Search

Your search keyword '"Walton, Jonathan D"' showing total 339 results
Start Over Author "Walton, Jonathan D"
339 results on '"Walton, Jonathan D"'

1. Target highlights in CASP13: Experimental target structures through the eyes of their authors

Author

Lepore, Rosalba, Kryshtafovych, Andriy, Alahuhta, Markus, Veraszto, Harshul A, Bomble, Yannick J, Bufton, Joshua C, Bullock, Alex N, Caba, Cody, Cao, Hongnan, Davies, Owen R, Desfosses, Ambroise, Dunne, Matthew, Fidelis, Krzysztof, Goulding, Celia W, Gurusaran, Manickam, Gutsche, Irina, Harding, Christopher J, Hartmann, Marcus D, Hayes, Christopher S, Joachimiak, Andrzej, Leiman, Petr G, Loppnau, Peter, Lovering, Andrew L, Lunin, Vladimir V, Michalska, Karolina, Mir‐Sanchis, Ignacio, Mitra, AK, Moult, John, Phillips, George N, Pinkas, Daniel M, Rice, Phoebe A, Tong, Yufeng, Topf, Maya, Walton, Jonathan D, and Schwede, Torsten

Subjects
Biochemistry and Cell Biology, Biological Sciences, Arabidopsis, Bacterial Proteins, Computational Biology, Crystallography, X-Ray, Humans, Models, Molecular, Protein Conformation, Proteins, CASP, protein structure prediction, cryo-EM, X-ray crystallography, CASP, protein structure prediction, Mathematical Sciences, Information and Computing Sciences, Bioinformatics, Biological sciences, Mathematical sciences
Abstract

The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.

Published
2019

2. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white rot/ brown rot paradigm for wood decay fungi

Author

Riley, Robert, Salamov, Asaf, Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitris, Held, Benjamin, Levasseur, Anthony, Lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika, Sun, Hui, LaButti, Kurt, Schmutz, Jeremy, Jabbour, Dina, Luo, Hong, Baker, Scott E., Pisabarro, Antonio, Walton, Jonathan D., Blanchette, Robert, Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David, and Grigoriev, Igor V.

Abstract

Basidiomycota (basidiomycetes) make up 32percent of the described fungi and include most wood decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white rot/brown rot classification paradigm we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically-informed Principal Components Analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs, but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown rot fungi. Our results suggest a continuum rather than a dichotomy between the white rot and brown rot modes of wooddecay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.

Published
2014

17. Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Author

Riley, Robert, Salamov, Asaf A., Brown, Daren W., Nagy, Laszlo G., Floudas, Dimitrios, Held, Benjamin W., Levasseur, Anthony, Lombard, Vincent, Morin, Emmanuelle, Otillar, Robert, Lindquist, Erika A., Sun, Hui, LaButti, Kurt M., Schmutz, Jeremy, Jabbour, Dina, Luoi, Hong, Baker, Scott E., Pisabarro, Antonio G., Walton, Jonathan D., Blanchette, Robert A., Henrissat, Bernard, Martin, Francis, Cullen, Dan, Hibbett, David S., and Grigoriev, Igor V.

Published
2014

26. The Fusarium graminearum Genome Reveals a Link between Localized Polymorphism and Pathogen Specialization

Author

Cuomo, Christina A., Güldener, Ulrich, Xu, Jin-Rong, Trail, Frances, Turgeon, B. Gillian, Di Pietro, Antonio, Walton, Jonathan D., Ma, Li-Jun, Baker, Scott E., Rep, Martijn, Adam, Gerhard, Antoniw, John, Baldwin, Thomas, Calvo, Sarah, Chang, Yueh-Long, DeCaprio, David, Gale, Liane R., Gnerre, Sante, Goswami, Rubella S., Hammond-Kosack, Kim, Harris, Linda J., Hilburn, Karen, Kennell, John C., Kroken, Scott, Magnuson, Jon K., Mannhaupt, Gertrud, Mauceli, Evan, Mewes, Hans-Werner, Mitterbauer, Rudolf, Muehlbauer, Gary, Münsterkötter, Martin, Nelson, David, O'Donnell, Kerry, Ouellet, Thérèse, Qi, Weihong, Quesneville, Hadi, Roncero, M. Isabel G., Seong, Kye-Yong, Tetko, Igor V., Urban, Martin, Waalwijk, Cees, Ward, Todd J., Yao, Jiqiang, Birren, Bruce W., and Kistler, H. Corby

Published
2007
Full Text
View/download PDF

49. An inhibitor-resistant histone deacetylase in the plant pathogenic fungus Cochliobolus carbonum

Author

Brosch, Gerald, Dangl, Markus, Graessle, Stefan, Loidl, Adele, Trojer, Patrick, Brandtner, Eva-Maria, Mair, Karin, Walton, Jonathan D., Baidyaroy, Dipnath, and Loidl, Peter

Subjects
Fungi -- Physiological aspects, Enzymes -- Structure-activity relationship, Toxins -- Physiological aspects, Histones -- Physiological aspects, Biological sciences, Chemistry
Abstract

Results reveal that Cochliobolus carbonum produces two types of histone deacetylases, a toxin-resistant and other toxin-sensitive forms. Data indicate that inhibitor-resistant activity is displayed by the toxin-producing form.

Published
2001

50. RPD3-type histone deacetylases in maize embryos

Author

Lechner, Thomas, Lusser, Alexandra, Pipal, Alexandra, Brosch, Gerald, Loidl, Adele, Goralik-Schramel, Maria, Sendra, Ramon, Wegener, Sigrun, Walton, Jonathan D., and Loidl, Peter

Subjects
Biochemistry -- Research, Histones -- Research, Corn -- Analysis, DNA -- Research, Cloning -- Research, Biological sciences, Chemistry
Abstract

Research has been conducted on the posttranslational core histone acetylation. The identification of two maize histone deacetylase forms by purification and cDNA cloning is described.

Published
2000

Catalog

Books, media, physical & digital resources
See catalog results