Free Radicals and Biomarkers Related to the Diagnosis of Cardiorenal Syndrome

The National Heart, Lung, and Blood Institute Working Group has postulated the cardiorenal syndrome (CRS) as an interaction between the kidneys and the cardiovascular system in which therapy to relieve congestive heart failure (HF) symptoms is limited by the further worsening renal function. CRS is classified from type I to V, taking into account the progression of the symptoms in terms of mechanisms, clinical conditions, and biomarkers. Experimental and clinical studies have shown the kidney as both a trigger and a target to sympathetic nervous system (SNS) overactivity. Renal damage and ischemia, activation of the renin angiotensin aldosterone system (RAAS), and dysfunction of nitric oxide (NO) system are associated with kidney adrenergic activation. Indeed, the imbalances of RAAS and/or SNS share an important common process in CRS: the activation and production of free radicals, especially reactive oxygen species (ROS). The present chapter addresses connections of the free radicals as potential biomarkers as the imbalances in the RAAS and the SNS are developed. Understanding the involvement of free radicals in CRS may bring knowledge to design studies in order to develop accurate pharmacological interventions

Stressed, but not defenceless: no obvious influence of irradiation levels on antifeeding and antifouling defences of tropical macroalgae

The production of defence metabolites is assumed to be costly in metabolic terms. If this holds true, low-light stress should reduce the ability of seaweeds to defend themselves chemically against herbivory and fouling. We investigated the effect of energy limitation on the defensive status of seaweeds by assessing their attractiveness to mesograzers and their activity against a bivalve macrofouler in comparison with non-stressed conspecifics. The macroalgae Codium decorticatum (Woodw.) M. Howe, Osmundaria obtusiloba (C. Agardh) R. E. Norris, Pterocladiella capillacea (S. G. Gmel.) Santel. and Hommer., Sargassum vulgare C. Agardh and Stypopodium zonale (Lamour.) Papenf. collected at the southeastern Brazilian coast were exposed to six levels of irradiation (between 1 and 180 μmol photons m−2 s−1) for 10–14 days. After this period, algae from all treatment levels were: (a) processed as artificial food and offered to an amphipod community dominated by Elasmopus brasiliensis Dana and (b) extracted to test for differences in settlement rates of the fouling mussel Perna perna L. on filter paper loaded with the crude extracts. Generally, photosynthesis rates and growth were reduced under low light conditions. Attractiveness to herbivores and macrofoulers, however, was insensitive to energy limitation. We discuss possible explanations for the observed absence of a relationship between light availability and algal defence including the change in nutritional value of the algal tissue, the allocation of resources towards defence instead of growth and the absence of costs for defence

Surface and electronic structure of MOCVD-grown Ga(0.92)In(0.08)N investigated by UV and X-ray photoelectron spectroscopies

The surface and electronic structure of MOCVD-grown layers of Ga(0.92)In(0.08)N have been investigated by means of photoemission. An additional feature at the valence band edge, which can be ascribed to the presence of In in the layer, has been revealed. A clean (0001)-(1x1) surface was prepared by argon ion sputtering and annealing. Stability of chemical composition of the investigated surface subjected to similar ion etching was proven by means of X-ray photoemission spectroscopy.Comment: 13 pages, 6 figure

Genome And Secretome Analysis Of The Hemibiotrophic Fungal Pathogen, Moniliophthora Roreri, Which Causes Frosty Pod Rot Disease Of Cacao: Mechanisms Of The Biotrophic And Necrotrophic Phases

Background: The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp.Results: We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase.Conclusions: Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. These genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease. © 2014 Meinhardt et al.; licensee BioMed Central Ltd.151USDA; U.S. Department of AgricultureLatunde-Dada, A.O., Colletotrichum: tales of forcible entry, stealth, transient confinement and breakout (2001) Mol Plant Pathol, 2 (4), pp. 187-198. , 10.1046/j.1464-6722.2001.00069.x, 20573006Oliver, R.P., Ipcho, S.V.S., Arabidopsis pathology breathes new life into the necrotrophs-vs.-biotrophs classification of fungal pathogens (2004) Mol Plant Pathol, 5 (4), pp. 347-352. , 10.1111/j.1364-3703.2004.00228.x, 20565602Catanzariti, A.M., Dodds, P.N., Lawrence, G.J., Ayliffe, M.A., Ellis, J.G., Haustorially expressed secreted proteins from flax rust are highly enriched for avirulence elicitors (2006) Plant Cell, 18 (1), pp. 243-256. , 10.1105/tpc.105.035980, 1323496, 16326930Link, T.I., Voegele, R.T., Secreted proteins of Uromyces fabae: similarities and stage specificity (2008) Mol Plant Pathol, 9 (1), pp. 59-66Brown, N.A., Antoniw, J., Hammond-Kosack, K.E., The predicted secretome of the plant pathogenic fungus Fusarium graminearum: a refined comparative analysis (2012) Plos One, 7 (4), pp. e33731. , 10.1371/journal.pone.0033731, 3320895, 22493673Thomma, B.P., Alternaria spp.: from general saprophyte to specific parasite (2003) Mol Plant Pathol, 4 (4), pp. 225-236. , 10.1046/j.1364-3703.2003.00173.x, 20569383Evans, H.C., Stalpers, J.A., Samson, R.A., Benny, G.L., Taxonomy of Monilia-Roreri, an important pathogen of theobroma-cacao in South-America (1978) Can J Bot, 56 (20), pp. 2528-2532Aime, M.C., Phillips-Mora, W., The causal agents of witches' broom and frosty pod rot of cacao (chocolate, Theobroma cacao) form a new lineage of Marasmiaceae (2005) Mycologia, 97 (5), pp. 1012-1022. , 10.3852/mycologia.97.5.1012, 16596953Phillips-Mora, W., Wilkinson, M.J., Frosty pod of cacao: a disease with a limited geographic range but unlimited potential for damage (2007) Phytopathology, 97 (12), pp. 1644-1647. , 10.1094/PHYTO-97-12-1644, 18943726Meinhardt, L.W., Rincones, J., Bailey, B.A., Aime, M.C., Griffith, G.W., Zhang, D.P., Pereira, G.A.G., Moniliophthora perniciosa, the causal agent of witches' broom disease of cacao: what's new from this old foe? (2008) Mol Plant Pathol, 9 (5), pp. 577-588. , 10.1111/j.1364-3703.2008.00496.x, 19018989Ferreira, L.F.R., Duarte, K.M.R., Gomes, L.H., Carvalho, R.S., Leal, G.A., Aguiar, M.M., Armas, R.D., Tavares, F.C.A., Genetic diversity of polysporic isolates of Moniliophthora perniciosa (Tricholomataceae) (2012) Genet Mol Res, 11 (3), pp. 2559-2568. , 10.4238/2012.July.10.11, 22869076Phillips-Mora, W., Wilkinson, M.J., Frosty pod: a disease of limited geographic distribution but unlimited potential for damage (2006) Phytopathology, 96 (6), pp. S138-S138Evans, H.C., (1981) Pod Rot of Cacao caused by Moniliophthora (Monilia) roreri, , London: Commonwealth Agricultural Bureau, 24Joosten, M., de Wit, P., THE TOMATO-CLADOSPORIUM FULVUM INTERACTION: a versatile experimental system to study plant-pathogen interactions (1999) Annu Rev Phytopathol, 37, pp. 335-367. , 10.1146/annurev.phyto.37.1.335, 11701827Perfect, S.E., Green, J.R., Infection structures of biotrophic and hemibiotrophic fungal plant pathogens (2001) Mol Plant Pathol, 2 (2), pp. 101-108. , 10.1046/j.1364-3703.2001.00055.x, 20572997Scarpari, L.M., Meinhardt, L.W., Mazzafera, P., Pomella, A.W.V., Schiavinato, M.A., Cascardo, J.C.M., Pereira, G.A.G., Biochemical changes during the development of witches' broom: the most important disease of cocoa in Brazil caused by Crinipellis perniciosa (2005) J Exp Bot, 56 (413), pp. 865-877. , 10.1093/jxb/eri079, 15642708Melnick, R.L., Marelli, J., Bailey, B.A., The molecular interaction of Theobroma cacao and Moniliophthora perniciosa, causal agent of witches' broom, during infection of young pods (2011) Phytopathology, 101 (6), pp. S274-S274Melnick, R.L., Marelli, J.P., Sicher, R.C., Strem, M.D., Bailey, B.A., The interaction of Theobroma cacao and Moniliophthora perniciosa, the causal agent of witches' broom disease, during parthenocarpy (2012) Tree Genet Genomes, 8 (6), pp. 1261-1279Thomazella, D.P., Teixeira, P.J., Oliveira, H.C., Saviani, E.E., Rincones, J., Toni, I.M., Reis, O., Pereira, G.A., The hemibiotrophic cacao pathogen Moniliophthora perniciosa depends on a mitochondrial alternative oxidase for biotrophic development (2012) New Phytol, 194 (4), pp. 1025-1034. , 10.1111/j.1469-8137.2012.04119.x, 3415677, 22443281Mondego, J.M., Carazzolle, M.F., Costa, G.G., Formighieri, E.F., Parizzi, L.P., Rincones, J., Cotomacci, C., Pereira, G.A.G., A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom disease of cacao (2008) Bmc Genomics, 9, p. 548. , 10.1186/1471-2164-9-548, 2644716, 19019209Bailey, B.A., Crozier, J., Sicher, R.C., Strem, M.D., Melnick, R., Carazzolle, M.F., Costa, G.G.L., Meinhardt, L., Dynamic changes in pod and fungal physiology associated with the shift from biotrophy to necrotrophy during the infection of Theobroma cacao by Moniliophthora roreri (2013) Physiol Mol Plant P, 81, pp. 84-96Henrissat, B., A classification of glycosyl hydrolases based on amino acid sequence similarities (1991) Biochem J, 280 (PART 2), pp. 309-316. , 1130547, 1747104Dias, F.M., Vincent, F., Pell, G., Prates, J.A., Centeno, M.S., Tailford, L.E., Ferreira, L.M., Gilbert, H.J., Insights into the molecular determinants of substrate specificity in glycoside hydrolase family 5 revealed by the crystal structure and kinetics of Cellvibrio mixtus mannosidase 5A (2004) J Biol Chem, 279 (24), pp. 25517-25526. , 10.1074/jbc.M401647200, 15014076Fibriansah, G., Masuda, S., Koizumi, N., Nakamura, S., Kumasaka, T., The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96 (2007) Proteins, 69 (3), pp. 683-690. , 10.1002/prot.21589, 17879342Markovic, O., Janecek, S., Pectin degrading glycoside hydrolases of family 28: sequence-structural features, specificities and evolution (2001) Protein Eng, 14 (9), pp. 615-631. , 10.1093/protein/14.9.615, 11707607Vandermarliere, E., Bourgois, T.M., Winn, M.D., van Campenhout, S., Volckaert, G., Delcour, J.A., Strelkov, S.V., Courtin, C.M., Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family (2009) Biochem J, 418 (1), pp. 39-47. , 10.1042/BJ20081256, 18980579Tiels, P., Baranova, E., Piens, K., De Visscher, C., Pynaert, G., Nerinckx, W., Stout, J., Callewaert, N., A bacterial glycosidase enables mannose-6-phosphate modification and improved cellular uptake of yeast-produced recombinant human lysosomal enzymes (2012) Nat Biotechnol, 30 (12), pp. 1225-1231. , 10.1038/nbt.2427, 23159880Ferreira, P., Hernandez-Ortega, A., Herguedas, B., Martinez, A.T., Medina, M., Aryl-alcohol oxidase involved in lignin degradation: a mechanistic study based on steady and pre-steady state kinetics and primary and solvent isotope effects with two alcohol substrates (2009) J Biol Chem, 284 (37), pp. 24840-24847. , 10.1074/jbc.M109.011593, 2757187, 19574215Mayer, A.M., Staples, R.C., Laccase: new functions for an old enzyme (2002) Phytochemistry, 60 (6), pp. 551-565. , 10.1016/S0031-9422(02)00171-1, 12126701Kersten, P.J., Glyoxal oxidase of Phanerochaete chrysosporium: its characterization and activation by lignin peroxidase (1990) Proc Natl Acad Sci U S A, 87 (8), pp. 2936-2940. , 10.1073/pnas.87.8.2936, 53808, 11607073Henrissat, B., Callebaut, I., Fabrega, S., Lehn, P., Mornon, J.P., Davies, G., Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases (1995) Proc Natl Acad Sci U S A, 92 (15), pp. 7090-7094. , 10.1073/pnas.92.15.7090, 41477, 7624375Wostemeyer, J., Kreibich, A., Repetitive DNA elements in fungi (Mycota): impact on genomic architecture and evolution (2002) Curr Genet, 41 (4), pp. 189-198. , 10.1007/s00294-002-0306-y, 12172959Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Oliver, S.G., Life with 6000 genes (1996) Science, 274 (5287), pp. 546-563. , 547, 10.1126/science.274.5287.546, 8849441Dean, R.A., Talbot, N.J., Ebbole, D.J., Farman, M.L., Mitchell, T.K., Orbach, M.J., Thon, M., Nicol, R., The genome sequence of the rice blast fungus Magnaporthe grisea (2005) Nature, 434 (7036), pp. 980-986. , 10.1038/nature03449, 15846337Labbe, J., Murat, C., Morin, E., Tuskan, G.A., Le Tacon, F., Martin, F., Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor (2012) Plos One, 7 (8), pp. e40197. , 10.1371/journal.pone.0040197, 3411680, 22870194Adomako, D., Cocoa pod husk pectin (1972) Phytochemistry, 11 (3), p. 1145Gan, P., Ikeda, K., Irieda, H., Narusaka, M., O'Connell, R.J., Narusaka, Y., Takano, Y., Shirasu, K., Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi (2013) New Phytol, 197 (4), pp. 1236-1249. , 10.1111/nph.12085, 23252678Garcia, O., Macedo, J.A.N., Tiburcio, R., Zaparoli, G., Rincones, J., Bittencourt, L.M.C., Ceita, G.O., Cascardo, J.C., Characterization of necrosis and ethylene-inducing proteins (NEP) in the basidiomycete Moniliophthora perniciosa, the causal agent of witches' broom in Theobroma cacao (2007) Mycol Res, 111, pp. 443-455. , 10.1016/j.mycres.2007.01.017, 17512713Pemberton, C.L., Salmond, G.P., The Nep1-like proteins-a growing family of microbial elicitors of plant necrosis (2004) Mol Plant Pathol, 5 (4), pp. 353-359. , 10.1111/j.1364-3703.2004.00235.x, 20565603Zaparoli, G., Barsottini, M.R., de Oliveira, J.F., Dyszy, F., Teixeira, P.J., Barau, J.G., Garcia, O., Dias, S.M., The crystal structure of necrosis-and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity (2011) Biochemistry-Us, 50 (45), pp. 9901-9910Cabral, A., Oome, S., Sander, N., Kufner, I., Nurnberger, T., Van den Ackerveken, G., Nontoxic Nep1-like proteins of the downy mildew pathogen Hyaloperonospora arabidopsidis: repression of necrosis-inducing activity by a surface-exposed region (2012) Mol Plant Microbe Interact, 25 (5), pp. 697-708. , 10.1094/MPMI-10-11-0269, 22235872Mosquera, G., Giraldo, M.C., Khang, C.H., Coughlan, S., Valent, B., Interaction transcriptome analysis identifies magnaporthe oryzae BAS1-4 as Biotrophy-associated secreted proteins in rice blast disease (2009) Plant Cell, 21 (4), pp. 1273-1290. , 10.1105/tpc.107.055228, 2685627, 19357089Paper, J.M., Scott-Craig, J.S., Adhikari, N.D., Cuomo, C.A., Walton, J.D., Comparative proteomics of extracellular proteins in vitro and in planta from the pathogenic fungus Fusarium graminearum (2007) Proteomics, 7 (17), pp. 3171-3183. , 10.1002/pmic.200700184, 17676664van den Burg, H.A., Harrison, S.J., Joosten, M.H., Vervoort, J., de Wit, P.J., Cladosporium fulvum Avr4 protects fungal cell walls against hydrolysis by plant chitinases accumulating during infection (2006) Mol Plant Microbe Interact, 19 (12), pp. 1420-1430. , 10.1094/MPMI-19-1420, 17153926Roby, D., Gadelle, A., Toppan, A., Chitin oligosaccharides as elicitors of chitinase activity in melon plants (1987) Biochem Biophys Res Commun, 143 (3), pp. 885-892. , 10.1016/0006-291X(87)90332-9, 3566760Deising, H., Siegrist, J., Chitin deacetylase activity of the rust uromyces-viciae-fabae is controlled by fungal morphogenesis (1995) Fems Microbiol Lett, 127 (3), pp. 207-211Teixeira, P.J.P.L., Thomazella, D.P.T., Vidal, R.O., Do Prado, P.F.V., Reis, O., Baroni, R.M., Franco, S.F., Mondego, J.M.C., The fungal pathogen moniliophthora perniciosa has genes similar to plant PR-1 that are highly expressed during its interaction with cacao (2012) Plos One, 7 (9)Riviere, M.P., Marais, A., Ponchet, M., Willats, W., Galiana, E., Silencing of acidic pathogenesis-related PR-1 genes increases extracellular beta-(1→ 3)-glucanase activity at the onset of tobacco defence reactions (2008) J Exp Bot, 59 (6), pp. 1225-1239. , 10.1093/jxb/ern044, 18390849Levy, A., Guenoune-Gelbart, D., Epel, B.L., Beta-1,3-Glucanases: plasmodesmal gate keepers for intercellular communication (2007) Plant Signal Behav, 2 (5), pp. 404-407. , 10.4161/psb.2.5.4334, 2634228, 19704615Prados-Rosales, R.C., Roldan-Rodriguez, R., Serena, C., Lopez-Berges, M.S., Guarro, J., Martinez-del-Pozo, A., Di Pietro, A., A PR-1-like protein of fusarium oxysporum functions in virulence on mammalian hosts (2012) J Biol Chem, 287 (26), pp. 21970-21979. , 10.1074/jbc.M112.364034, 3381157, 22553200Kershaw, M.J., Talbot, N.J., Hydrophobins and repellents: proteins with fundamental roles in fungal morphogenesis (1998) Fungal Genet Biol, 23 (1), pp. 18-33. , 10.1006/fgbi.1997.1022, 9501475Zelena, K., Takenberg, M., Lunkenbein, S., Woche, S.K., Nimtz, M., Berger, R.G., PfaH2: a novel hydrophobin from the ascomycete Paecilomyces farinosus (2013) Biotechnol Appl Biochem, 60 (2), pp. 147-154. , 10.1002/bab.1077, 23600571Wosten, H.A., Hydrophobins: multipurpose proteins (2001) Annu Rev Microbiol, 55, pp. 625-646. , 10.1146/annurev.micro.55.1.625, 11544369Bayry, J., Aimanianda, V., Guijarro, J.I., Sunde, M., Latge, J.P., Hydrophobins-unique fungal proteins (2012) PLoS Pathog, 8 (5), pp. e1002700. , 10.1371/journal.ppat.1002700, 3364958, 22693445De Oliveira, A.L., Gallo, M., Pazzagli, L., Benedetti, C.E., Cappugi, G., Scala, A., Pantera, B., Cicero, D.O., The structure of the elicitor cerato-platanin (CP), the first member of the CP fungal protein family, reveals a double psi beta-barrel fold and carbohydrate binding (2011) J Biol Chem, 286 (20), pp. 17560-17568. , 10.1074/jbc.M111.223644, 3093830, 21454637Baccelli, I., Comparini, C., Bettini, P.P., Martellini, F., Ruocco, M., Pazzagli, L., Bernardi, R., Scala, A., The expression of the cerato-platanin gene is related to hyphal growth and chlamydospores formation in Ceratocystis platani (2012) Fems Microbiol Lett, 327 (2), pp. 155-163. , 10.1111/j.1574-6968.2011.02475.x, 22136757Zaparoli, G., Cabrera, O.G., Medrano, F.J., Tiburcio, R., Lacerda, G., Pereira, G.G., Identification of a second family of genes in Moniliophthora perniciosa, the causal agent of witches' broom disease in cacao, encoding necrosis-inducing proteins similar to cerato-platanins (2009) Mycol Res, 113, pp. 61-72. , 10.1016/j.mycres.2008.08.004, 18796332Lombardi, L., Faoro, F., Luti, S., Baccelli, I., Martellini, F., Bernardi, R., Picciarelli, P., Pazzagli, L., Differential timing of defense-related responses induced by cerato-platanin and cerato-populin, two non-catalytic fungal elicitors (2013) Physiol Plant, 149, pp. 408-421Yang, Y., Zhang, H., Li, G., Li, W., Wang, X., Song, F., Ectopic expression of MgSM1, a Cerato-platanin family protein from Magnaporthe grisea, confers broad-spectrum disease resistance in Arabidopsis (2009) Plant Biotechnol J, 7 (8), pp. 763-777. , 10.1111/j.1467-7652.2009.00442.x, 19754836Bhadauria, V., Banniza, S., Vandenberg, A., Selvaraj, G., Wei, Y., EST mining identifies proteins putatively secreted by the anthracnose pathogen Colletotrichum truncatum (2011) Bmc Genomics, 12, p. 327. , 10.1186/1471-2164-12-327, 3149586, 21699715Frischmann, A., Neudl, S., Gaderer, R., Bonazza, K., Zach, S., Gruber, S., Spadiut, O., Seidl-Seiboth, V., Self-assembly at air/water interfaces and carbohydrate binding properties of the small secreted protein EPL1 from the fungus trichoderma atroviride (2013) J Biol Chem, 288 (6), pp. 4278-4287. , 10.1074/jbc.M112.427633, 3567679, 23250741Jeong, J.S., Mitchell, T.K., Dean, R.A., The magnaporthe grisea snodprot1 homolog, MSP1, is required for virulence (2007) Fems Microbiol Lett, 273 (2), pp. 157-165. , 10.1111/j.1574-6968.2007.00796.x, 17590228Peter, M., Courty, P.E., Kohler, A., Delaruelle, C., Martin, D., Tagu, D., Frey-Klett, P., Martin, F., Analysis of expressed sequence tags from the ectomycorrhizal basidiomycetes Laccaria bicolor and Pisolithus microcarpus (2003) New Phytol, 159 (1), pp. 117-129Cosgrove, D.J., Loosening of plant cell walls by expansins (2000) Nature, 407 (6802), pp. 321-326. , 10.1038/35030000, 11014181Quiroz-Castaneda, R.E., Martinez-Anaya, C., Cuervo-Soto, L.I., Segovia, L., Folch-Mallol, J.L., Loosenin, a novel protein with cellulose-disrupting activity from Bjerkandera adusta (2011) Microb Cell Fact, 10, p. 8. , 10.1186/1475-2859-10-8, 3050684, 21314954Brotman, Y., Briff, E., Viterbo, A., Chet, I., Role of swollenin, an expansin-like protein from Trichoderma, in plant root colonization (2008) Plant Physiol, 147 (2), pp. 779-789. , 10.1104/pp.108.116293, 2409044, 18400936Yamada, M., Sakuraba, S., Shibata, K., Taguchi, G., Inatomi, S., Okazaki, M., Shimosaka, M., Isolation and analysis of genes specifically expressed during fruiting body development in the basidiomycete Flammulina velutipes by fluorescence differential display (2006) Fems Microbiol Lett, 254 (1), pp. 165-172. , 10.1111/j.1574-6968.2005.00023.x, 16451195Rincones, J., Scarpari, L.M., Carazzolle, M.F., Mondego, J.M.C., Formighieri, E.F., Barau, J.G., Costa, G.G.L., Pereira, G.A., Differential gene expression between the biotrophic-like and saprotrophic mycelia of the witches' broom pathogen Moniliophthora perniciosa (2008) Mol Plant Microbe In, 21 (7), pp. 891-908Zerbino, D.R., Birney, E., Velvet: algorithms for de novo short read assembly using de Bruijn graphs (2008) Genome Res, 18 (5), pp. 821-829. , 10.1101/gr.074492.107, 2336801, 18349386Sommer, D.D., Delcher, A.L., Salzberg, S.L., Pop, M., Minimus: a fast, lightweight genome assembler (2007) BMC Bioinforma, 8, p. 64Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y.O., Borodovsky, M., Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training (2008) Genome Res, 18 (12), pp. 1979-1990. , 10.1101/gr.081612.108, 2593577, 18757608Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., Morgenstern, B., AUGUSTUS: ab initio prediction of alternative transcripts (2006) Nucleic Acids Res, 34, pp. W435-W439. , Web Server issue, 1538822, 16845043Stanke, M., Tzvetkova, A., Morgenstern, B., AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome (2006) Genome Biol, 7 (SUPPL. 1), pp. S11 11-18Slater, G.S., Birney, E., Automated generation of heuristics for biological sequence comparison (2005) BMC Bioinforma, 6, p. 31Borodovsky, M., Lomsadze, A., Ivanov, N., Mills, R., Eukaryotic gene prediction using GeneMark.hmm (2003) Curr Protoc Bioinformatics, , Chapter 4, Unit4 6Haas, B.J., Salzberg, S.L., Zhu, W., Pertea, M., Allen, J.E., Orvis, J., White, O., Wortman, J.R., Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments (2008) Genome Biol, 9 (1), pp. R7. , 10.1186/gb-2008-9-1-r7, 2395244, 18190707Koski, L.B., Gray, M.W., Lang, B.F., Burger, G., AutoFACT: an automatic functional annotation and classification tool (2005) BMC Bioinforma, 6, p. 151Suzek, B.E., Huang, H., McGarvey, P., Mazumder, R., Wu, C.H., UniRef: comprehensive and non-redundant UniProt reference clusters (2007) Bioinformatics, 23 (10), pp. 1282-1288. , 10.1093/bioinformatics/btm098, 17379688Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Sonnhammer, E.L., The Pfam protein families database (2002) Nucleic Acids Res, 30 (1), pp. 276-280. , 10.1093/nar/30.1.276, 99071,

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