Overall Picture Of Expressed Heat Shock Factors In Glycine Max, Lotus Japonicusand Medicago Truncatula

Heat shock (HS) leads to the activation of molecular mechanisms, known as HS-response, that prevent damage and enhance survival under stress. Plants have a flexible and specialized network of Heat Shock Factors (HSFs), which are transcription factors that induce the expression of heat shock proteins. The present work aimed to identify and characterize the Glycine maxHSF repertory in the Soybean Genome Project (GENOSOJA platform), comparing them with other legumes (Medicago truncatulaand Lotus japonicus) in view of current knowledge of Arabidopsis thaliana. The HSF characterization in leguminous plants led to the identification of 25, 19 and 21 candidate ESTs in soybean, Lotusand Medicago, respectively. A search in the SuperSAGE libraries revealed 68 tags distributed in seven HSF gene types. From the total number of obtained tags, more than 70% were related to root tissues (water deficit stress libraries vs.controls), indicating their role in abiotic stress responses, since the root is the first tissue to sense and respond to abiotic stress. Moreover, as heat stress is related to the pressure of dryness, a higher HSF expression was expected at the water deficit libraries. On the other hand, expressive HSF candidates were obtained from the library inoculated with Asian Soybean Rust, inferring crosstalk among genes associated with abiotic and biotic stresses. Evolutionary relationships among sequences were consistent with different HSF classes and subclasses. Expression profiling indicated that regulation of specific genes is associated with the stage of plant development and also with stimuli from other abiotic stresses pointing to the maintenance of HSF expression at a basal level in soybean, favoring its activation under heat-stress conditions. © 2012, Sociedade Brasileira de Genética.35SUPPL.1247259Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J., Basic local alignment search tool (1990) J Mol Biol, 215, pp. 403-410Baniwal, S.K., Chan, K.Y., Scharf, K.-D., Nover, L., Role of heat stress transcription factor HsfA5 as specific repressor of HsfA4* (2007) J Biol Chem, 282, pp. 3605-3613Bharti, K., Schimidt, E., Lyck, R., Bublak, D., Scharf, K.-D., Isolation and characterization of HsfA3, a new heat stress transcription factor of Lycopersicon peruvianum (2000) Plant J, 22, pp. 355-365Bharti, K., von Koskull-Döring, P., Bharti, S., Kumar, P., Tintschl-Körbitzer, A., Treuter, E., Nover, L., Tomato heat stress transcription factor HsfB1 represents a novel type of general transcription coactivator with a histone-like motif interacting with HAC1/CBP (2004) Plant Cell, 16, pp. 1521-1535Efeoglu, B., Heat shock proteins and heat shock response in plants (2009) G U J Sci, 22, pp. 67-75Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, D., Cluster analysis and display of genome-wide expression patterns (1998) Proc Natl Acad Sci USA, 95, pp. 14863-14868Fehr, W.R., Caviness, C.E., Burmood, D.T., Pennington, I.S., Stage of development descriptions for soybeans, Glycine max (L.) Merrill (1971) Crop Sci, 11, pp. 929-931Fehr, W.R., Caviness, C.E., (1977) Stage of Soybean Development, p. 12. , Special Report n. 80. Ames, Iowa State University of Science and Technology, IowaGlombitza, S., Dubuis, P.-H., Thulke, O., Welzl, G., Bovet, L., Götz, M., Affenzeller, M., Asnaghi, C., Crosstalk and differential response to abiotic and biotic stressors reflected at the transcriptional level of effector genes from secondary metabolism (2004) Plant Mol Biol, 54, pp. 817-835Heerklotz, D., Doring, P., Bonzelius, F., Winkelhaus, S., Nover, L., The balance of nuclear import and export determines the intracellular distribution and function of tomato heat stress transcription factor HsfA2 (2001) Mol Cell Biol, 21, pp. 1759-1768Hoagland, D., Arnon, D.I., The water culture method for growing plants without soil (1950) Calif Agric Exp Stn Circ, 347, pp. 1-32Hsu, S.-F., Lai, H.-C., Jinn, T.-L., Cytosol-localized heat shock factor-binding protein, AtHSBP, functions as a negative regulator of heat shock response by translocation to the nucleus and is required for seed development in Arabidopsis (2010) Plant Physiol, 153, pp. 773-784Hu, W., Hu, G., Han, B., Genome-wide survey and expression profiling of heat shock proteins and heat shock factors revealed overlapped and stress specific response under abiotic stresses in rice (2009) Plant Sci, 176, pp. 583-590Kido, E.A., Barbosa, P.K., Ferreira Neto, J.C.R., Pandolfi, V., Houllou-Kido, L.M., Crovella, S., Benko-Iseppon, A.M., Identification of plant protein kinases in response to abiotic and biotic stresses using SuperSAGE (2011) Curr Prot Pept Sci, 12, pp. 643-656Kotak, S., Port, M., Ganguli, A., Bicker, F., von Koskull-Doring, P., Characterization of C-terminal domains of Arabidopsis heat stress transcription factors (Hsfs) and identification of a new signature combination of plant class a Hsfs with AHA and NES motifs essential for activator function and intracellular localization (2004) Plant J, 39, pp. 98-112Kotak, S., Larkindale, J., Lee, U., von Koskull-Doring, P., Vierling, E., Scharf, K.D., Complexity of the heat stress response in plants (2007) Curr Opin Plant Biol, 10, pp. 310-316Li, H.-Y., Chang, C.-S., Lu, L.-S., Liu, C.-A., Chan, M.-T., Charng, Y.-Y., Over-expression of Arabidopsis thaliana heat shock factor gene (AtHsfA1b) enhances chilling tolerance in transgenic tomato (2004) Bot Bull Acad Sin, 44, pp. 129-140Li, M., Berendzen, K.W., Schoffl, F., Promoter specificity and interactions between early and late Arabidopsis heat shock factors (2010) Plant Mol Biol, 73, pp. 559-567McClean, P.E., Mamidi, S., McConnell, M., Chikara, S., Lee, R., Synteny mapping between common bean and soybean reveals extensive blocks of shared loci (2010) BMC Genomics, 11, pp. e184Miller, G., Mittler, R., Could heat shock transcription factors function as hydrogen peroxide sensors in plant? (2006) Ann Bot, 98, pp. 279-288Mittal, D., Chakrabarti, S., Sarkar, A., Singh, A., Grover, A., Heat shock factor gene family in rice: Genomic organization and transcript expression profiling in response to high temperature, low temperature and oxidative stresses (2009) Plant Physiol Biochem, 47, pp. 785-795Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K., Tran, L.-S.P., In silico analysis of transcription factor repertoire and prediction of stress responsive transcription factors in soybean (2009) DNA Res, 16, pp. 353-369Mochida, K., Yoshida, T., Sakurai, T., Yamaguchi-Shinozaki, K., Shinozaki, K., Tran, L.-S.P., LegumeTFDB: An in-tegrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors (2009) Bioinformatics, 26, pp. 290-291Nascimento, L.C., Costa, G.G.L., Binneck, E., Pereira, G.A.G., Caraz-Zolle, M.F., A web-based bioinformatics interface applied to Genosoja Project: Databases and pipelines (2012) Genet Mol Biol, 35 (SUPPL. 1), pp. 203-211Nover, L., Bharti, K., Doring, P., Mishra, S.K., Ganguli, A., Scharf, K.-D., Arabidopsis and the heat stress transcription factor world: How many heat stress transcription factors do we need? (2001) Cell Stress Chap, 6, pp. 177-189Pirkkala, L., Nykanen, I., Sistonen, L., Roles of the heat shock transcription factors in regulation of the heat shock response and beyond (2001) FASEB J, 15, pp. 1118-1131Ruelland, E., Zachowski, A., How plants sense temperature (2010) Environ Exp Bot, 69, pp. 225-232Sato, Y., Yokoya, S., Enhanced tolerance to drought stress in transgenic rice plants overexpressing a small heat-shock protein, sHSP17.7 (2008) Plant Cell Rep, 27, pp. 329-334Scharf, K.-D., Rose, S., Thierfelder, J., Nover, L., Two cDNAs for tomato heat stress transcription factors (1993) Plant Physiol, 102, pp. 1355-1356Scharf, K.-D., Rose, S., Zott, W., Schoffl, F., Nover, L., Three tomato genes code for heat stress transcription factors with a regionofremarkable homology to the DNA-binding domain of the yeast HSF (1990) EMBO J, 9, pp. 4495-4501Schöff, F., Prändl, R., Reindl, A., Regulation of the heat-shock response (1998) Plant Physiol, 117, pp. 1135-1141Sung, D.-Y., Kaplan, F., Lee, K.-J., Guy, C.L., Acquired tolerance to temperature extremes (2003) Trends Plant Sci, 8, pp. 179-187Swindell, W.R., Huebner, M., Weber, A.P., Transcriptional profiling of Arabidopsis heat shock proteins and transcription factors reveals extensive overlap between heat and non-heat stress response pathways (2007) BMC Genomics, 8, pp. e125Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S., MEGA5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods (2011) Mol Biol Evol, 28, pp. 2731-2739Treshow, M., (1970) Environment and Plant Response, p. 421. , McGraw-Hill Company, New YorkTreuter, E., Nover, L., Ohme, K., Scharf, K.-D., Promoter specificity and deletion analysis of three tomato heat stress transcription factors (1993) Mol Gen Genet, 240, pp. 113-125Yamada, K., Fukao, Y., Hayashi, M., Fukazawa, M., Suzuki, I., Nishimura, M., Cytosolic HSP90 regulated the heat shock response that is responsible for heat acclimation in Arabidopsis thaliana (2007) J Biol Chem, 282, pp. 37794-3780

Density functional study of the adsorption of K on the Ag(111) surface

Full-potential gradient corrected density functional calculations of the adsorption of potassium on the Ag(111) surface have been performed. The considered structures are Ag(111) (root 3 x root 3) R30degree-K and Ag(111) (2 x 2)-K. For the lower coverage, fcc, hcp and bridge site; and for the higher coverage all considered sites are practically degenerate. Substrate rumpling is most important for the top adsorption site. The bond length is found to be nearly identical for the two coverages, in agreement with recent experiments. Results from Mulliken populations, bond lengths, core level shifts and work functions consistently indicate a small charge transfer from the potassium atom to the substrate, which is slightly larger for the lower coverage.Comment: to appear in Phys Rev

An Overall Evaluation Of The Resistance (r) And Pathogenesis-related (pr) Super Families In Soybean, As Compared With Medicago And Arabidopsis

Plants have the ability to recognize and respond to a multitude of pathogens, resulting in a massive reprogramming of the plant to activate defense responses including Resistance (R) and Pathogenesis-Related (PR) genes. Abiotic stresses can also activate PR genes and enhance pathogen resistance, representing valuable genes for breeding purposes. The present work offers an overview of soybean Rand PR genes present in the GENOSOJA (Brazilian Soybean Genome Consortium) platform, regarding their structure, abundance, evolution and role in the plant-pathogen metabolic pathway, as compared with Medicago and Arabidopsis. Searches revealed 3,065 R candidates (756 in Soybean, 1,142 in Medicago and 1,167 in Arabidopsis), and PR candidates matching to 1,261 sequences (310, 585 and 366 for the three species, respectively). The identified transcripts were also evaluated regarding their expression pattern in 65 libraries, showing prevalence in seeds and developing tissues. Upon consulting the Super SAGE libraries, 1,072 Rand 481 PR tags were identified in association with the different libraries. Multiple alignments were generated forXa21andPR-2genes, allowing inferences about their evolution. The results revealed interesting insights regarding the variability and complexity of defense genes in soybean, as compared with Medicago and Arabidopsis. © 2012, Sociedade Brasileira de Genética.35SUPPL.1260271Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., Walter, P., (2002) Molecular Biology of the Cell, p. 1616. , 4th edition. Garland Publishing Company, New York & LondonAltschul, S.F., Gish, W., Miller, W., Myers, E., Basic local alignment search tool (1990) J Mol Biol, 215, pp. 403-410Ashfield, T., Bocian, A., Held, D., Henk, A.D., Marek, L.F., Danesh, D., Penuela, S., Young, N.D., Genetic and physical localization of the soybean Rpg1-b disease resistance gene reveals a complex locus containing several tightly linked families of NBS-LRR genes (2003) Mol Plant Microbe Interact, 16, pp. 817-826Atici, O., Nalbantoglu, B., Antifreeze proteins in higher plants (2003) Phytochemistry, 64, pp. 1187-1196Barbosa-da-Silva, A., Wanderley-Nogueira, A.C., Silva, R.R.M., Belarmino, L.C., Soares-Cavalcanti, N.M., Benko-Iseppon, A.M., In silico survey of resistance (R) genes in Eucalyptus transcriptome (2005) Genet Mol Biol, 28, pp. 562-574Benko-Iseppon, A.M., Galdino, S.L., Calsa, T., Kido, E.A., Tossi, A., Belarmino, L.C., Crovella, S., Overview of plant antimicrobial peptides (2010) Curr Prot Pept Sci, 11, pp. 181-188Bent, A.F., Plant disease resistance genes: Function meets structure (1996) Plant Cell, 8, pp. 1751-1771Bolton, M., Primary metabolism and plant defense-Fuel for the fire (2009) Mol Plant Microbe Interact, 22, pp. 487-497Bonas, U., Anckerveken, G.V., Gene-for-gene interactions: Bacterial avirulence proteins specify plant disease resistance (1999) Curr Opin Plant Biol, 2, pp. 94-98Bonasera, J.M., Kim, J.F., Beer, S.V., PR genes of apple: Identification and expression in response to elicitors and inoculation with Erwinia amylovora (2006) BMC Plant Biol, 6, pp. 23-34Cannon, S.B., May, G.D., Jackson, S.A., Three sequenced legume genomes and many crop species: Rich opportunities for translational genomics (2009) Plant Physiol, 151, pp. 970-977Chester, K.S., The problem of acquired physiological immunity in plants (1933) Quart Rev Phytopathol, 42, pp. 185-209Dafny-Yelin, M., Tzfira, T., Delivery of multiple trans-genes to plant cells (2007) Plant Physiol, 145, pp. 1118-1128Dinesh-Kumar, S.P., Whitham, S., Choi, D., Hehl, R., Corr, C., Baker, B., Transposon tagging of tobacco mosaic virus resistance gene N:I its possible role in the TMV-N-mediated signal transduction pathway (1995) Proc Natl Acad Sci USA, 92, pp. 4175-4180Dixon, M.S., Jones, D.A., Keddie, J.S., Thomas, C.T., Harrison, K., Jones, J.D.G., The tomato Cf2 disease resistance locus comprises two functional genes encoding leucine rich repeats proteins (1996) Cell, 84, pp. 451-459Durrant, W.E., Dong, X., Systemic acquired resistance (2004) Annu Rev Plant Pathol, 42, pp. 185-209Eisen, M.B., Spellman, P.T., Brown, P.O., Botstein, B., Cluster analysis and display of genome-wide expression patterns (1998) Genetics, 25, pp. 14863-14868Ellis, J., Jones, D., Structure and function of proteins controlling strain-specific pathogen resistance in plants (2000) Curr Opin Plant Biol, 1, pp. 288-293Ellis, J., Lawrence, G.J., Finnegan, E.J., Anderson, P.A., Contrasting complexity of two rust resistance loci in flax (1995) Proc Natl Acad Sci USA, 92, pp. 4185-4188Ellis, J., Dodds, P., Pryor, T., Structure, function and evolution of plant disease resistance genes (2000) Curr Opin Plant Biol, 3, pp. 278-284Gaffney, T., Friedrich, L., Vernooij, B., Negrotto, D., Nye, G., Ukness, S., Ward, E., Kessman Hand Ryals, J., Requirementofsalicylic acid for the induction of systemic acquired resistance (1993) Science, 261, pp. 754-756Glombitza, S., Dubuis, P.-H., Thulke, O., Welzl, G., Bovet, L., Götz, M., Affenzeller, M., Asnaghi, C., Crosstalk and differential response to abiotic and biotic stressors reflected at the transcriptional level of effector genes from secondary metabolism (2004) Plant Mol Biol, 54, pp. 817-835Griffith, M., Yaish, M.W.F., Antifreeze proteins in overwintering plants: A tale of two activities (2004) Trends Plant Sci, 9, pp. 399-405Hammond-Kosack, K.E., Jones, J.D.G., Plant disease resistance genes (1997) Annu Rev Plant Physiol, 48, pp. 575-607Hon, W.C., Griffith, M., Mlynarz, A., Kwok, Y.C., Yang, D.S.C., Antifreeze proteins in winter rye are similar to pathogenesis-related proteins (1995) Plant Physiol, 109, pp. 879-889Hulbert, S.H., Webb, C.A., Smith, S.M., Sun, Q., Resistance gene complexes: Evolution and utilization (2001) Annu Rev Phytopathol, 39, pp. 285-312Joahal, G.S., Briggs, S.P., Reductase activity encodes by the Hm1 resistance gene in maize (1992) Science, 198, pp. 985-987Kanazin, V., Marek, L.F., Shoemaker, R.C., Resistance gene analogs are conserved and clustered in soybean (1996) Proc Natl Acad Sci USA, 93, pp. 11746-11750Kido, E.A., Barbosa, P.K., Ferreira Neto, J.C.R., Pandolfi, V., Houllou-Kido, L.M., Crovella, S., Benko-Iseppon, A.M., Identification of plant protein kinases in response to abiotic and biotic stresses using Super SAGE (2011) Curr Prot Pept Sci, 12, pp. 643-656Kitajima, S., Sato, F., Plant pathogenesis-related proteins: Molecular mechanisms of gene expression and protein function (1999) J Biochem, 125, pp. 1-8Lavin, M., Herendeen, P.S., Wojciechowski, M.F., Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary (2005) Syst Biol, 54, pp. 575-594Lawrence, G.J., Finnegan, E.J., Ayliffe, M.A., Ellis, J.G., The L6 gene for flax rust resistance is related to the Arabidopsis bacterial resistance gene RPS2 and the tobacco viral resistance gene (1995) N. Plant Cell, 7, pp. 1195-1206Leubner-Metzger, G., β-1,3-glucanase gene expression in low-hydrated seeds as a mechanism for dormancy release during tobacco after-ripening (2005) Plant J, 41, pp. 133-145Li, L., He, H., Zhang, J., Wang, X., Bai, S., Stolc, V., Tongprasit, W., Deng, X.W., Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays (2008) Genome Biol, 9, pp. R57Libault, M., Farmer, A., Joshi, T., Takahashi, K., Langley, R.J., Franklin, L.D., He, J., Stacey, G., An integrated transcriptome atlas of the crop model Glycine max and its use in comparative analyses in plants (2010) Plant J, 63, pp. 86-99Liu, B., Zhang, S., Zhu, X., Yang, Q., Wu, S., Mei, M., Mauleon, R., Leung, H., Candidate defense genes as predictors of quantitative blast resistance in rice (2004) Mol Plant Microbe Int, 17, pp. 1146-1152Maisonneuve, B., Bellec, Y., Anderson, P., Michelmore, R.W., Rapid mapping of two genes for resistance to downy mildew from Lactuca serriola to existing clusters of resistance genes (1994) Theor Appl Genet, 89, pp. 96-104Matsumura, H., Kruger, D.H., Kahl, G., Terauchi, R., SuperSAGE: A modern platform for genome-wide quantitative transcript profiling (2008) Curr Pharm Biotechnol, 9, pp. 368-374Melotto, M., Coelho, M.F., Pedrosa-Harand, A., Kelly, J.D., Camargo, L.E., The anthracnose resistance locus Co-4 of common bean is located on chromosome 3 and contains putative disease resistance-related genes (2004) Theor Appl Genet, 109, pp. 690-699Metzler, M.C., Cutt, J.R., Klessig, D.F., Isolation and characterization of a gene encoding a PR-1 like protein from Arabidopsis thaliana (1991) Plant Physiol, 96, pp. 346-348Michelmore, R.W., Meyers, B.C., Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process (1998) Genome Res, 8, pp. 1113-1130Mindrinos, M., Katagiri, F., Yu, G.L., Ausubel, F.M., The Arabidopsis thaliana disease resistance gene encodes a protein containing a nucleotide-binding site and leucine rich repeats (1994) Cell, 78, pp. 1089-1099Mudge, J., Cannon, S.B., Kalo, P., Oldroyd, G.E., Roe, B.A., Town, C.D., Young, N.D., Highly syntenic regions in the genomes of soybean, Medicago truncatula and Arabidopsis thaliana (2005) BMC Plant Biol, 5, pp. e15Nanda, A.K., Andrio, E., Marino, D., Pauly, N., Dunand, C., Reactive Oxygen Species during plant-microorganism early interactions (2010) J Integr Plant Biol, 52, pp. 195-204Nurnberg, T., Brunner, F., Innate immunity in plants and animals: Emerging parallels between the recognition of general elicitors and pathogen-associated molecular patterns (2002) Curr Opin Plant Biol, 5, pp. 318-324Page, R.D., (1996) Comp Appl Biosci, 12, pp. 357-358Rayapati, P.J., Lee, M., Gregory, J.W., Wise, R.P., A linkage map of diploid Avena based on RFLP loci and a locus conferring resistance to nine isolates of Puccinia coronata var. 'avenae' (1994) Theor Appl Genet, 89, pp. 831-837Salmeron, J.M., Oldroyd, G.E.D., Romens, C.M.T., Scofield, S.R., Kim, H.S., Lavelle, D.T., Dahlbeck, D., Staskawicz, B.J., Tomato Prf is a member of the leucine rich repeats class of plant disease resistance genes and lies embedded within the Pto kinase gene cluster (1996) Cell, 86, pp. 123-133Shoemaker, R.C., Schlueter, J., Doyle, J.J., Paleopolyploidy and gene duplication in soybean and other legumes (2006) Curr Opin Plant Biol, 9, pp. 104-109Song, W.Y., Pi, L.Y., Wang, G.L., Gardner, J., Holsten, T., Ronald, P.C., Evolution of the rice Xa21 disease resistance genes family (1997) Plant Cell, 9, pp. 1279-1287Song, W.Y., Wang, G.L., Kim, H.S., Pi, L.Y., Gardner, J., Wang, B., Holsten, T., Fauquet, C., A receptor kinase-like protein encoded by the rice disease resistance gene Xa21 (1995) Science, 270, pp. 1804-1806Sparla, F., Rotino, L., Valgimigli, M.C., Pupillo, P., Trost, P., Systemic resistance induced by benzothisdizole in pear inoculated with the agent of fire blight (2004) Sci Hortic, 101, pp. 269-279Tamura, K., Dudley, J., Nei, M., Kumar, S., MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software ver. 4.0 (2007) Mol Biol Evol, 24, pp. 1596-1599Tang, X., Xie, M., Kim, Y.J., Zhou, J., Klessing, D.F., Martin, G.B., Overexpression of Pto activates defense responses and confers broad resistance (1999) Plant Cell, 11, pp. 15-29Thiel, T., Graner, A., Waugh, R., Grosse, I., Close, T.J., Stein, N., Evidence and evolutionary of ancient whole-genome duplication in barley predating the divergence from rice (2009) BMC Evol Biol, 9, pp. 209-227Tornero, P., Gadea, J., Conejero, V., Vera, P., Two PR-1 genes from tomato are differentially regulated and reveal a novel mode of expression for a pathogenesis-related gene during the hypersensitive response and development (1997) Plant Microbe Interact, 10, pp. 624-634Van-Loon, L.C., Geraats, B.P.J., Linthorst, H.J.M., Ethylene as a modulator of disease resistance in plants (2006) Trends Plant Sci, 11, pp. 184-191Van-Loon, L.C., Pierpoint, W.S., Boller, T., Conejero, V., Recommendations for naming plant pathogenesis-related proteins (1999) Plant Mol Biol Rep, 12, pp. 245-264Velazhahan, R., Muthukrishnan, S., Transgenic tobacco plants constitutively overexpressing a rice thaumatin-like protein (PR-5) show enhanced resistance to Alternaria alternata (2003) Plant Biol, 47, pp. 347-354Vergne, E., Grand, X., Ballini, R., Chalvon, V., Saindrenan, P., Tharreau, D., Nottéghem, J.-L., Morel, J.-B., Preformed expression of defense is a hallmark of partial resistance to rice blast fungal pathogen Magnaporthe oryzae (2010) BMC Plant Biol, 10, pp. e206Wanderley-Nogueira, A.C., Mota, N., Lima-Morais, D., Silva, L.C.B., Silva, A.B., Benko-Iseppon, A.M., Abundance and diversity of resistance (R) genes in the sugarcane trans-criptome (2007) Genet Mol Res, 6, pp. 866-889Wang, G.L., Holsten, T.E., Song, W.Y., Wang, H.P., Ronald, P.C., Construction of a rice bacterial artificial chromosome library and identification of clones linked to the Xa21 disease resistance locus (1995) Plant J, 7, pp. 525-533Wendell, J., Genome evolution in polyploids (2000) Plant Mol Biol, 42, pp. 225-249Weng, J.K., Banks, J.A., Chapple, C., Parallels in lignin biosynthesis: A study in Selaginella moellendorffii reveals convergence across 400 million years of evolution (2008) Comm Int Biol, 1, pp. 20-22Wilkstrom, N., Savolainen, V., Chase, M.W., Evolution of the angiosperms: Calibrating the family tree (2001) Proc Soc Biol Sci, 268, pp. 2211-2220Zeier, J., Pink, B., Mueller, M.J., Berger, S., Light conditions influence specific defense responses in incompatible plant-pathogen interactions: Uncoupling systemic resistance from salicylic acid and PR-1 accumulation (2004) Planta, 219, pp. 673-68

Green manure in coffee systems in the region of Zona da Mata, Minas Gerais: characteristics and kinetics of carbon and nitrogen mineralization.

The use of green manure may contribute to reduce soil erosion and increase the soil organic matter content and N availability in coffee plantations in the Zona da Mata, State of Minas Gerais, in Southeastern Brazil. The potential of four legumes (A. pintoi, C. mucunoides, S. aterrimum and S. guianensis)to produce above-ground biomass, accumulate nutrients and mineralize N was studied in two coffee plantations of subsistence farmers under different climate conditions. The biomass production of C. mucunoides was influenced by the shade of the coffee plantation.C. mucunoides tended to mineralize more N than the other legumes due to the low polyphenol content and polyphenol/N ratio. In the first year, the crop establishment of A. pintoi in the area took longer than of the other legumes, resulting in lower biomass production and N2 fixation. In the long term, cellulose was the main factor controlling N mineralization. The biochemical characteristics, nutrient accumulation and biomass production of the legumes were greatly influenced by the altitude and position of the area relative to the sun

Search for lepton-flavor violation at HERA

A search for lepton-flavor-violating interactions $e p \to \mu X$ and $e p\to \tau X$ has been performed with the ZEUS detector using the entire HERA I data sample, corresponding to an integrated luminosity of 130 pb^{-1}. The data were taken at center-of-mass energies, $\sqrt{s}$, of 300 and 318 GeV. No evidence of lepton-flavor violation was found, and constraints were derived on leptoquarks (LQs) that could mediate such interactions. For LQ masses below $\sqrt{s}$, limits were set on $\lambda_{eq_1} \sqrt{\beta_{\ell q}}$, where $\lambda_{eq_1}$ is the coupling of the LQ to an electron and a first-generation quark $q_1$, and $\beta_{\ell q}$ is the branching ratio of the LQ to the final-state lepton $\ell$ ($\mu$ or $\tau$) and a quark $q$. For LQ masses much larger than $\sqrt{s}$, limits were set on the four-fermion interaction term $\lambda_{e q_\alpha} \lambda_{\ell q_\beta} / M_{\mathrm{LQ}}^2$ for LQs that couple to an electron and a quark $q_\alpha$ and to a lepton $\ell$ and a quark $q_\beta$, where $\alpha$ and $\beta$ are quark generation indices. Some of the limits are also applicable to lepton-flavor-violating processes mediated by squarks in $R$-Parity-violating supersymmetric models. In some cases, especially when a higher-generation quark is involved and for the process $e p\to \tau X$, the ZEUS limits are the most stringent to date.Comment: 37 pages, 10 figures, Accepted by EPJC. References and 1 figure (Fig. 6) adde

Multijet production in neutral current deep inelastic scattering at HERA and determination of alpha_s

Multijet production rates in neutral current deep inelastic scattering have been measured in the range of exchanged boson virtualities 10 < Q2 < 5000 GeV2. The data were taken at the ep collider HERA with centre-of-mass energy sqrt(s) = 318 GeV using the ZEUS detector and correspond to an integrated luminosity of 82.2 pb-1. Jets were identified in the Breit frame using the k_T cluster algorithm in the longitudinally invariant inclusive mode. Measurements of differential dijet and trijet cross sections are presented as functions of jet transverse energy E_{T,B}{jet}, pseudorapidity eta_{LAB}{jet} and Q2 with E_{T,B}{jet} > 5 GeV and -1 < eta_{LAB}{jet} < 2.5. Next-to-leading-order QCD calculations describe the data well. The value of the strong coupling constant alpha_s(M_Z), determined from the ratio of the trijet to dijet cross sections, is alpha_s(M_Z) = 0.1179 pm 0.0013(stat.) {+0.0028}_{-0.0046}(exp.) {+0.0064}_{-0.0046}(th.)Comment: 22 pages, 5 figure

Measurement of the open-charm contribution to the diffractive proton structure function

Production of D*+/-(2010) mesons in diffractive deep inelastic scattering has been measured with the ZEUS detector at HERA using an integrated luminosity of 82 pb^{-1}. Diffractive events were identified by the presence of a large rapidity gap in the final state. Differential cross sections have been measured in the kinematic region 1.5 < Q^2 < 200 GeV^2, 0.02 < y < 0.7, x_{IP} < 0.035, beta 1.5 GeV and |\eta(D*+/-)| < 1.5. The measured cross sections are compared to theoretical predictions. The results are presented in terms of the open-charm contribution to the diffractive proton structure function. The data demonstrate a strong sensitivity to the diffractive parton densities.Comment: 35 pages, 11 figures, 6 table

Measurement of beauty production in deep inelastic scattering at HERA

The beauty production cross section for deep inelastic scattering events with at least one hard jet in the Breit frame together with a muon has been measured, for photon virtualities Q^2 > 2 GeV^2, with the ZEUS detector at HERA using integrated luminosity of 72 pb^-1. The total visible cross section is sigma_b-bbar (ep -> e jet mu X) = 40.9 +- 5.7 (stat.) +6.0 -4.4 (syst.) pb. The next-to-leading order QCD prediction lies about 2.5 standard deviations below the data. The differential cross sections are in general consistent with the NLO QCD predictions; however at low values of Q^2, Bjorken x, and muon transverse momentum, and high values of jet transverse energy and muon pseudorapidity, the prediction is about two standard deviations below the data.Comment: 18 pages, 4 figure