Coupling Virus-Induced Gene Silencing to Exogenous Green Fluorescence Protein Expression Provides a Highly Efficient System for Functional Genomics in Arabidopsis and across All Stages of Tomato Fruit Development

Since the advent of the postgenomic era, efforts have focused on the development of rapid strategies for annotating plant genes of unknown function. Given its simplicity and rapidity, virus-induced gene silencing (VIGS) has become one of the preeminent approaches for functional analyses. However, several problems remain intrinsic to the use of such a strategy in the study of both metabolic and developmental processes. The most prominent of these is the commonly observed phenomenon of ""sectoring"" the tissue regions that are not effectively targeted by VIGS. To better discriminate these sectors, an effective marker system displaying minimal secondary effects is a prerequisite. Utilizing a VIGS system based on the tobacco rattle virus vector, we here studied the effect of silencing the endogenous phytoene desaturase gene (pds) and the expression and subsequent silencing of the exogenous green fluorescence protein (gfp) on the metabolism of Arabidopsis (Arabidopsis thaliana) leaves and tomato (Solanum lycopersicum) fruits. In leaves, we observed dramatic effects on primary carbon and pigment metabolism associated with the photobleached phenotype following the silencing of the endogenous pds gene. However, relatively few pleiotropic effects on carbon metabolism were observed in tomato fruits when pds expression was inhibited. VIGS coupled to gfp constitutive expression revealed no significant metabolic alterations after triggering of silencing in Arabidopsis leaves and a mild effect in mature green tomato fruits. By contrast, a wider impact on metabolism was observed in ripe fruits. Silencing experiments with an endogenous target gene of interest clearly demonstrated the feasibility of cosilencing in this system; however, carefully constructed control experiments are a prerequisite to prevent erroneous interpretation.

Cell coupling in mouse pancreatic beta-cells measured in intact islets of Langerhans

The perforated whole-cell configuration of the patch-clamp technique was applied to functionally identified beta-cells in intact mouse pancreatic islets to study the extent of cell coupling between adjacent beta-cells. Using a combination of current- and voltage-clamp recordings, the total gap junctional conductance between beta-cells in an islet was estimated to be 1.22 nS. The analysis of the current waveforms in a voltage-clamped cell ( due to the. ring of an action potential in a neighbouring cell) suggested that the gap junctional conductance between a pair of beta-cells was 0.17 nS. Subthreshold voltage-clamp depolarization (to -55 mV) gave rise to a slow capacitive current indicative of coupling between beta-cells, but not in non-beta-cells, with a time constant of 13.5 ms and a total charge movement of 0.2 pC. Our data suggest that a superficial beta-cell in an islet is in electrical contact with six to seven other beta-cells. No evidence for dye coupling was obtained when cells were dialysed with Lucifer yellow even when electrical coupling was apparent. The correction of the measured resting conductance for the contribution of the gap junctional conductance indicated that the whole-cell K(ATP) channel conductance (G(K,ATP)) falls from approximately 2.5 nS in the absence of glucose to 0.1 nS at 15 mM glucose with an estimated IC(50) of approximately 4 mM. Theoretical considerations indicate that the coupling between beta-cells within the islet is sufficient to allow propagation of [Ca(2+)](i) waves to spread with a speed of approximately 80 mu m s(-1), similar to that observed experimentally in confocal [Ca(2+)](i) imaging.

Impaired phagocytosis by alveolar macrophages from diabetic rats is related to the deficient coupling of LTs to the Fe gamma R signaling cascade

Diabetic individuals are more susceptible to infections and this seems to be related to impaired phagocyte function. Alveolar macrophages (AMs) are the first barrier to prevent respiratory infections Leukotrienes (LTs) increase AM phagocytic activity via Fc gamma R. In this study, we compared AMs from diabetic and nondiabetic rats for phagocytosis via Fc gamma R and the roles of LTs and insulin Diabetes was induced in male Wistar rats by alloxan (42 mg/kg, i.v); macrophages were obtained by bronchoalveolar lavage and IgG-opsonised sheep red blood cells (IgG-SRBC) were used as targets. LTs were added to the AMs 5 min before the addition of IgG-SRBC. AMs were treated with a LT synthesis inhibitor (zileuton, 10 mu M), or antagonists of the LTB(4) receptor (CP105 696, 10 mu M) cys-LT receptor (MK571, 10 mu M), 30 or 20 min before the addition of IgG-SRBC, respectively. We found that the phagocytosis of IgG-SRBC by AMs from diabetic rats is impaired compared with non-diabetic rats. Treatment with the LT inhibitor/antagonists significantly reduced AM phagocytosis in non-diabetic but not diabetic rats. During the phagocytosis of IgG-SRBC LTB(4) and LTC(4) were produced by AMs from both groups. The addition of exogenous LTB(4) or LTD(4) potentiated phagocytosis similarly in both groups Phagocytosis was followed by the phosphorylation of PKC-delta. ERK and Akt This was reduced by zileuton treatment in AMs from non-diabetic but not diabetic rats The addition of insulin to AMs further increased the phagocytosis by increasing PKC-delta phosphorylation These results suggest that the impaired phagocytosis found in AMs from diabetic rats is related to a deficient coupling of LTs to the Fc gamma R signaling cascade and that insulin has a key role in this coupling An essential role for insulin in Innate immunity is suggested (C) 2010 Elsevier Ltd. All rights reserved.

Glucocorticoids in Vivo Induce Both Insulin Hypersecretion and Enhanced Glucose Sensitivity of Stimulus-Secretion Coupling in Isolated Rat Islets

Although glucocorticoids are widely used as antiinflammatory agents in clinical therapies, they may cause serious side effects that include insulin resistance and hyperinsulinemia. To study the potential functional adaptations of the islet of Langerhans to in vivo glucocorticoid treatment, adult Wistar rats received dexamethasone (DEX) for 5 consecutive days, whereas controls (CTL) received only saline. The analysis of insulin release in freshly isolated islets showed an enhanced secretion in response to glucose in DEX-treated rats. The study of Ca(2+) signals by fluorescence microscopy also demonstrated a higher response to glucose in islets from DEX-treated animals. However, no differences in Ca(2+) signals were found between both groups with tolbutamide or KCl, indicating that the alterations were probably related to metabolism. Thus, mitochondrial function was explored by monitoring oxidation of nicotinamide dinucleotide phosphate autofluorescence and mitochondrial membrane potential. Both parameters revealed a higher response to glucose in islets from DEX-treated rats. The mRNA and protein content of glucose transporter-2, glucokinase, and pyruvate kinase was similar in both groups, indicating that changes in these proteins were probably not involved in the increased mitochondrial function. Additionally, we explored the status of Ca(2+)-dependent signaling kinases. Unlike calmodulin kinase II, we found an augmented phosphorylation level of protein kinase C alpha as well as an increased response of the phospholipase C/inositol 1,4,5-triphosphate pathway in DEX-treated rats. Finally, an increased number of docked secretory granules were observed in the beta-cells of DEX animals using transmission electron microscopy. Thus, these results demonstrate that islets from glucocorticoid-treated rats develop several adaptations that lead to an enhanced stimulus-secretion coupling and secretory capacity. (Endocrinology 151: 85-95, 2010)

Iterative strong coupling of dimensionally heterogeneous models

In this article we address decomposition strategies especially tailored to perform strong coupling of dimensionally heterogeneous models, under the hypothesis that one wants to solve each submodel separately and implement the interaction between subdomains by boundary conditions alone. The novel methodology takes full advantage of the small number of interface unknowns in this kind of problems. Existing algorithms can be viewed as variants of the `natural` staggered algorithm in which each domain transfers function values to the other, and receives fluxes (or forces), and vice versa. This natural algorithm is known as Dirichlet-to-Neumann in the Domain Decomposition literature. Essentially, we propose a framework in which this algorithm is equivalent to applying Gauss-Seidel iterations to a suitably defined (linear or nonlinear) system of equations. It is then immediate to switch to other iterative solvers such as GMRES or other Krylov-based method. which we assess through numerical experiments showing the significant gain that can be achieved. indeed. the benefit is that an extremely flexible, automatic coupling strategy can be developed, which in addition leads to iterative procedures that are parameter-free and rapidly converging. Further, in linear problems they have the finite termination property. Copyright (C) 2009 John Wiley & Sons, Ltd.

A coupling cutting stock-lot sizing problem in the paper industry

An important production programming problem arises in paper industries coupling multiple machine scheduling with cutting stocks. Concerning machine scheduling: how can the production of the quantity of large rolls of paper of different types be determined. These rolls are cut to meet demand of items. Scheduling that minimizes setups and production costs may produce rolls which may increase waste in the cutting process. On the other hand, the best number of rolls in the point of view of minimizing waste may lead to high setup costs. In this paper, coupled modeling and heuristic methods are proposed. Computational experiments are presented.

Clustering and diffusion in a symplectic map lattice with non-local coupling

We study a symplectic chain with a non-local form of coupling by means of a standard map lattice where the interaction strength decreases with the lattice distance as a power-law, in Such a way that one can pass continuously from a local (nearest-neighbor) to a global (mean-field) type of coupling. We investigate the formation of map clusters, or spatially coherent structures generated by the system dynamics. Such clusters are found to be related to stickiness of chaotic phase-space trajectories near periodic island remnants, and also to the behavior of the diffusion coefficient. An approximate two-dimensional map is derived to explain some of the features of this connection. (C) 2008 Elsevier Ltd. All rights reserved.

A single-step procedure for the preparation of palladium nanoparticles and a phosphine-functionalized support as catalyst for Suzuki cross-coupling reactions

We here report the preparation of supported palladium nanoparticles (NPs) stabilized by pendant phosphine groups by reacting a palladium complex containing the ligand 2-(diphenylphosphino)benzaldehyde with an amino-functionalized silica surface The Pd nanocatalyst is active for Suzuki cross-coupling reaction avoiding any addition of other sources of phosphine ligands The Pd intermediates and Pd NPs were characterized by solid-state nuclear magnetic resonance and transmission electron microscopy techniques The synthetic method was also applied to prepare magnetically recoverable Pd NPs leading to a catalyst that could be reused for up to 10 recycles In summary we gathered the advantages of heterogeneous catalysis magnetic separation and enhanced catalytic activity of palladium promoted by phosphine ligands to synthesize a new catalyst for Suzuki cross-coupling reactions The Pd NP catalyst prepared on the phosphine-functionalized support was more active and selective than a similar Pd NP catalyst prepared on an amino-functionalized support (C) 2010 Elsevier Inc All rights reserved

NMR Chemical Shielding and Spin-Spin Coupling Constants of Liquid NH(3): A Systematic Investigation using the Sequential QM/MM Method

The NMR spin coupling parameters, (1)J(N,H) and (2)J(H,H), and the chemical shielding, sigma((15)N), of liquid ammonia are studied from a combined and sequential QM/MM methodology. Monte Carlo simulations are performed to generate statistically uncorrelated configurations that are submitted to density functional theory calculations. Two different Lennard-Jones potentials are used in the liquid simulations. Electronic polarization is included in these two potentials via an iterative procedure with and without geometry relaxation, and the influence on the calculated properties are analyzed. B3LYP/aug-cc-pVTZ-J calculations were used to compute the V(N,H) constants in the interval of -67.8 to -63.9 Hz, depending on the theoretical model used. These can be compared with the experimental results of -61.6 Hz. For the (2)J(H,H) coupling the theoretical results vary between -10.6 to -13.01 Hz. The indirect experimental result derived from partially deuterated liquid is -11.1 Hz. Inclusion of explicit hydrogen bonded molecules gives a small but important contribution. The vapor-to-liquid shifts are also considered. This shift is calculated to be negligible for (1)J(N,H) in agreement with experiment. This is rationalized as a cancellation of the geometry relaxation and pure solvent effects. For the chemical shielding, U(15 N) Calculations at the B3LYP/aug-pcS-3 show that the vapor-to-liquid chemical shift requires the explicit use of solvent molecules. Considering only one ammonia molecule in an electrostatic embedding gives a wrong sign for the chemical shift that is corrected only with the use of explicit additional molecules. The best result calculated for the vapor to liquid chemical shift Delta sigma((15)N) is -25.2 ppm, in good agreement with the experimental value of -22.6 ppm.

Observational constraints on the dark energy and dark matter mutual coupling

We examine different phenomenological interaction models for Dark Energy and Dark Matter by performing statistical joint analysis with observational data arising from the 182 Gold type la supernova samples, the shift parameter of the Cosmic Microwave Background given by the three-year Wilkinson Microwave Anisotropy Probe observations, the baryon acoustic oscillation measurement from the Sloan Digital Sky Survey and age estimates of 35 galaxies. Including the time-dependent observable, we add sensitivity of measurement and give complementary results for the fitting. The compatibility among three different data sets seem to imply that the coupling between dark energy and dark matter is a small positive value, which satisfies the requirement to solve the coincidence problem and the second law of thermodynamics, being compatible with previous estimates. (c) 2008 Elsevier B.V. All rights reserved.

An alternative approach for general covariant Horava-Lifshitz gravity and matter coupling

Recently, in [3] Horava and Melby-Thompson proposed a nonrelativistic gravity theory with extended gauge symmetry that is free of the spin-0 graviton. We propose a minimal substitution recipe to implement this extended gauge symmetry which reproduces the results obtained by them. Our prescription has the advantage of being manifestly gauge invariant and immediately generalizable to other fields, like matter. We briefly discuss the coupling of gravity with scalar and vector fields found by our method. We show also that the extended gauge invariance in gravity does not force the value of. to be lambda = 1 as claimed in [3]. However, the spin-0 graviton is eliminated even for general lambda.

The effect of the negative coupling parameter on the spectrum of a trapped Bose gas

The interest in attractive Bose-Einstein Condensates arises due to the chemical instabilities generate when the number of trapped atoms is above a critical number. In this case, recombination process promotes the collapse of the cloud. This behavior is normally geometry dependent. Within the context of the mean field approximation, the system is described by the Gross-Pitaevskii equation. We have considered the attractive Bose-Einstein condensate, confined in a nonspherical trap, investigating numerically and analytically the solutions, using controlled perturbation and self-similar approximation methods. This approximation is valid in all interval of the negative coupling parameter allowing interpolation between weak-coupling and strong-coupling limits. When using the self-similar approximation methods, accurate analytical formulas were derived. These obtained expressions are discussed for several different traps and may contribute to the understanding of experimental observations.

One-dimensional trapped atoms: critical coupling parameter and critical number of particles

In this paper we consider the case of a Bose gas in low dimension in order to illustrate the applicability of a method that allows us to construct analytical relations, valid for a broad range of coupling parameters, for a function which asymptotic expansions are known. The method is well suitable to investigate the problem of stability of a collection of Bose particles trapped in one- dimensional configuration for the case where the scattering length presents a negative value. The eigenvalues for this interacting quantum one-dimensional many particle system become negative when the interactions overcome the trapping energy and, in this case, the system becomes unstable. Here we calculate the critical coupling parameter and apply for the case of Lithium atoms obtaining the critical number of particles for the limit of stability.

Systematic structural studies of iron superoxide dismutases from human parasites and a statistical coupling analysis of metal binding specificity

Superoxide dismutases (SODs) are a crucial class of enzymes in the combat against intracellular free radical damage. They eliminate superoxide radicals by converting them into hydrogen peroxide and oxygen. In spite of their very different life cycles and infection strategies, the human parasites Plasmodium falciparum, Trypanosoma cruzi and Trypanosoma brucei are known to be sensitive to oxidative stress. Thus the parasite Fe-SODs have become attractive targets for novel drug development. Here we report the crystal structures of FeSODs from the trypanosomes T. brucei at 2.0 angstrom and T. cruzi at 1.9 angstrom resolution, and that from P. falciparum at a higher resolution (2.0 angstrom) to that previously reported. The homodimeric enzymes are compared to the related human MnSOD with particular attention to structural aspects which are relevant for drug design. Although the structures possess a very similar overall fold, differences between the enzymes at the entrance to the channel which leads to the active site could be identified. These lead to a slightly broader and more positively charged cavity in the parasite enzymes. Furthermore, a statistical coupling analysis (SCA) for the whole Fe/MnSOD family reveals different patterns of residue coupling for Mn and Fe SODs, as well as for the dimeric and tetrameric states. In both cases, the statistically coupled residues lie adjacent to the conserved core surrounding the metal center and may be expected to be responsible for its fine tuning, leading to metal ion specificity.