A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens

Understanding the mechanisms by which plants trigger host defenses in response to viruses has been a challenging problem owing to the multiplicity of factors and complexity of interactions involved. The advent of genomic techniques, however, has opened the possibility to grasp a global picture of the interaction. Here, we used Arabidopsis thaliana to identify and compare genes that are differentially regulated upon infection with seven distinct (+)ssRNA and one ssDNA plant viruses. In the first approach, we established lists of genes differentially affected by each virus and compared their involvement in biological functions and metabolic processes. We found that phylogenetically related viruses significantly alter the expression of similar genes and that viruses naturally infecting Brassicaceae display a greater overlap in the plant response. In the second approach, virus-regulated genes were contextualized using models of transcriptional and protein-protein interaction networks of A. thaliana. Our results confirm that host cells undergo significant reprogramming of their transcriptome during infection, which is possibly a central requirement for the mounting of host defenses. We uncovered a general mode of action in which perturbations preferentially affect genes that are highly connected, central and organized in modules. © 2012 Rodrigo et al.This work was supported by the Spanish Ministerio de Ciencia e Innovacion (MICINN) grants BFU2009-06993 (S. F. E.) and BIO2006-13107 (C. L.) and by Generalitat Valenciana grant PROMETEO2010/016 (S. F. E.). G. R. is supported by a graduate fellowship from the Generalitat Valenciana (BFPI2007-160) and J.C. by a contract from MICINN grant TIN2006-12860. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Rodrigo Tarrega, G.; Carrera Montesinos, J.; Ruiz-Ferrer, V.; Del Toro, F.; Llave, C.; Voinnet, O.; Elena Fito, SF. (2012). A meta-analysis reveals the commonalities and differences in Arabidopsis thaliana response to different viral pathogens. PLoS ONE. 7(7):40526-40526. https://doi.org/10.1371/journal.pone.0040526S405264052677Peng, X., Chan, E. Y., Li, Y., Diamond, D. L., Korth, M. J., & Katze, M. G. (2009). Virus–host interactions: from systems biology to translational research. Current Opinion in Microbiology, 12(4), 432-438. doi:10.1016/j.mib.2009.06.003Dodds, P. N., & Rathjen, J. P. (2010). Plant immunity: towards an integrated view of plant–pathogen interactions. Nature Reviews Genetics, 11(8), 539-548. doi:10.1038/nrg2812Maule, A., Leh, V., & Lederer, C. (2002). The dialogue between viruses and hosts in compatible interactions. 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Effect of contact plasticity on the seismic response of a 7-duct bundle immersed in fluid

In the reactor core, the ducts, submerged under fluid, are closely packed. As a result, the collision between ducts is inevitable during the seismic load. Understanding seismic response of the ducts needs to consider both the collision between ducts and the inertial effect from the surrounding fluid. For the collision model, we proposed a nonlinear contact model from a full scale simulation to consider the plastic effect during collision; For the fluid effect, we built an acoustic-structural model to obtain the added mass coefficient depending on the duct's location. Next, we integrated the effects from plastic collision and the fluid inertia into a beam model to study the seismic response of a 7-duct bundle, and then discussed the plastic effect on the contact forces, contact durations and duct acceleration. Results show that although contact plasticity hardly affects the ducts' motion, it has a noticeable effect on both contact force and contact energy dissipation. In addition, our result shows that the contact duration for one typical type of collisions tends to be constant

Identification and mRNA Expression of Antioxidant Enzyme Genes in the Mud Crab (Scylla paramamosain) in Response to Acute Ammonia and Nitrite Exposure

Thioredoxin reductase (TrxR) is a conserved protein that is involved in protecting organisms against various oxidative stresses. In this study, a thioredoxin reductase gene was cloned from the mud crab Scylla paramamosain (SpTrxR). The full-length cDNA of SpTrxR is comprised of 2724 bp with a 1791 bp open reading frame that encodes a putative protein of 596 amino acids. The deduced amino acid sequence of SpTrxR contains the typical TrxR domain. Quantitative real-time PCR analysis revealed that the SpTrxR mRNA was distributed abundantly in mud crabs, while strong expression was observed mainly in the gills. The expression of antioxidant enzyme genes (SpTrxR, SpTrx, SpSOD, and SpCAT) was measured using quantitative real-time PCR after acute ammonia and nitrite exposure. The results show that antioxidant enzyme genes (SpTrxR, SpTrx, SpSOD, and SpCAT) were modulated by acute ammonia and nitrite exposure. These results suggest that antioxidant enzyme genes play an important role in protecting organisms against oxidative stres