Proton coupled electron transfer reaction of phenols with excited state ruthenium(II) - polypyridyl complexes

The reaction of phenols with the excited state, *[Ru(bpy)3]2+ (E0 = 0.76V) and *[Ru(H2dcbpy)3]2+, (dcbpy = 4,4'-dicarboxy-2,2'-bipyridine) (E0 = 1.55 V vs. SCE) complexes in CH3CN has been studied by luminescence quenching technique and the quenching is dynamic. The formation of phenoxyl radical as a transient is confirmed by its characteristic absorption at 400 nm. The kq value is highly sensitive to the change of pH of the medium and ΔG0 of the reaction. Based on the treatment of kq data in terms of energetics of the reaction and pH of the medium, proton coupled electron transfer (PCET) mechanism has been proposed for the reaction

A robust nitrobenzene electrochemical sensor based on chitin hydrogel entrapped graphite composite

© 2017 An amperometric nitrobenzene (NB) sensor has been developed based on a glassy carbon electrode (GCE) modified with the composite of chitin hydrogel stabilized graphite (GR-CHI) composite. The physicochemical characterization confirmed the formation of GR-CHI composite and was formed by the strong interaction between GR and CHI. Furthermore, GR-CHI composite modified GCE was used to study the electrochemical reduction behavior of NB by cyclic voltammetry (CV) and compared with GR and CHI modified GCEs. The CV results confirmed that GR-CHI composite modified electrode has high catalytic ability and lower reduction potential toward NB than other modified electrodes due to the combined unique properties of exfoliated GR and CHI. The GR-CHI composite modified electrode can be able to detect the NB in the linear response range from 0.1 to 594.6 µM with the lower detection limit of 37 nM by amperometric i–t method. The selectivity of the sensor is evaluated in the presence of nitroaromatic, biologically active and dihydroxybenzene compounds. The sensor shows appropriate practicality and good repeatability toward detection of NB in lab water samples

An endophyte Paenibacillus dendritiformis strain APL3 promotes Amaranthus polygonoides L. sprout growth and their extract inhibits food-borne pathogens

Green leafy vegetables are rich sources of antioxidants and minerals, which prevent food-borne pathogen infections during our diet. This study was aimed to isolate and identify the plant growth-promoting endophytic bacterium from several plant species to enhance the growth of Amaranthus polygonoides L. and their antimicrobial potential against food-borne pathogens. Seven endophytic bacterial isolates were tested on two Amaranthus species to identify the suitable beneficial bacterium. The antioxidants capacity and antimicrobial activity of bacterial isolate (APL3) treated plants were analyzed. The bacterial isolate, APL3 showed a significantly higher growth of A. polygonoides L. than other isolates. It was identified as Paenibacillus dendritiformis strain APL3 by 16S rRNA gene sequencing and phylogenetic analysis. The endophyte (APL3) treated A. polygonoides L. sprouts had higher antioxidants potentials and significantly inhibited the growth of Escherichia coli, Salmonella sp., Staphylococcus sp. and Pseudomonas sp. The results of the present study suggest that utilization of P. dendritiformis strain APL3 triggers the growth of A. polygonoides L. and induces metabolic changes in plants to improve their antimicrobial properties to prevent foodborne pathogens

Effectiveness of pharmacogenomic tests including CYP2D6 and CYP2C19 genomic variants for guiding the treatment of depressive disorders: Systematic review and meta-analysis of randomized controlled trials

Major depressive disorders are prevalent conditions with limited treatment response and remission. Pharmacogenomics tests including CYP2D6 and CYP2C19 genomic variants provide the most reliable actionable approach to guide choice and dosing of antidepressants in major depression to improve outcome. We carried out a meta-analysis and meta-regression analyses of randomised controlled trials evaluating pharmacogenomic tests with CYP2D6 and CYP2C19 polymorphisms in major depression. A systematic review was conducted according to PRISMA and Cochrane guidelines to search several electronic databases. Logarithmically transformed odds ratios (OR) and confidence intervals (CI) for improvement, response and remission were calculated. A random-effects meta-analysis and meta-regression analyses were subsequently carried out. Twelve randomised controlled trials were included. Pharmacogenomic tests in the treatment of depression were more effective than treatment as usual for improvement (OR:1.63, CI: 1.19-2.24), response (OR: 1.46; CI: 1.16-1.85) and remission (OR: 1.85; CI: 1.23-2.76) with no evidence of publication bias. Remission was less favourable in recent studies. The results are promising but cautious use of pharmacogenomics in major depression is advisable. PROSPERO registration ID: CRD42021261143

Melt blending and characterization of carbon nanoparticles-filled thermoplastic polyurethane elastomers

In this work, thermoplastic polyurethane (TPU) elastomers reinforced with carbon nanosized particles were produced by a special melt blending technique. A TPU was melt blended with high-structured carbon black and carbon nanofibres (1 wt%). A miniature asymmetric batch mixer, which applies high shear levels to the melt, ensured good particles dispersion. The TPU material systems were then thoroughly characterized using thermogravimetric analysis, differential scanning calorimetry, tensile mechanical testing, electrical resistance measurements and flammability tests. The different nanofillers exhibited different influences on the TPU properties, these materials featuring interesting and improved multifunctional behaviours, with high propensity for large deformation sensors applications.This work was supported by FCT – Portuguese Foundation for Science and Technology through projects NANOSens – PTDC/CTM/73465/2006

The Usefulness of Gridded Climate Data Products in Characterizing Climate Variability and Assessing Crop Production

A sparse rain gauge network in dryland regions has been a major challenge for accessing high quality observed data needed to understand variability and trends in climate. Gridded estimates of weather parameters produced through data assimilation algorithms that integrate satellite and irregularly distributed on-ground observations from multiple observing networks are a potential alternative. Questions remain about the application of such climate data sources for assessing climate variability and crop productivity. This study assessed the usefulness and limitations of gridded data from four different sources i.e. AgMERRA, CHIRPS, NASA Power, and TAMSAT in estimating climate impacts on crop productivity using Agricultural Production Systems Simulator (APSIM). The study used data for 11 locations from Africa and India. The agreement between these data sets and observed data both in the amount and distribution of rainfall was evaluated before and after bias correction statistically. A deviation of more than 100 mm per season was observed in 13%, 20%, 25%, and 40% of the seasons in CHIRPS, AgMERRA, NASA Power, and TAMSAT data sets respectively. The differences were reduced significantly when data sets were bias-corrected. The number of rainy days is better estimated by TAMSAT and CHIRPS with a deviation of 4% and 6% respectively while AgMERRA and NASA Power overestimated by 28% and 67% respectively. The influence of these differences on crop growth and productivity was estimated by simulating maize yields with APSIM. Simulated crop yields with all gridded data sets were poorly correlated with observed data. The normalized root-mean-square error (NRMSE) of maize yield simulated with observed and gridded data was <30% for two locations in the case of AgMERRA and CHIRPS and three locations in the case of NASA Power. The NRMSE was > 30% for all locations with TAMSAT data. When yields were simulated with data after bias correction using the linear scaling technique, results were slightly improved. The results of our study thus indicate that the gridded data sets are usefully applied for characterizing climate variability, i.e. trends and seasonality in rainfall, however their use in driving crop model simulations of smallholder farm level production should be carefully interpreted

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Abstract Background Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome. Results Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable – estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation. Conclusions Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation

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,

Hybrid assembly with long and short reads improves discovery of gene family expansions

BACKGROUND: Long-read and short-read sequencing technologies offer competing advantages for eukaryotic genome sequencing projects. Combinations of both may be appropriate for surveys of within-species genomic variation. METHODS: We developed a hybrid assembly pipeline called "Alpaca" that can operate on 20X long-read coverage plus about 50X short-insert and 50X long-insert short-read coverage. To preclude collapse of tandem repeats, Alpaca relies on base-call-corrected long reads for contig formation. RESULTS: Compared to two other assembly protocols, Alpaca demonstrated the most reference agreement and repeat capture on the rice genome. On three accessions of the model legume Medicago truncatula, Alpaca generated the most agreement to a conspecific reference and predicted tandemly repeated genes absent from the other assemblies. CONCLUSION: Our results suggest Alpaca is a useful tool for investigating structural and copy number variation within de novo assemblies of sampled populations

RF Sputtered Nb-Doped MoS2 Thin Film for Effective Detection of NO2 Gas Molecules: Theoretical and Experimental Studies

This is the final version. Available on open access from the American Chemical Society via the DOI in this recordDoping plays a significant role in affecting the physical and chemical properties of two-dimensional (2D) dichalcogenide materials. Controllable doping is one of the major factors in the modification of the electronic and mechanical properties of 2D materials. MoS2 2D materials have gained significant attention in gas sensing owing to their high surface-to-volume ratio. However, low response and recovery time hinder their application in practical gas sensors. Herein, we report the enhanced gas response and recovery of Nb-doped MoS2 gas sensor synthesized through physical vapor deposition (PVD) toward NO2 at different temperatures. The electronic states of MoS2 and Nb-doped MOS2 monolayers grown by PVD were analyzed based on their work functions. Doping with Nb increases the work function of MoS2 and its electronic properties. The Nb-doped MoS2 showed an ultrafast response and recovery time of t rec = 30/85 s toward 5 ppm of NO2 at their optimal operating temperature (100 °C). The experimental results complement the electron difference density functional theory calculation, showing both physisorption and chemisorption of NO2 gas molecules on niobium substitution doping in MoS2.Japan Society for the Promotion of ScienceJapan Advanced Institute of Science and Technology, JapanEngineering and Physical Sciences Research Council (EPSRC