W emission. Assuming that the hints for a light Higgs do not yet constitute an evidence, we work in a scenario where a heavy Higgs is viable. A Higgs heavier than similar to 800 GeV would in fact necessitate either a heavy quark decay channel t' -> b'W/b' -> t'W or a heavy lepton decay channel tau' -> nu'W as long as the mixing between the third and fourth generations is small. This mixing tends to suppress the mass splittings and hence the W-emission channels. The possibility of the W-emission channel could substantially change the search strategies of fourth-generation fermions at the LHC and impact the currently reported mass limits.

Higgs boson in the MSSM in light of the LHC

We investigate the expectations for the light Higgs signal in the minimal supersymmetric standard model in different search channels at the LHC. After taking into account dark matter and flavor constraints in the minimal supersymmetric standard model with 11 free parameters as well as LHC results on the Higgs sector, we show that the light Higgs signal in the gamma channel is expected to be at most at the level of the standard model Higgs, while the h -> b (b) over bar from W fusion and/or the h -> tau(tau) over bar can be enhanced. For the main discovery mode, we show that a strong suppression of the signal occurs in two different cases: low M-A or large invisible width. The former is however strongly constrained by the recent LHC results. A more modest suppression is associated with the effect of light supersymmetric particles. Looking for such modification of the Higgs properties and searching directly for supersymmetric partners and pseudoscalar Higgs offer two complementary probes of supersymmetry at the LHC.

Flavored co-annihilations

Neutralino dark matter in supersymmetric models is revisited in the presence of flavor violation in the soft supersymmetry breaking sector. We focus on flavor violation the sleptonic sector and study the implications for the co-annihilation regions. Flavor is introduced by a single (mu) over tilde (R) - (T) over tilde (R) insertion in the slepton mass matrix. Limits on insertion from BR(tau -> mu + gamma) are weak in some regions of the parameter space where happen within the amplitudes. We look for overlaps in parameter space where the co-annihilation condition as well as the cancellations within the amplitudes occur. mSUGRA, such overlap regions are not existent, whereas they are present in models non-universal Higgs boundary conditions (NUHM). The effect of flavor violation is fold: (a) it shifts the co-annihilation regions towards lighter neutralino masses (b) co-annihilation cross sections would be modified with the inclusion of flavor violating which can contribute significantly. Even if flavor violation is within the presently limits, this is sufficient to modify the thermally averaged cross-sections by about 15)% in mSUGRA and (20{30)% in NUHM, depending on the parameter space. In overlap regions, the flavor violating cross sections become comparable and in some even dominant to the flavor conserving ones. A comparative study of the channels is for mSUGRA and NUHM cases.

Unraveling siRNA unzipping kinetics with graphene

Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides of RNA have stronger attractive interactions with graphene as compared to DNA residues. These stronger interactions force the double stranded siRNA to spontaneously unzip and bind to the graphene surface. Unzipping always nucleates at one end of the siRNA and propagates to the other end after few base-pairs get unzipped. While both the ends get unzipped, the middle part remains in double stranded form because of torsional constraint. Unzipping probability distributions fitted to single exponential function give unzipping time (tau) of the order of few nanoseconds which decrease exponentially with temperature. From the temperature variation of unzipping time we estimate the energy barrier to unzipping. (C) 2012 American Institute of Physics. http://dx.doi.org/10.1063/1.4742189]

Consistency tests of Ampcalculator and chiral amplitudes in SU(3) Chiral Perturbation Theory: A tutorial-based approach

Ampcalculator (AMPC) is a Mathematica (c) based program that was made publicly available some time ago by Unterdorfer and Ecker. It enables the user to compute several processes at one loop (upto O(p(4))) in SU(3) chiral perturbation theory. They include computing matrix elements and form factors for strong and non-leptonic weak processes with at most six external states. It was used to compute some novel processes and was tested against well-known results by the original authors. Here we present the results of several thorough checks of the package. Exhaustive checks performed by the original authors are not publicly available, and hence the present effort. Some new results are obtained from the software especially in the kaon odd-intrinsic parity non-leptonic decay sector involving the coupling G(27). Another illustrative set of amplitudes at tree level we provide is in the context of tau-decays with several mesons including quark mass effects, of use to the BELLE experiment. All eight meson-meson scattering amplitudes have been checked. The Kaon-Compton amplitude has been checked and a minor error in the published results has been pointed out. This exercise is a tutorial-based one, wherein several input and output notebooks are also being made available as ancillary files on the arXiv. Some of the additional notebooks we provide contain explicit expressions that we have used for comparison with established results. The purpose is to encourage users to apply the software to suit their specific needs. An automatic amplitude generator of this type can provide error-free outputs that could be used as inputs for further simplification, and in varied scenarios such as applications of chiral perturbation theory at finite temperature, density and volume. This can also be used by students as a learning aid in low-energy hadron dynamics.

Flavoured co-annihilation

In minimal supergravity (mSUGRA) or CMSSM, one of the main co-annihilating partners of the neutralino is the lightest stau, (tau) over tilde (1). In the presence of flavour violation in the right-handed sector, the co-annihilating partner would be a flavour mixed state. The flavour effect is two-fold: (a) It changes the mass of (tau) over tilde (1) thus modifying the parameter space of the co-annihilation and (b) flavour violating scatterings could now contribute to the cross-sections in the early Universe. In fact, it is shown that for large enough delta similar to 0.2, these processes would constitute the dominant channels in co-annihilation regions. The amount of flavour mixing permissible is constrained by flavour violating tau -> mu or tau -> e processes. For Delta(RR) mass insertions, the constraints from flavour violation are not strong enough in some regions of the parameter space due to partial cancellations in the amplitudes. In mSUGRA, the regions with cancelations within LFV amplitudes do not overlap with the regions of co-annihilations. In non-universal Higgs model (NUHM), however, these regions do overlap leading to significant flavoured co-annihilations. At the LHC and other colliders, these regions can constitute for interesting signals.

Model independent bounds on the modulus of the pion form factor on the unitarity cut below the omega pi threshold

We calculate upper and lower bounds on the modulus of the pion electromagnetic form factor on the unitarity cut below the omega pi inelastic threshold, using as input the phase in the elastic region known via the Fermi-Watson theorem from the pi pi P-wave phase shift, and a suitably weighted integral of the modulus squared above the inelastic threshold. The normalization at t = 0, the pion charge radius and experimental values at spacelike momenta are used as additional input information. The bounds are model independent, in the sense that they do not rely on specific parametrizations and do not require assumptions on the phase of the form factor above the inelastic threshold. The results provide nontrivial consistency checks on the recent experimental data on the modulus available below the omega pi threshold from e(+)e(-) annihilation and tau-decay experiments. In particular, at low energies the calculated bounds offer a more precise description of the modulus than the experimental data.