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58. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Author

Seshadri, R, Leahy, SC, Attwood, GT, Teh, KH, Lambie, SC, Cookson, AL, Eloe-Fadrosh, EA, Pavlopoulos, GA, Hadjithomas, M, Varghese, NJ, Paez-Espino, D, Perry, R, Henderson, G, Creevey, CJ, Terrapon, N, Lapebie, P, Drula, E, Lombard, V, Rubin, E, Kyrpides, NC, Henrissat, B, Woyke, T, Ivanova, NN, Kelly, WJ, Palevic, N, Janssen, PH, Ronimus, RS, Noel, S, Soni, P, Reilly, K, Atherly, T, Ziemer, C, Wright, AD, Ishaq, S, Cotta, M, Thompson, S, Crosley, K, McKain, N, Wallace, JJ, Flint, HJ, Martin, JC, Forster, RJ, Gruninger, RJ, McAllister, T, Gilbert, R, Ouwerkerk, DJ, Klieve, AJ, Jassim, RA, Denman, S, McSweeney, C, Rosewarne, C, Koike, S, Kobayashi, Y, Mitsumori, M, Shinkai, T, Cravero, S, and Cerón Cucchi, M

Subjects
animal structures, food and beverages
Abstract

© 2018 Nature Publishing Group. All rights reserved. Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents â 1/475% of the genus-level bacterial and archaeal taxa present in the rumen.

Published
2018

59. Learning Temporal Strategic Relationships using Generative Adversarial Imitation Learning

Author

Tharindu Fernando, Denman, S., Sridharan, S., and Fookes, C.

Subjects
FOS: Computer and information sciences, Computer Vision and Pattern Recognition (cs.CV), Computer Science - Computer Vision and Pattern Recognition
Abstract

This paper presents a novel framework for automatic learning of complex strategies in human decision making. The task that we are interested in is to better facilitate long term planning for complex, multi-step events. We observe temporal relationships at the subtask level of expert demonstrations, and determine the different strategies employed in order to successfully complete a task. To capture the relationship between the subtasks and the overall goal, we utilise two external memory modules, one for capturing dependencies within a single expert demonstration, such as the sequential relationship among different sub tasks, and a global memory module for modelling task level characteristics such as best practice employed by different humans based on their domain expertise. Furthermore, we demonstrate how the hidden state representation of the memory can be used as a reward signal to smooth the state transitions, eradicating subtle changes. We evaluate the effectiveness of the proposed model for an autonomous highway driving application, where we demonstrate its capability to learn different expert policies and outperform state-of-the-art methods. The scope in industrial applications extends to any robotics and automation application which requires learning from complex demonstrations containing series of subtasks., Comment: International Foundation for Autonomous Agents and Multiagent Systems, 2018

Published
2018
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60. New and Interesting Fungi. 1

Author

Crous, P.W., Schumacher, R.K., Wingfield, M.J., Akulov, A., Denman, S., Roux, J., Braun, U., Burgess, T.I., Carnegie, A.J., Váczy, K.Z., Guatimosim, E., Schwartsburd, P.B., Barreto, R.W., Hernández-Restrepo, M., Lombard, L., Groenewald, J.Z., Crous, P.W., Schumacher, R.K., Wingfield, M.J., Akulov, A., Denman, S., Roux, J., Braun, U., Burgess, T.I., Carnegie, A.J., Váczy, K.Z., Guatimosim, E., Schwartsburd, P.B., Barreto, R.W., Hernández-Restrepo, M., Lombard, L., and Groenewald, J.Z.

Abstract

This study introduces two new families, one new genus, 22 new species, 10 new combinations, four epitypes, and 16 interesting new host and / or geographical records. Cylindriaceae (based on Cylindrium elongatum) is introduced as new family, with three new combinations.Xyladictyochaetaceae (based on Xyladictyochaetalusitanica) is introduced to accommodate Xyladictyochaeta. Pseudoanungitea gen. nov. (based on P.syzygii)is described on stems of Vaccinium myrtillus(Germany). New species include: Exophiala eucalypticola on Eucalyptus obliqua leaf litter, Phyllosticta hakeicola on leaves of Hakea sp.,Setophaeosphaeriacitricola on leaves of Citrus australasica, and Sirastachyscyperacearum on leaves of Cyperaceae(Australia); Polyscytalum chilense on leaves of Eucalyptus urophylla (Chile); Pseudoanungitea vaccinii on Vaccinium myrtillus (Germany); Teichospora quercus on branch tissue of Quercus sp. (France); Fusiconidiumlycopodiellae on stems of Lycopodiella inundata,Monochaetiajunipericola on twig of Juniperus communis,Myrmecridiumsorbicola on branch tissues of Sorbus aucuparia, Parathyridariaphiladelphi on twigs of Philadelphus coronarius, and Wettsteininaphiladelphi on twigs of Philadelphus coronarius (Germany); Zygosporium pseudogibbum on leaves of Eucalyptus pellita (Malaysia); Pseudoanungiteavariabilis on dead wood (Spain); Alfaria acaciae on leaves of Acacia propinqua, Dictyochaeta mimusopis on leaves of Mimusops caffra,and Pseudocercosporabreonadiae on leaves of Breonadia microcephala (South Africa); Colletotrichumkniphofiae on leaves of Kniphofia uvaria,Subplenodomusiridicola on Iris sp., and Trochila viburnicola on twig cankers on Viburnum sp. (UK); Polyscytalum neofecundissimum on Quercus robur leaf litter, and Roussoellaeuonymi on fallen branches of Euonymus europaeus (Ukraine). New combinations include: Cylindrium algarvense on leaves of Eucalyptus sp. (Portugal), Cylindrium purgamentum on leaf litter (USA), Cylindrium syzygii on leaves of Syzygium sp. (Australi

Published
2018

61. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Author

Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Hadjithomas, M., Varghese, N. J., Paez-Espino, D., Perry, R., Henderson, G., Creevey, C. J., Terrapon, N., Lapebie, P., Drula, E., Lombard, V., Rubin, E., Kyrpides, N. C., Henrissat, B., Woyke, T., Ivanova, N. N., Kelly, W. J., Palevic, N., Janssen, P. H., Ronimus, R. S., Noel, S., Soni, P., Reilly, K., Atherly, T., Ziemer, C., Wright, A., Ishaq, S., Cotta, S., Thompson, S., Crosley, K., McKain, S., Wallace, R. J., Flint, H. J., Martin, J. C., Forster, R. J., Gruninger, R. J., McAllister, T., Gilbert, Rosalind A., Ouwerkerk, Diane, Klieve, Athol, Jassim, R. A., Denman, S., McSweeney, C., Rosewarne, S., Koike, S., Kobayashi, Y., Mitsumori, M., Shinkai, T., Cravero, S., Cerón Cucchi, T., Seshadri, R., Leahy, S. C., Attwood, G. T., Teh, K. H., Lambie, S. C., Cookson, A. L., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Hadjithomas, M., Varghese, N. J., Paez-Espino, D., Perry, R., Henderson, G., Creevey, C. J., Terrapon, N., Lapebie, P., Drula, E., Lombard, V., Rubin, E., Kyrpides, N. C., Henrissat, B., Woyke, T., Ivanova, N. N., Kelly, W. J., Palevic, N., Janssen, P. H., Ronimus, R. S., Noel, S., Soni, P., Reilly, K., Atherly, T., Ziemer, C., Wright, A., Ishaq, S., Cotta, S., Thompson, S., Crosley, K., McKain, S., Wallace, R. J., Flint, H. J., Martin, J. C., Forster, R. J., Gruninger, R. J., McAllister, T., Gilbert, Rosalind A., Ouwerkerk, Diane, Klieve, Athol, Jassim, R. A., Denman, S., McSweeney, C., Rosewarne, S., Koike, S., Kobayashi, Y., Mitsumori, M., Shinkai, T., Cravero, S., and Cerón Cucchi, T.

Abstract

Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B 12, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents â 1/475% of the genus-level bacterial and archaeal taxa present in the rumen. © 2018 Nature Publishing Group. All rights reserved.

Published
2018

62. Variation in lung function as a marker of adherence to oral and inhaled medication in cystic fibrosis

Author

White, H, Shaw, N, Denman, S, Pollard, K, Wynne, S, and Peckham, DG

Abstract

Study aim: The aim of this study was to characterise adherence in an adult population with CF and to investigate if variation in lung function was a predictor of adherence to treatment. Patients and methods: Patients aged ≥ 16 years from an adult CF centre undertook adherence measures by medication possession ratio (MPR) and self-report and were assigned to one of three adherence categories (

Published
2017

64. New and Interesting Fungi. 1

Author

Crous, P.W., primary, Schumacher, R.K., additional, Wingfield, M.J., additional, Akulov, A., additional, Denman, S., additional, Roux, J., additional, Braun, U., additional, Burgess, T.I., additional, Carnegie, A.J., additional, Váczy, K.Z., additional, Guatimosim, E., additional, Schwartsburd, P.B., additional, Barreto, R.W., additional, Hernández-Restrepo, M., additional, Lombard, L., additional, and Groenewald, J.Z., additional

Published
2018
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66. Fungal Planet description sheets: 625–715

Author

Crous, P.W., Wingfield, M.J., Burgess, T.I., Carnegie, A.J., Hardy, G.E.St.J., Smith, D., Summerell, B.A., Cano-Lira, J.F., Guarro, J., Houbraken, J., Lombard, L., Martín, M.P., Sandoval-Denis, M., Alexandrova, A.V., Barnes, C.W., Baseia, I.G., Bezerra, J.D.P., Guarnaccia, V., May, T.W., Hernández-Restrepo, M., Stchigel, A.M., Miller, A.N., Ordoñez, M.E., Abreu, V.P, Accioly, T., Agnello, C., Agustin Colmán, A., Albuquerque, C.C., Alfredo, D.S., Alvarado, P., Araújo-Magalhães, G.R, Arauzo, S., Atkinson, Thomas, Barili, A., Barreto, R.W., Bezerra, J.L., Cabral, T.S., Camello Rodríguez, F., Cruz, R.H.S.F., Daniëls, P.P., da Silva, B.D.B., de Almeida, D.A.C., de Carvalho Júnior, A.A., Decock, C.A., Delgat, L., Denman, S., Dimitrov, R.A., Edwards, J., Fedosova, A.G., Ferreira, R.J., Firmino, A.L., Flores, J.A., Garcia, D., Gené, J., Giraldo, A., Góis, J.S., Gomes, A.A.M., Gonçalves, C.M., Gouliamova, D.E., Groenewald, M., Guéorguiev, B.V., Guevara-Suarez, M., Gusmao, L.F.P., Hosaka, K., Hubka, V., Huhndorf, S.M., Jadan, M., Jurjević, Ž., Kraak, B., Kučera, V., Kumar, T.K.A., Kušan, I., Lacerda, S.R., Lamlertthon, S., Lisboa, W.S., Loizides, M., Luangsa-ard, J.J., Lysková, P., Mac Cormack, W.P., Macedo, D.M., Machado, A.R., Malysheva, E.F., Marinho, P., Matočec, N., Meijer, M., Mešić, A., Mongkolsamrit, S., Moreira, K.A., Morozova, O.V., Nair, K.U., Nakamura, N., Noisripoom, W., Olariaga, I., Oliveira, R.J.V., Paiva, L.M., Pawar, Pranita, Pereira, O.L., Peterson, S.W., Prieto, M., Rodríguez-Andrade, E., Rojo De Blas, C., Roy, M., Santos, E.S., Sharma, R., Silva, G.A., Souza-Motta, C.M., Takeuchi-Kaneko, Y., Tanaka, C., Thakur, A., Smith, M.TH., Tkalčec, Z., Valenzuela-Lopez, N., van der Kleij, P., Verbeken, A., Viana, M.G., Wang, X.W., Groenewald, J.Z., Crous, P.W., Wingfield, M.J., Burgess, T.I., Carnegie, A.J., Hardy, G.E.St.J., Smith, D., Summerell, B.A., Cano-Lira, J.F., Guarro, J., Houbraken, J., Lombard, L., Martín, M.P., Sandoval-Denis, M., Alexandrova, A.V., Barnes, C.W., Baseia, I.G., Bezerra, J.D.P., Guarnaccia, V., May, T.W., Hernández-Restrepo, M., Stchigel, A.M., Miller, A.N., Ordoñez, M.E., Abreu, V.P, Accioly, T., Agnello, C., Agustin Colmán, A., Albuquerque, C.C., Alfredo, D.S., Alvarado, P., Araújo-Magalhães, G.R, Arauzo, S., Atkinson, Thomas, Barili, A., Barreto, R.W., Bezerra, J.L., Cabral, T.S., Camello Rodríguez, F., Cruz, R.H.S.F., Daniëls, P.P., da Silva, B.D.B., de Almeida, D.A.C., de Carvalho Júnior, A.A., Decock, C.A., Delgat, L., Denman, S., Dimitrov, R.A., Edwards, J., Fedosova, A.G., Ferreira, R.J., Firmino, A.L., Flores, J.A., Garcia, D., Gené, J., Giraldo, A., Góis, J.S., Gomes, A.A.M., Gonçalves, C.M., Gouliamova, D.E., Groenewald, M., Guéorguiev, B.V., Guevara-Suarez, M., Gusmao, L.F.P., Hosaka, K., Hubka, V., Huhndorf, S.M., Jadan, M., Jurjević, Ž., Kraak, B., Kučera, V., Kumar, T.K.A., Kušan, I., Lacerda, S.R., Lamlertthon, S., Lisboa, W.S., Loizides, M., Luangsa-ard, J.J., Lysková, P., Mac Cormack, W.P., Macedo, D.M., Machado, A.R., Malysheva, E.F., Marinho, P., Matočec, N., Meijer, M., Mešić, A., Mongkolsamrit, S., Moreira, K.A., Morozova, O.V., Nair, K.U., Nakamura, N., Noisripoom, W., Olariaga, I., Oliveira, R.J.V., Paiva, L.M., Pawar, Pranita, Pereira, O.L., Peterson, S.W., Prieto, M., Rodríguez-Andrade, E., Rojo De Blas, C., Roy, M., Santos, E.S., Sharma, R., Silva, G.A., Souza-Motta, C.M., Takeuchi-Kaneko, Y., Tanaka, C., Thakur, A., Smith, M.TH., Tkalčec, Z., Valenzuela-Lopez, N., van der Kleij, P., Verbeken, A., Viana, M.G., Wang, X.W., and Groenewald, J.Z.

Abstract

Novel species of fungi described in this study include those from various countries as follows: Antarctica: Cadophora antarctica from soil. Australia: Alfaria dandenongensis on Cyperaceae, Amphosoma persooniae on Persoonia sp., Anungitea nullicana on Eucalyptus sp., Bagadiella eucalypti on Eucalyptus globulus, Castanediella eucalyptigena on Eucalyptus sp., Cercospora dianellicola on Dianella sp., Cladoriella kinglakensis on Eucalyptus regnans, Cladoriella xanthorrhoeae (incl. Cladoriellaceae fam. nov. and Cladoriellales ord. nov.) on Xanthorrhoea sp., Cochlearomyces eucalypti (incl. Cochlearomyces gen. nov. and Cochlearomycetaceae fam. nov.) on Eucalyptus obliqua, Codinaea lambertiae on Lambertia formosa, Diaporthe obtusifoliae on Acacia obtusifolia, Didymella acaciae on Acacia melanoxylon, Dothidea eucalypti on Eucalyptus dalrympleana, Fitzroyomyces cyperi (incl. Fitzroyomyces gen. nov.) on Cyperaceae, Murramarangomyces corymbiae (incl. Murramarangomyces gen. nov., Murramarangomycetaceae fam. nov. and Murramarangomycetales ord. nov.) on Corymbia maculata, Neoanungitea eucalypti (incl. Neoanungitea gen. nov.) on Eucalyptus obliqua, Neoconiothyrium persooniae (incl. Neoconiothyrium gen. nov.) on Persoonia laurina subsp. laurina, Neocrinula lambertiae (incl. Neocrinulaceae fam. nov.) on Lambertia sp., Ochroconis podocarpi on Podocarpus grayae, Paraphysalospora eucalypti (incl. Paraphysalospora gen. nov.) on Eucalyptus sieberi, Pararamichloridium livistonae (incl. Pararamichloridium gen. nov., Pararamichloridiaceae fam. nov. and Pararamichloridiales ord. nov.) on Livistona sp., Pestalotiopsis dianellae on Dianella sp., Phaeosphaeria gahniae on Gahnia aspera, Phlogicylindrium tereticornis on Eucalyptus tereticornis, Pleopassalora acaciae on Acacia obliquinervia, Pseudodactylaria xanthorrhoeae (incl. Pseudodactylaria gen. nov., Pseudodactylariaceae fam. nov. and Pseudodactylariales ord. nov.) on Xanthorrhoea sp., Pseudosporidesmium lambertiae (incl. Pseudosporidesmiaceae

Published
2017

67. Fungal Planet description sheets: 625–715

Author

Crous, P.W. (Pedro Willem), Wingfield, M.J., Burgess, T.I., Carnegie, A.J., Hardy, G.E.St.J., Smith, D., Summerell, B.A., Cano-Lira, J.F., Guarro, J., Houbraken, J., Lombard, L., Martín, M.P., Sandoval-Denis, M., Alexandrova, A.V., Barnes, C.W., Baseia, I.G., Bezerra, J.D.P., Guarnaccia, V., May, T.W., Hernández-Restrepo, M., Stchigel, A.M., Miller, A.N., Ordoñez, M.E., Abreu, V.P., Accioly, T., Agnello, C., Agustin Colmán, A., Albuquerque, C.C., Alfredo, D.S., Alvarado, P., Araújo-Magalhães, G.R., Arauzo, S., Atkinson, T., Barili, A., Barreto, R.W., Bezerra, J.L., Cabral, T.S., Camello Rodríguez, F., Cruz, R.H.S.F., Daniëls, P.P., da Silva, B.D.B., de Almeida, D.A.C., de Carvalho Júnior, A.A., Decock, C.A., Delgat, L., Denman, S., Dimitrov, R.A., Edwards, J., Fedosova, A.G., Ferreira, R.J., Firmino, A.L., Flores, J.A., García, D., Gené, J., Giraldo, A., Góis, J.S., Gomes, A.A.M., Gonçalves, C.M., Gouliamova, D.E., Groenewald, M., Guéorguiev, B.V., Guevara-Suarez, M., Gusmão, L.F.P., Hosaka, K., Hubka, V., Huhndorf, S.M., Jadan, M., Jurjević, Ž., Kraak, B., Kučera, V., Kumar, T.K.A., Kušan, I., Lacerda, S.R., Lamlertthon, S., Lisboa, W.S., Loizides, M., Luangsa-ard, J.J. (Janet), Lysková, P., Mac Cormack, W.P., Macedo, D.M., Machado, A.R., Malysheva, E.F., Marinho, P., Matočec, N., Meijer, M., Mešić, A., Mongkolsamrit, S., Moreira, K.A., Morozova, O.V., Nair, K.U., Nakamura, N., Noisripoom, W., Olariaga, I., Oliveira, R.J.V. de, Paiva, L.M., Pawar, P., Pereira, O.L., Peterson, S.W., Prieto, M., Rodríguez-Andrade, E., Rojo De Blas, C., Roy, M., Santos, E.S., Sharma, R., Silva, G.A., Souza-Motta, C.M., Takeuchi-Kaneko, Y., Tanaka, C., Thakur, A., Smith, M.Th., Tkalčec, Z., Valenzuela-Lopez, N., van der Kleij, P., Verbeken, A., Viana, M.G., Wang, X.W., Groenewald, J.Z., Crous, P.W. (Pedro Willem), Wingfield, M.J., Burgess, T.I., Carnegie, A.J., Hardy, G.E.St.J., Smith, D., Summerell, B.A., Cano-Lira, J.F., Guarro, J., Houbraken, J., Lombard, L., Martín, M.P., Sandoval-Denis, M., Alexandrova, A.V., Barnes, C.W., Baseia, I.G., Bezerra, J.D.P., Guarnaccia, V., May, T.W., Hernández-Restrepo, M., Stchigel, A.M., Miller, A.N., Ordoñez, M.E., Abreu, V.P., Accioly, T., Agnello, C., Agustin Colmán, A., Albuquerque, C.C., Alfredo, D.S., Alvarado, P., Araújo-Magalhães, G.R., Arauzo, S., Atkinson, T., Barili, A., Barreto, R.W., Bezerra, J.L., Cabral, T.S., Camello Rodríguez, F., Cruz, R.H.S.F., Daniëls, P.P., da Silva, B.D.B., de Almeida, D.A.C., de Carvalho Júnior, A.A., Decock, C.A., Delgat, L., Denman, S., Dimitrov, R.A., Edwards, J., Fedosova, A.G., Ferreira, R.J., Firmino, A.L., Flores, J.A., García, D., Gené, J., Giraldo, A., Góis, J.S., Gomes, A.A.M., Gonçalves, C.M., Gouliamova, D.E., Groenewald, M., Guéorguiev, B.V., Guevara-Suarez, M., Gusmão, L.F.P., Hosaka, K., Hubka, V., Huhndorf, S.M., Jadan, M., Jurjević, Ž., Kraak, B., Kučera, V., Kumar, T.K.A., Kušan, I., Lacerda, S.R., Lamlertthon, S., Lisboa, W.S., Loizides, M., Luangsa-ard, J.J. (Janet), Lysková, P., Mac Cormack, W.P., Macedo, D.M., Machado, A.R., Malysheva, E.F., Marinho, P., Matočec, N., Meijer, M., Mešić, A., Mongkolsamrit, S., Moreira, K.A., Morozova, O.V., Nair, K.U., Nakamura, N., Noisripoom, W., Olariaga, I., Oliveira, R.J.V. de, Paiva, L.M., Pawar, P., Pereira, O.L., Peterson, S.W., Prieto, M., Rodríguez-Andrade, E., Rojo De Blas, C., Roy, M., Santos, E.S., Sharma, R., Silva, G.A., Souza-Motta, C.M., Takeuchi-Kaneko, Y., Tanaka, C., Thakur, A., Smith, M.Th., Tkalčec, Z., Valenzuela-Lopez, N., van der Kleij, P., Verbeken, A., Viana, M.G., Wang, X.W., and Groenewald, J.Z.

Abstract

Novel species of fungi described in this study include those from various countries as follows: Antarctica: Cadophora antarctica from soil. Australia: Alfaria dandenongensis on Cyperaceae, Amphosoma persooniae on Persoonia sp., Anungitea nullicana on Eucalyptus sp., Bagadiella eucalypti on Eucalyptus globulus, Castanediella eucalyptigena on Eucalyptus sp., Cercospora dianellicola on Dianella sp., Cladoriella kinglakensis on Eucalyptus regnans, Cladoriella xanthorrhoeae (incl. Cladoriellaceae fam. nov. and Cladoriellales ord. nov.) on Xanthorrhoea sp., Cochlearomyces eucalypti (incl. Cochlearomyces gen. nov. and Cochlearomycetaceae fam. nov.) on Eucalyptus obliqua, Codinaea lambertiae on Lambertia formosa, Diaporthe obtusifoliae on Acacia obtusifolia, Didymella acaciae on Acacia melanoxylon, Dothidea eucalypti on Eucalyptus dalrympleana, Fitzroyomyces cyperi (incl. Fitzroyomyces gen. nov.) on Cyperaceae, Murramarangomyces corymbiae (incl. Murramarangomyces gen. nov., Murramarangomycetaceae fam. nov. and Murramarangomycetales ord. nov.) on Corymbia maculata, Neoanungitea eucalypti (incl. Neoanungitea gen. nov.) on Eucalyptus obliqua, Neoconiothyrium persooniae (incl. Neoconiothyrium gen. nov.) on Persoonia laurina subsp. laurina, Neocrinula lambertiae (incl. Neocrinulaceae fam. nov.) on Lambertia sp., Ochroconis podocarpi on Podocarpus grayae, Paraphysalospora eucalypti (incl. Paraphysalospora gen. nov.) on Eucalyptus sieberi, Pararamichloridium livistonae (incl. Pararamichloridium gen. nov., Pararamichloridiaceae fam. nov. and Pararamichloridiales ord. nov.) on Livistona sp., Pestalotiopsis dianellae on Dianella sp., Phaeosphaeria gahniae on Gahnia aspera, Phlogicylindrium tereticornis on Eucalyptus tereticornis, Pleopassalora acaciae on Acacia obliquinervia, Pseudodactylaria xanthorrhoeae (incl. Pseudodactylaria gen. nov., Pseudodactylariaceae fam. nov. and Pseudodactylariales ord. nov.) on Xanthorrhoea sp., Pseudosporidesmium lambertiae (incl. Pseudosporidesmiaceae

Published
2017
Full Text
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68. Fungal Planet description sheets: 625–715

Author

Ministry of Education, Youth and Sports (Czech Republic), European Commission, Secretaría de Educación Superior, Ciencia, Tecnología e Innovación (Ecuador), Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Fundação de Amparo à Pesquisa do Estado de São Paulo Minas Gerais, Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco, Russian Science Foundation, Russian Academy of Sciences, Russian Foundation for Basic Research, Agence Nationale de la Recherche (France), Department of Biotechnology (India), National Centre for Microbial Resource (India), Bulgarian National Science Fund, Fédération Wallonie-Bruxelles, Northern Velebit National Park, VEGA Agency (Slovakia), National Science and Technology Development Agency (Thailand), Martín, María P. [0000-0002-1235-4418], Crous, P. W., Wingfield, M. J., Burgess, T.I., Carnegie, A. J., Hardy, G. E. St. J., Smith, D., Summerell, B. A., Cano-Lira, J.F., Guarro, J., Houbraken, J., Lombard, L., Kuera, V., Kumar, T. K. A., Kušan, I., Lacerda, S. R., Lamlertthon, S., Lisboa, W. S., Loizides, M., Luangsa-Ard, J. J., Lysková, P., Maccormack, W. P., Meši, A., Macedo, D. M., Machado, Alexandre R., Malysheva, E. F., Marinho, P., Matoec, N., Meijer, M., Mongkolsamrit, S., Moreira, K. A., Morozova, O. V., Nair, K. U., Nakamura, N., Noisripoom, W., Olariaga, I., Oliveira, R. J. V., Paiva, L. M., Roy, M., Pawar, P., Pereira, O. L., Peterson, S. W., Prieto, M., Rodríguez-Andrade, E., Rojodeblas, C., Santos, E. S., Sharma, R., Silva, G. A., Souza-Motta, C. M., Takeuchi-Kaneko, Y., Tanaka, C., Thakur, A., Smith, M. Th., Tkalec, Z., Martín, María P., Valenzuela-Lopez, N., Vanderkleij, P., Verbeken, A., Viana, M. G., Wang, X. W., Groenewald, J. Z., Sandoval Denis, M., Alexandrova, A. V., Barnes, C. W., Baseia, I.G., Bezerra, J. D. P., Guarnaccia, Vladimiro, May, T. W., Hernández-Restrepo, M., Stchigel, A. M., Miller, A. N., Ordoñez, M. E., Abreu, V. P., Accioly, Thiago, Agnello, C., Agustincolmán, A., Albuquerque, C. C., Alfredo, D. S., Alvarado, P., Araújo-Magalhães, G. R., Arauzo, S., Atkinson, T., Barili, A., Barreto, R. W., Bezerra, J. L., Cabral, T. S., Rodríguez, F. Camello, Cruz, R. H. S. F., Daniëls, Pablo P., Silva, Bianca D. B., Almeida, D. A. C., Carvalhojúnior, A. A., Decock, C. A., Delgat, L., Denman, S., Dimitrov, R. A., Edwards, J., Fedosova, A. G., Ferreira, Renato Juciano, Firmino, A. L., Flores, J. A., García, D., Gené, J., Giraldo, A., Góis, J. S., Gomes, A.M.P., Gonçalves, C. M., Gouliamova, D. E., Groenewald, M., Guéorguiev, B. V., Guevara-Suarez, M., Gusmão, L. F. P., Hosaka, K., Hubka, V., Huhndorf, S. M., Jadan, M. Jurjevi, Kraak, B., Ministry of Education, Youth and Sports (Czech Republic), European Commission, Secretaría de Educación Superior, Ciencia, Tecnología e Innovación (Ecuador), Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Fundação de Amparo à Pesquisa do Estado de São Paulo Minas Gerais, Fundação de Amparo à Ciência e Tecnologia do Estado de Pernambuco, Russian Science Foundation, Russian Academy of Sciences, Russian Foundation for Basic Research, Agence Nationale de la Recherche (France), Department of Biotechnology (India), National Centre for Microbial Resource (India), Bulgarian National Science Fund, Fédération Wallonie-Bruxelles, Northern Velebit National Park, VEGA Agency (Slovakia), National Science and Technology Development Agency (Thailand), Martín, María P. [0000-0002-1235-4418], Crous, P. W., Wingfield, M. J., Burgess, T.I., Carnegie, A. J., Hardy, G. E. St. J., Smith, D., Summerell, B. A., Cano-Lira, J.F., Guarro, J., Houbraken, J., Lombard, L., Kuera, V., Kumar, T. K. A., Kušan, I., Lacerda, S. R., Lamlertthon, S., Lisboa, W. S., Loizides, M., Luangsa-Ard, J. J., Lysková, P., Maccormack, W. P., Meši, A., Macedo, D. M., Machado, Alexandre R., Malysheva, E. F., Marinho, P., Matoec, N., Meijer, M., Mongkolsamrit, S., Moreira, K. A., Morozova, O. V., Nair, K. U., Nakamura, N., Noisripoom, W., Olariaga, I., Oliveira, R. J. V., Paiva, L. M., Roy, M., Pawar, P., Pereira, O. L., Peterson, S. W., Prieto, M., Rodríguez-Andrade, E., Rojodeblas, C., Santos, E. S., Sharma, R., Silva, G. A., Souza-Motta, C. M., Takeuchi-Kaneko, Y., Tanaka, C., Thakur, A., Smith, M. Th., Tkalec, Z., Martín, María P., Valenzuela-Lopez, N., Vanderkleij, P., Verbeken, A., Viana, M. G., Wang, X. W., Groenewald, J. Z., Sandoval Denis, M., Alexandrova, A. V., Barnes, C. W., Baseia, I.G., Bezerra, J. D. P., Guarnaccia, Vladimiro, May, T. W., Hernández-Restrepo, M., Stchigel, A. M., Miller, A. N., Ordoñez, M. E., Abreu, V. P., Accioly, Thiago, Agnello, C., Agustincolmán, A., Albuquerque, C. C., Alfredo, D. S., Alvarado, P., Araújo-Magalhães, G. R., Arauzo, S., Atkinson, T., Barili, A., Barreto, R. W., Bezerra, J. L., Cabral, T. S., Rodríguez, F. Camello, Cruz, R. H. S. F., Daniëls, Pablo P., Silva, Bianca D. B., Almeida, D. A. C., Carvalhojúnior, A. A., Decock, C. A., Delgat, L., Denman, S., Dimitrov, R. A., Edwards, J., Fedosova, A. G., Ferreira, Renato Juciano, Firmino, A. L., Flores, J. A., García, D., Gené, J., Giraldo, A., Góis, J. S., Gomes, A.M.P., Gonçalves, C. M., Gouliamova, D. E., Groenewald, M., Guéorguiev, B. V., Guevara-Suarez, M., Gusmão, L. F. P., Hosaka, K., Hubka, V., Huhndorf, S. M., Jadan, M. Jurjevi, and Kraak, B.

Abstract

Novel species of fungi described in this study include those from various countries as follows: Antarctica: Cadophora antarctica from soil. Australia: Alfaria dandenongensis on Cyperaceae, Amphosoma persooniae on Persoonia sp., Anungitea nullicana on Eucalyptus sp., Bagadiella eucalypti on Eucalyptus globulus, Castanediella eucalyptigena on Eucalyptus sp., Cercospora dianellicola on Dianella sp., Cladoriella kinglakensis on Eucalyptus regnans, Cladoriella xanthorrhoeae (incl. Cladoriellaceae fam. nov. and Cladoriellales ord. nov.) on Xanthorrhoea sp., Cochlearomyces eucalypti (incl. Cochlearomyces gen. nov. and Cochlearomycetaceae fam. nov.) on Eucalyptus obliqua, Codinaea lambertiae on Lambertia formosa, Diaporthe obtusifoliae on Acacia obtusifolia, Didymella acaciae on Acacia melanoxylon, Dothidea eucalypti on Eucalyptus dalrympleana, Fitzroyomyces cyperi (incl. Fitzroyomyces gen. nov.) on Cyperaceae, Murramarangomyces corymbiae (incl. Murramarangomyces gen. nov., Murramarangomycetaceae fam. nov. and Murramarangomycetales ord. nov.) on Corymbia maculata, Neoanungitea eucalypti (incl. Neoanungitea gen. nov.) on Eucalyptus obliqua, Neoconiothyrium persooniae (incl. Neoconiothyrium gen. nov.) on Persoonia laurina subsp. laurina, Neocrinula lambertiae (incl. Neocrinulaceae fam. nov.) on Lambertia sp., Ochroconis podocarpi on Podocarpus grayae, Paraphysalospora eucalypti (incl. Paraphysalospora gen. nov.) on Eucalyptus sieberi, Pararamichloridium livistonae (incl. Pararamichloridium gen. nov., Pararamichloridiaceae fam. nov. and Pararamichloridiales ord. nov.) on Livistona sp., Pestalotiopsis dianellae on Dianella sp., Phaeosphaeria gahniae on Gahnia aspera, Phlogicylindrium tereticornis on Eucalyptus tereticornis, Pleopassalora acaciae on Acacia obliquinervia, Pseudodactylaria xanthorrhoeae (incl. Pseudodactylaria gen. nov., Pseudodactylariaceae fam. nov. and Pseudodactylariales ord. nov.) on Xanthorrhoea sp., Pseudosporidesmium lambertiae (incl. Pseudosporidesmiaceae, Brazil: Achaetomium lippiae on Lippia gracilis, Cyathus isometricus on decaying wood, Geastrum caririense on soil, Lycoperdon demoulinii (incl. Lycoperdon subg. Arenicola) on soil, Megatomentella cristata (incl. Megatomentella gen. nov.) on unidentified plant, Mutinus verrucosus on soil, Paraopeba schefflerae (incl. Paraopeba gen. nov.) on Schefflera morototoni, Phyllosticta catimbauensis on Mandevilla catimbauensis, Pseudocercospora angularis on Prunus persica, Pseudophialophora sorghi on Sorghum bicolor, Spumula piptadeniae on Piptadenia paniculata. Bulgaria: Yarrowia parophonii from gut of Parophonus hirsutulus. Croatia: Pyrenopeziza velebitica on Lonicera borbasiana. Cyprus: Peziza halophila on coastal dunes Czech Republic: Aspergillus contaminans from human fingernail. Ecuador: Cuphophyllus yacurensis on forest soil, Ganoderma podocarpense on fallen tree trunk. England: Pilidium anglicum (incl. Chaetomellales ord. nov.) on Eucalyptus sp. France: Planamyces parisiensis (incl. Planamyces gen. nov.) on wood inside a house. French Guiana: Lactifluus ceraceus on soil. Germany: Talaromyces musae on Musa sp. India: Hyalocladosporiella cannae on Canna indica, Nothophoma raii from soil. Italy: Setophaeosphaeria citri on Citrus reticulata, Yuccamyces citri on Citrus limon. Japan: Glutinomyces brunneus (incl. Glutinomyces gen. nov.) from roots of Quercus sp. Netherlands (all from soil): Collariella hilkhuijsenii, Fusarium petersiae, Gamsia kooimaniorum, Paracremonium binnewijzendii, Phaeoisaria annesophieae, Plectosphaerella niemeijerarum, Striaticonidium deklijnearum, Talaromyces annesophieae, Umbelopsis wiegerinckiae, Vandijckella johannae (incl. Vandijckella gen. nov. and Vandijckellaceae fam. nov.), Verhulstia trisororum (incl. Verhulstia gen. nov.). New Zealand: Lasiosphaeria similisorbina on decorticated wood. Papua New Guinea: Pseudosubramaniomyces gen. nov. (based on Pseudosubramaniomyces fusisaprophyticus comb. nov.). Slovakia: Hemileucoglossum pusillum on soil.

Published
2017

69. Fungal Planet description sheets: 625-715.

Author

Universitat Rovira i Virgili, Crous, P.W.; Wingfield, M.J.; Burgess, T.I.; Carnegie, A.J.; St.J. Hardy, G.E.; Smith, D.; Summerell, B.A.; Cano-Lira, J.F.; Guarro, J.; Houbraken, J.; Lombard, L.; Martín, M.P.; Sandoval-Denis, M.; Alexandrova, A.V.; Barnes, C.W.; Baseia, I.G.; Bezerra, J.D.P.; Guarnaccia, V.; May, T.W.; Hernández-Restrepo, M.; Stchigel, A.M.; Miller, A.N.; Ordoñez, M.E.; Abreu, V.P.; Accioly, T.; Agnello, C.; Agustincolmán, A.; Albuquerque, C.C.; Alfredo, D.S.; Alvarado, P.; Araújo-Magalhães, G.R.; Arauzo, S.; Atkinson, T.; Barili, A.; Barreto, R.W.; Bezerra, J.L.; Cabral, T.S.; Rodríguez, F. Camello; Cruz, R.H.S.F.; Daniëls, P.P.; da silva, B.D.B.; de Almeida, D.A.C.; de Carvalhojúnior, A.A.; Decock, C.A.; Delgat, L.; Denman, S.; Dimitrov, R.A.; Edwards, J.; Fedosova, A.G.; Ferreira, R.J.; Firmino, A.L.; Flores, J.A.; García, D.; Gené, J.; Giraldo, A.; Góis, J.S.; Gomes, A.A.M.; Gonçalves, C.M.; Gouliamova, D.E.; Groenewald, M.; Guéorguiev, B.V.; Guevara-Suarez, M.; Gusmão, L.F.P.; Hosaka, K.; Hubka, V.; Huhndorf, S.M.; Jadan, M.; Jurjevi; Kraak, B.; Kuera, V.; Kumar, T.K.A.; Kušan, I.; Lacerda, S.R.; Lamlertthon, S.; Lisboa, W.S.; Loizides, M.; Luangsa-Ard, J.J.; Lysková, P.; Maccormack, W.P.; Macedo, D.M.; Machado, A.R.; Malysheva, E.F.; Marinho, P.; Matoec, N.; Meijer, M.; Meši, A.; Mongkolsamrit, S.; Moreira, K.A.; Morozova, O.V.; Nair, K.U.; Nakamura, N.; Noisripoom, W.; Olariaga, I.; Oliveira, R.J.V.; Paiva, L.M.; Pawar, P.; Pereira, O.L.; Peterson, S.W.; Prieto, M.; Rodríguez-Andrade, E.; Rojodeblas, C.; Roy, M.; Santos, E.S.; Sharma, R.; Silva, G.A.; Souza-Motta, C.M.; Takeuchi-Kaneko, Y.; Tanaka, C.; Thakur, A.; Smith, M.TH.; Tkalec, Z.; Valenzuela-Lopez, N.; Vanderkleij, P.; Verbeken, A.; Viana, M.G.; Wang, X.W.; Groenewald, J.Z., Universitat Rovira i Virgili, and Crous, P.W.; Wingfield, M.J.; Burgess, T.I.; Carnegie, A.J.; St.J. Hardy, G.E.; Smith, D.; Summerell, B.A.; Cano-Lira, J.F.; Guarro, J.; Houbraken, J.; Lombard, L.; Martín, M.P.; Sandoval-Denis, M.; Alexandrova, A.V.; Barnes, C.W.; Baseia, I.G.; Bezerra, J.D.P.; Guarnaccia, V.; May, T.W.; Hernández-Restrepo, M.; Stchigel, A.M.; Miller, A.N.; Ordoñez, M.E.; Abreu, V.P.; Accioly, T.; Agnello, C.; Agustincolmán, A.; Albuquerque, C.C.; Alfredo, D.S.; Alvarado, P.; Araújo-Magalhães, G.R.; Arauzo, S.; Atkinson, T.; Barili, A.; Barreto, R.W.; Bezerra, J.L.; Cabral, T.S.; Rodríguez, F. Camello; Cruz, R.H.S.F.; Daniëls, P.P.; da silva, B.D.B.; de Almeida, D.A.C.; de Carvalhojúnior, A.A.; Decock, C.A.; Delgat, L.; Denman, S.; Dimitrov, R.A.; Edwards, J.; Fedosova, A.G.; Ferreira, R.J.; Firmino, A.L.; Flores, J.A.; García, D.; Gené, J.; Giraldo, A.; Góis, J.S.; Gomes, A.A.M.; Gonçalves, C.M.; Gouliamova, D.E.; Groenewald, M.; Guéorguiev, B.V.; Guevara-Suarez, M.; Gusmão, L.F.P.; Hosaka, K.; Hubka, V.; Huhndorf, S.M.; Jadan, M.; Jurjevi; Kraak, B.; Kuera, V.; Kumar, T.K.A.; Kušan, I.; Lacerda, S.R.; Lamlertthon, S.; Lisboa, W.S.; Loizides, M.; Luangsa-Ard, J.J.; Lysková, P.; Maccormack, W.P.; Macedo, D.M.; Machado, A.R.; Malysheva, E.F.; Marinho, P.; Matoec, N.; Meijer, M.; Meši, A.; Mongkolsamrit, S.; Moreira, K.A.; Morozova, O.V.; Nair, K.U.; Nakamura, N.; Noisripoom, W.; Olariaga, I.; Oliveira, R.J.V.; Paiva, L.M.; Pawar, P.; Pereira, O.L.; Peterson, S.W.; Prieto, M.; Rodríguez-Andrade, E.; Rojodeblas, C.; Roy, M.; Santos, E.S.; Sharma, R.; Silva, G.A.; Souza-Motta, C.M.; Takeuchi-Kaneko, Y.; Tanaka, C.; Thakur, A.; Smith, M.TH.; Tkalec, Z.; Valenzuela-Lopez, N.; Vanderkleij, P.; Verbeken, A.; Viana, M.G.; Wang, X.W.; Groenewald, J.Z.

Abstract

© 2017 Naturalis Biodiversity Center & Westerdijk Fungal Biodiversity Institute. Novel species of fungi described in this study include those from various countries as follows: Australia:Apiognomonia lasiopetali on Lasiopetalum sp Blastacervulus eucalyptorum on Eucalyptus adesmophloia,Bullanockia australis (incl. Bullanockia gen. nov.) on Kingia australis, Caliciopsis eucalypti on Eucalyptus marginata, Celerioriella petrophiles on Petrophile teretifolia, Coleophoma xanthosiae on Xanthosia rotundifolia, Coniothyrium hakeae on Hakea sp Diatrypella banksiae on Banksia formosa, Disculoides corymbiae on Corymbia calophylla, Elsinoë eelemani on Melaleuca alternifolia, Elsinoë eucalyptigena onEucalyptus kingsmillii, Elsinoë preissianae on Eucalyptus preissiana, Eucasphaeria rustici on Eucalyptus creta, Hyweljonesia queenslandica (incl. Hyweljonesia gen. nov.) on the cocoon of an unidentified microlepidoptera, Mycodiella eucalypti (incl. Mycodiella gen. nov.) on Eucalyptus diversicolor,Myrtapenidiella sporadicae on Eucalyptus sporadica, Neocrinula xanthorrhoeae (incl. Neocrinula gen. nov.) on Xanthorrhoea sp, Ophiocordyceps nooreniae on dead ant, Phaeosphaeriopsis agavacearum on Agavesp, Phlogicylindrium mokarei on Eucalyptus sp, Phyllosticta acaciigena on Acacia suaveolens,Pleurophoma acaciae on Acacia glaucoptera, Pyrenochaeta hakeae on Hakea sp, Readeriella lehmannii onEucalyptus lehmannii, Saccharata banksiae on Banksia grandis, Saccharata daviesiae on Daviesia pachyphylla, Saccharata eucalyptorum on Eucalyptus bigalerita, Saccharata hakeae on Hakea baxteri,Saccharata hakeicola on Hakea victoria, Saccharata lambertiae on Lambertia ericifolia, Saccharata petrophiles on Petrophile sp, Saccharata petrophilicola on Petrophile fastigiata, Sphaerellopsis hakeae onHakea sp, and

Published
2017

70. Responses of the two-spotted oak buprestid, Agrilus biguttatus (Coleoptera:Buprestidae) to host tree volatiles

Author

Vuts, J., Woodcock, C. M., Sumner, M. E., Caulfield, J. C., Reed, K., Inward, D. J. G., Leather, S. R., Pickett, J. A., Birkett, M. A., and Denman, S.

Subjects
Entomology, Agronomy
Abstract

BACKGROUNDAgrilus bigutattus (Fabricius) is a forest pest of increasing importance in the United Kingdom. The larvae damage weakened native oaks and are thought to contribute to premature tree death. Suspected links with acute oak decline (AOD) are not yet confirmed, but AOD-predisposed trees appear to become more susceptible to A. biguttatus attack. Thus, management may be necessary for control of this insect. To explore the possibility of monitoring beetle populations by baited traps, the host tree volatiles regulating A. biguttatus-oak interactions were studied. RESULTSBiologically active volatile organic compounds in dynamic headspace extracts of oak foliage and bark were identified initially by coupled gas chromatography-electroantennography (GC-EAG) and GC-mass spectrometry (GC-MS), and the structures were confirmed by GC coinjection with authentic compounds. Of two synthetic blends of these compounds comprising the active leaf volatiles, the simpler one containing three components evoked strongly positive behavioural responses in four-arm olfactometer tests with virgin females and males, although fresh leaf material was more efficient than the blend. The other blend, comprising a five-component mixture made up of bark volatiles, proved to be as behaviourally active for gravid females as bark tissue. CONCLUSIONSThese initial results on A. biguttatus chemical ecology reveal aspects of the role of attractive tree volatiles in the host-finding of beetles and underpin the development of semiochemically based surveillance strategies for this forest insect. (c) 2015 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Published
2016

73. Fungal Planet description sheets: 625–715

Author

Crous, P.W., primary, Wingfield, M.J., additional, Burgess, T.I., additional, Carnegie, A.J., additional, Hardy, G.E.St.J., additional, Smith, D., additional, Summerell, B.A., additional, Cano-Lira, J.F., additional, Guarro, J., additional, Houbraken, J., additional, Lombard, L., additional, Martín, M.P., additional, Sandoval-Denis, M., additional, Alexandrova, A.V., additional, Barnes, C.W., additional, Baseia, I.G., additional, Bezerra, J.D.P., additional, Guarnaccia, V., additional, May, T.W., additional, Hernández-Restrepo, M., additional, Stchigel, A.M., additional, Miller, A.N., additional, Ordoñez, M.E., additional, Abreu, V.P., additional, Accioly, T., additional, Agnello, C., additional, Agustin Colmán, A., additional, Albuquerque, C.C., additional, Alfredo, D.S., additional, Alvarado, P., additional, Araújo-Magalhães, G.R., additional, Arauzo, S., additional, Atkinson, T., additional, Barili, A., additional, Barreto, R.W., additional, Bezerra, J.L., additional, Cabral, T.S., additional, Camello Rodríguez, F., additional, Cruz, R.H.S.F., additional, Daniëls, P.P., additional, da Silva, B.D.B., additional, de Almeida, D.A.C., additional, de Carvalho Júnior, A.A., additional, Decock, C.A., additional, Delgat, L., additional, Denman, S., additional, Dimitrov, R.A., additional, Edwards, J., additional, Fedosova, A.G., additional, Ferreira, R.J., additional, Firmino, A.L., additional, Flores, J.A., additional, García, D., additional, Gené, J., additional, Giraldo, A., additional, Góis, J.S., additional, Gomes, A.A.M., additional, Gonçalves, C.M., additional, Gouliamova, D.E., additional, Groenewald, M., additional, Guéorguiev, B.V., additional, Guevara-Suarez, M., additional, Gusmão, L.F.P., additional, Hosaka, K., additional, Hubka, V., additional, Huhndorf, S.M., additional, Jadan, M., additional, Jurjević, Ž., additional, Kraak, B., additional, Kučera, V., additional, Kumar, T.K.A., additional, Kušan, I., additional, Lacerda, S.R., additional, Lamlertthon, S., additional, Lisboa, W.S., additional, Loizides, M., additional, Luangsa-ard, J.J., additional, Lysková, P., additional, Mac Cormack, W.P., additional, Macedo, D.M., additional, Machado, A.R., additional, Malysheva, E.F., additional, Marinho, P., additional, Matočec, N., additional, Meijer, M., additional, Mešić, A., additional, Mongkolsamrit, S., additional, Moreira, K.A., additional, Morozova, O.V., additional, Nair, K.U., additional, Nakamura, N., additional, Noisripoom, W., additional, Olariaga, I., additional, Oliveira, R.J.V., additional, Paiva, L.M., additional, Pawar, P., additional, Pereira, O.L., additional, Peterson, S.W., additional, Prieto, M., additional, Rodríguez-Andrade, E., additional, Rojo De Blas, C., additional, Roy, M., additional, Santos, E.S., additional, Sharma, R., additional, Silva, G.A., additional, Souza-Motta, C.M., additional, Takeuchi-Kaneko, Y., additional, Tanaka, C., additional, Thakur, A., additional, Smith, M.Th., additional, Tkalčec, Z., additional, Valenzuela-Lopez, N., additional, van der Kleij, P., additional, Verbeken, A., additional, Viana, M.G., additional, Wang, X.W., additional, and Groenewald, J.Z., additional

Published
2017
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74. Review: The application of omics to rumen microbiota function.

Author

Denman, S. E., Morgavi, D. P., McSweeney, C. S., Cassar-Malek, Isabelle, Baumont, René, Bannink, Andre, Teixeira, Izabelle, Mayberry, Dianne, and Kyriazakis, Ilias

Abstract

Rumen microbiome profiling uses 16S rRNA (18S rRNA, internal transcribed spacer) gene sequencing, a method that usually sequences a small portion of a single gene and is often biased and varies between different laboratories. Functional information can be inferred from this data, but only for those that are closely related to known annotated species, and even then may not truly reflect the function performed within the environment being studied. Genome sequencing of isolates and metagenome-assembled genomes has now reached a stage where representation of the majority of rumen bacterial genera are covered, but this still only represents a portion of rumen microbial species. The creation of a microbial genome (bins) database with associated functional annotations will provide a consistent reference to allow mapping of RNA-Seq reads for functional gene analysis from within the rumen microbiome. The integration of multiple omic analytics is linking functional gene activity, metabolic pathways and rumen metabolites with the responsible microbiota, supporting our biological understanding of the rumen system. The application of these techniques has advanced our understanding of the major microbial populations and functional pathways that are used in relation to lower methane emissions, higher feed efficiencies and responses to different feeding regimes. Continued and more precise use of these tools will lead to a detailed and comprehensive understanding of compositional and functional capacity and design of techniques for the directed intervention and manipulation of the rumen microbiota towards a desired state. [ABSTRACT FROM AUTHOR]

Published
2018
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76. High fat diets induce colonic epithelial cell stress and inflammation that is reversed by IL-22

Author

Gulhane, M, Murray, L, Lourie, R, Tong, H, Kang, A, Schreiber, V, Magor, G, Denman, S, Begun, J, Florin, T, Perkins, A, Cuiv, OP, Mcguckin, M, Hasnain, SZ, Gulhane, M, Murray, L, Lourie, R, Tong, H, Kang, A, Schreiber, V, Magor, G, Denman, S, Begun, J, Florin, T, Perkins, A, Cuiv, OP, Mcguckin, M, and Hasnain, SZ

Abstract

Prolonged high fat diets (HFD) induce low-grade chronic intestinal inflammation in mice, and diets high in saturated fat are a risk factor for the development of human inflammatory bowel diseases. We hypothesized that HFD-induced endoplasmic reticulum (ER)/oxidative stress occur in intestinal secretory goblet cells, triggering inflammatory signaling and reducing synthesis/secretion of proteins that form the protective mucus barrier. In cultured intestinal cells non-esterified long-chain saturated fatty acids directly increased oxidative/ER stress leading to protein misfolding. A prolonged HFD elevated the intestinal inflammatory cytokine signature, alongside compromised mucosal barrier integrity with a decrease in goblet cell differentiation and Muc2, a loss in the tight junction protein, claudin-1 and increased serum endotoxin levels. In Winnie mice, that develop spontaneous colitis, HFD-feeding increased ER stress, further compromised the mucosal barrier and increased the severity of colitis. In obese mice IL-22 reduced ER/oxidative stress and improved the integrity of the mucosal barrier, and reversed microbial changes associated with obesity with an increase in Akkermansia muciniphila. Consistent with epidemiological studies, our experiments suggest that HFDs are likely to impair intestinal barrier function, particularly in early life, which partially involves direct effects of free-fatty acids on intestinal cells, and this can be reversed by IL-22 therapy.

Published
2016

77. Characterization ofColletotrichumspecies associated with diseases of Proteaceae

Author

Lubbe, C.M., Denman, S., Cannon, P.F., Groenewald, J.Z., Lamprecht, S.C., and Crous, P.W.

Subjects
0106 biological sciences, 0301 basic medicine, Physiology, fungi, EPS-4, food and beverages, Cell Biology, General Medicine, 030108 mycology & parasitology, 010603 evolutionary biology, 01 natural sciences, Laboratorium voor Phytopathologie, 03 medical and health sciences, Laboratory of Phytopathology, Genetics, Molecular Biology, fusarium, Ecology, Evolution, Behavior and Systematics
Abstract

Colletotrichum spp. are known to occur on and cause diseases of Proteaceae, but their identities are confused and poorly understood. The aim of the present study thus was to identify accurately the Colletotrichum spp. associated with diseases of cultivated Proteaceae. Colletotrichum spp. associated with proteaceous hosts growing in various parts of the world were identified based on morphology, sequence data of the internal transcribed spacer region (ITS-1, ITS-2), the 5.8S gene, and partial sequences of the ß-tubulin gene. Four species of Colletotrichum were found to be associated with Proteaceae. Colletotrichum gloeosporioides, a cosmopolitan species known to occur on numerous hosts, was isolated from Protea cynaroides cultivated in South Africa and Zimbabwe, and from a Leucospermum sp. in Portugal. A recently described species, C. boninense was associated with Zimbabwean and Australian Proteaceae but also occurred on a Eucalyptus sp. in South Africa. This represents a major geographical and host extension for the species and a description of the African strains is provided. Colletotrichum crassipes was represented by a single isolate obtained from a Dryandra plant in Madeira. Colletotrichum acutatum was isolated from Protea and Leucadendron in South Africa as well as from other hosts occurring elsewhere. A pathologically distinct population of this species was found to occur on Hakea in South Africa. This population is described as C. acutatum f. sp. hakeae, and its relationship with other strains of C. acutatum is discussed. Contrary to earlier literature reports linking C. gloeosporioides to anthracnose of Proteaceae, the present study has shown that several distinct species of Colletotrichum are associated with different diseases of this crop, which has serious implications for quarantine and disease control practices

Published
2004

79. DO LONGITUDINAL MEASURES OF CLINICAL VARIATION CORRELATE WITH ADHERENCE IN CYSTIC FIBROSIS

Author

White, H, Denman, S, Shaw, N, Pollard, K, and Peckham, D

Abstract

Introduction: An electronic clinical record (ECR) coding for all variables of CF and capturing “real time” data from 2007 was used as a basis for this study. From this data, longitudinal patterns of clinical variation have emerged that suggest a relationship between variation in lung function and adherence. Our aim was to determine a) the accuracy of self-report adherence and its relationship with clinical variation, and b) whether objective measures, including clinical variation can predict adherence. Methods: Patients aged 16 years and over attending an adult regional CF centre were invited to complete an adherence questionnaire (CFQ-R) and consent to pharmacy script data collection (previous 6 months). Coefficient of variation for FEV1 (CoV FEV1) was calculated from all contacts within the previous year. Age, gender, microbiology, disease severity (banding status), medication, lung function and weight were noted at baseline. Self-reported adherence was calculated against prescribed medication (using ECR) and patients classified into one of 3 categories: low (80%) according to % calculated adherence. Ordinal regression was used to determine the contribution of age, gender, microbiology status, disease severity (Banding status), medication, genotype and CoV FEV1 to self-reported adherence. Results: Patients (n=250) [age 29.7 (±9.2) y, 58.6% (M), baseline BMI 22.5 kg/m2 (±3.8), FEV1 61.3% (±25.1), FVC 79.4% (±23.1)] completed the study. Pharmacy collection data were available for 106 (42%) patients. Pharmacy script collection was strongly correlated to self-reported adherence (Table). CoV FEV1 was inversely related to self-reported adherence (Table 1). Regression analysis revealed that CoV FEV1 [OR = 0.95; CI: 0.92-0.98, p=0.006], number of types of medication [OR = 1.18; CI: 1.11- 1.26, p

Published
2014

80. Objective predictors of self-report of adherence in adults with cystic fibrosis

Author

Denman, S, White, H, Shaw, N, Driffil, A, and Peckham, DG

Abstract

Objective: Self-reported adherence overestimates true adherence and is 14% above pharmacy script collection in our population. Our aim was to investigate the presence of objective measures which could predict self reported adherence. Methods: Patients completed a self-report of adherence (CFQ-R). They were subsequently classified into one of 3 categories: low (80%) according to a mean of their score from the CFQ-R adherence score and confirmation against prescribed medications. Coefficient of variation (CoV) for FEV1, weight and CRP were each calculated from all clinical contacts within the previous year. Age, gender, microbial status, disease severity, medication, respiratory and anthropometric measures were collected at baseline. Ordinal regression was used to determine the contribution of objective variables to adherence. Results: 249 patients [age 29.7(±9.2) yrs, 58.6% (M)] completed the study. Regression analysis revealed that FEV1 CoV [OR = 0.95; CI: 0.92-0.98, p=0.006], number of types of medication [OR = 1.18; CI: 1.11-1.26, p

Published
2014

87. Cultivation and diseases of Proteaceae: Leucadendron, Leucospermum and Protea

Author

Crous, P.W., Denman, S., Taylor, J.E., Swart, L., Bezuidenhout, C.M., Hoffman, L., Palm, M.E., and Groenewald, J.Z.

Subjects
disease control, plantenziekteverwekkende schimmels, fytosanitair beleid, taxonomie, leucospermum, phytosanitary policies, host range, plant pathogenic bacteria, ziektebestrijding, cut flowers, gastheerreeks, taxonomy, leucadendron, snijbloemen, root rots, wilts, identificatie, determinatietabellen, kanker (plantenziektekundig), cankers, plantenziekteverwekkende bacteriën, wortelrot, cultivation, teelt, plant pathogenic fungi, identification, proteaceae, keys, plantenziekten, verwelkingsziekten, protea, plant diseases
Abstract

Proteaceae represent a prominent family of flowering plants in the Southern Hemisphere. Because of their beauty, unique appearance, and relatively long shelf life, Proteaceae cut-flowers have become a highly desirable crop for the export market. The cultivation of Proteaceae is a thriving industry that provides employment in countries where these flowers are grown, often in areas that are otherwise unproductive agriculturally. Diseases cause a loss in yield, and also limit the export of these flowers due to strict phytosanitary regulations. In this publication the fungi that cause leaf, stem and root diseases on Leucadendron, Leucospermum and Protea are treated. Data are provided pertaining to the taxonomy, identification, host range, distribution, pathogenicity, molecular characteristics and control of these pathogens. Taxonomic descriptions and illustrations are provided and keys are included to distinguish species in genera where a number of species affect Proteaceae. Disease symptoms are described and colour photographs are included. Where known, factors that affect disease epidemiology are discussed. Disease management strategies are also presented that will assist growers and advisors in making appropriate choices for reducing disease in specific areas. Information is also provided relating to crop improvement, cultivation techniques, harvesting and export considerations. Further development and expansion of this industry depends on producing and obtaining disease-free germplasm from countries where these plants are indigenous. For that reason it is important to document the fungi that occur on Proteaceae, and to establish the distribution of these fungi. These data are essential for plant quarantine services for use in risk assessments.

Published
2013

88. Phytophthora taxa associated with cultivated Agathosma, with emphasis on the P. citricola complex and P. capensis sp. nov

Author

Bezuidenhout, C.M., Denman, S., Kirk, S.A., Botha, W.J., Mostert, L., McLeod, A., and Naturalis journals & series

Subjects
taxonomy, isozymes, fynbos, Avocado, malate dehydrogenase, pathogenicity, root-rot, glucose-6-phosphate isomerase, buchu, Research Article
Abstract

Agathosma species, which are indigenous to South Africa, are also cultivated for commercial use. Recently growers experienced severe plant loss, and symptoms shown by affected plants suggested that a soilborne disease could be the cause of death. A number of Phytophthora taxa were isolated from diseased plants, and this paper reports their identity, mating type, and pathogenicity to young Agathosma plants. Using morphological and sequence data seven Phytophthora taxa were identified: the A1 mating type of P. cinnamomi var. cinnamomi, P. cinnamomi var. parvispora and P. cryptogea, the A2 mating type of P. drechsleri and P. nicotianae, and two homothallic taxa from the P. citricola complex. The identity of isolates in the P. citricola complex was resolved using reference isolates of P. citricola CIT groups 1 to 5 sensu Oudemans et al. (1994) along with multi-locus phylogenies (three nuclear and two mitochondrial regions), isozyme analyses, morphological characteristics and temperature-growth studies. These analyses revealed the isolates from Agathosma to include P. multivora and a putative novel species, P. taxon emzansi. Furthermore, among the P. citricola reference isolates the presence of a new species was revealed, described here as P. capensis. Findings of our study, along with some recent other studies, have contributed to resolving some of the species complexity within the P. citricola complex, resulting in the identification of a number of phylogenetically distinct taxa. The pathogenicity of representative isolates of the taxa from Agathosma was tested on A. betulina seedlings. The putative novel species, P. taxon emzansi, and P. cinnamomi var. parvispora were non-pathogenic, whereas the other species were pathogenic to this host.

Published
2010

89. Letter to the Editor : Standardizing the nomenclature for clonal lineages of the sudden oak death pathogen, Phytophthora ramorum

Author

Grünwald, N.J., Goss, E.M., Ivors, K., Garbelotto, M., Martin, F.N., Prospero, S., Hansen, E., Bonants, P.J.M., Hamelin, R.C., Chastagner, M., Werres, S., Rizzo, D.M., Abad, G., Beales, P., Bilodeau, G.J., Blomquist, C.L., Brasier, C., Brière, S.C., Chandelier, A., Davidson, J.M., Denman, S., Elliott, M., Frankel, S.J., Goheen, E.M., de Gruyter, H., Heungens, K., James, D., Kanaskie, A., McWilliams, M.G., Man in't Veld, W., Moralejo, E., Osterbauer, N.K., Palm, M.E., Parke, J.L., Perez Sierra, A.M., Shamoun, S.F., Shishkoff, N., Tooley, P.W., Vettraino, A.M., Webber, J., and Widmer, T.L.

Subjects
north-american, toluca valley, european populations, Bioint Moleculair Phytopathology, genotypic diversity, central mexico, united-states, in-vitro, california, infestans, dna polymorphisms
Abstract

Phytophthora ramorum, the causal agent of sudden oak death and ramorum blight, is known to exist as three distinct clonal lineages which can only be distinguished by performing molecular marker-based analyses. However, in the recent literature there exists no consensus on naming of these lineages. Here we propose a system for naming clonal lineages of P. ramorum based on a consensus established by the P. ramorum research community. Clonal lineages are named with a two letter identifier for the continent on which they were first found (e.g., NA = North America; EU = Europe) followed by a number indicating order of appearance. Clonal lineages known to date are designated NA1 (mating type: A2; distribution: North America; environment: forest and nurseries), NA2 (A2; North America; nurseries), and EU1 (predominantly A1, rarely A2; Europe and North America; nurseries and gardens). It is expected that novel lineages or new variants within the existing three clonal lineages could in time emerge.

Published
2009

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