Search

Your search keyword '"Yoshinaga Y"' showing total 937 results
Start Over Author "Yoshinaga Y"
937 results on '"Yoshinaga Y"'

1. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens.

Author

Haridas, S, Albert, R, Binder, M, Bloem, J, LaButti, K, Salamov, A, Andreopoulos, B, Baker, SE, Barry, K, Bills, G, Bluhm, BH, Cannon, C, Castanera, R, Culley, DE, Daum, C, Ezra, D, González, JB, Henrissat, B, Kuo, A, Liang, C, Lipzen, A, Lutzoni, F, Magnuson, J, Mondo, SJ, Nolan, M, Ohm, RA, Pangilinan, J, Park, H-J, Ramírez, L, Alfaro, M, Sun, H, Tritt, A, Yoshinaga, Y, Zwiers, L-H, Turgeon, BG, Goodwin, SB, Spatafora, JW, Crous, PW, and Grigoriev, IV

Subjects
Aulographales Crous, Spatafora, Haridas & Grigoriev, Coniosporiaceae Crous, Spatafora, Haridas & Grigoriev, Coniosporiales Crous, Spatafora, Haridas & Grigoriev, Eremomycetales Crous, Spatafora, Haridas & Grigoriev, Fungal evolution, Genome-based prediction, Lineolataceae Crous, Spatafora, Haridas & Grigoriev, Lineolatales Crous, Spatafora, Haridas & Grigoriev, Machine-learning, New taxa, Rhizodiscinaceae Crous, Spatafora, Haridas & Grigoriev, Aulographales Crous, Spatafora, Haridas & Grigoriev, Coniosporiaceae Crous, Coniosporiales Crous, Eremomycetales Crous, Lineolataceae Crous, Lineolatales Crous, Rhizodiscinaceae Crous, Microbiology, Mycology & Parasitology
Abstract

Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species.

Published
2020

4. High throughput sequencing recovers the noval gene Megf8 as the ENU induced mutation causing single ventricle cardiac defect associated with randomized left-right patterning (Massively parallel sequencing identifies the gene Megf8 with ENU-induced mutation causing heterotaxy)

Author

Zhang, Z., Alpert, D., Francis, R., Chatterjee, B., Yu, Q., Tansey, T., Sabol, S., Cui, C., Bai, Y., Koriabine, M., Yoshinaga, Y., Cheng, J.-F., Martin, J., Schackwitz, W., Fujiwara, Y., Orkin, S., Gunn, T.M., Kramer, K.L., DeJong, P.J., Pennacchio, L.A., and Lo, C.W.

Abstract

Forward genetic screens with ENU (N-ethyl-N-nitrosourea) mutagenesis can facilitate gene discovery, but mutation identification is often difficult. We present the first study in which an ENU-induced mutation was identified by massively parallel DNA sequencing. This mutation causes heterotaxy and complex congenital heart defects and was mapped to a 2.2-Mb interval on mouse chromosome 7. Massively parallel sequencing of the entire 2.2-Mb interval identified 2 single-base substitutions, one in an intergenic region and a second causing replacement of a highly conserved cysteine with arginine (C193R) in the gene Megf8. Megf8 is evolutionarily conserved from human to fruit fly, and is observed to be ubiquitously expressed. Morpholino knockdown of Megf8 in zebrafish embryos resulted in a high incidence of heterotaxy, indicating a conserved role in laterality specification. Megf8(C193R) mouse mutants show normal breaking of symmetry at the node, but Nodal signaling failed to be propagated to the left lateral plate mesoderm. Videomicroscopy showed nodal cilia motility, which is required for left-right patterning, is unaffected. Although this protein is predicted to have receptor function based on its amino acid sequence, surprisingly confocal imaging showed it is translocated into the nucleus, where it is colocalized with Gfi1b and Baf60C, two proteins involved in chromatin remodeling. Overall, through the recovery of an ENU-induced mutation, we uncovered Megf8 as an essential regulator of left-right patterning

Published
2009

8. Mutations in the FUS/TLS Gene on Chromosome 16 Cause Familial Amyotrophic Lateral Sclerosis

Author

Kwiatkowski,, T. J., Bosco, D. A., LeClerc, A. L., Tamrazian, E., Vanderburg, C. R., Russ, C., Davis, A., Gilchrist, J., Kasarskis, E. J., Munsat, T., Valdmanis, P., Rouleau, G. A., Hosler, B. A., Cortelli, P., de Jong, P. J., Yoshinaga, Y., Haines, J. L., Pericak-Vance, M. A., Yan, J., Ticozzi, N., Siddique, T., McKenna-Yasek, D., Sapp, P. C., Horvitz, H. R., Landers, J. E., and Brown,, R. H.

Published
2009
Full Text
View/download PDF

15. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens

Author

Haridas, S., Albert, R., Binder, M., Bloem, J., LaButti, K., Salamov, A., Andreopoulos, B., Baker, S. E., Barry, K., Bills, G., Bluhm, B. H., Cannon, C., Castanera, R., Culley, D. E., Daum, C., Ezra, D., González, J. B., Henrissat, B., Kuo, A., Liang, C., Lipzen, A., Lutzoni, F., Magnuson, J., Mondo, S. J., Nolan, M., Ohm, R. A., Pangilinan, J., Park, H. J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L. H., Turgeon, B. G., Goodwin, S. B., Spatafora, J. W., Crous, P. W., Grigoriev, I. V., Haridas, S., Albert, R., Binder, M., Bloem, J., LaButti, K., Salamov, A., Andreopoulos, B., Baker, S. E., Barry, K., Bills, G., Bluhm, B. H., Cannon, C., Castanera, R., Culley, D. E., Daum, C., Ezra, D., González, J. B., Henrissat, B., Kuo, A., Liang, C., Lipzen, A., Lutzoni, F., Magnuson, J., Mondo, S. J., Nolan, M., Ohm, R. A., Pangilinan, J., Park, H. J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L. H., Turgeon, B. G., Goodwin, S. B., Spatafora, J. W., Crous, P. W., and Grigoriev, I. V.

Abstract

Dothideomycetes is the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetes and they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomycetes has significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetes introducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetes phylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species.

Published
2020

16. Gastric cancer mortality rates by occupation and industry among male and female workers aged 25–64 years in Japan

Author

Yoshinaga, Y. (Yoko), Tanaka, H. (Hirokazu), Wada, K. (Koji), Ikeda, S. (Shunya), Yoshinaga, Y. (Yoko), Tanaka, H. (Hirokazu), Wada, K. (Koji), and Ikeda, S. (Shunya)

Abstract

Differences in risk for gastric cancer exist among occupations and industries in Japan. Using a 2015 national dataset, we estimated the mortality rates due to gastric cancer in Japanese male and female workers aged 25–64 yr. Regression models were used to estimate the mortality rate ratios separately for men and women with adjustment for age. The occupation with the high-est risk ratio was “Service” in men (2.06, 95% confidence interval: 1.63–2.61) and “Construction and Mining” in women compared with “Sales”. For industries, workers in “Mining”, “Electricity, Gas, Heat supply and Water”, “Fisheries”, “Agriculture and Forestry”, and “Construction” had a higher mortality risk. Our results showed that occupations and industries with higher mortality rates in men had the same trend as the results from 2010, and occupations and industries with higher mortality rates in women were almost the same as those in men. The analyses also indicated that managerial and professional workers in Japan had higher mortality as opposed to developed Western countries. In conclusion, this study suggests that occupations and industries still impact men and women’s health in terms of mortality due to gastric cancer in Japan.

Published
2020
Full Text
View/download PDF

17. 101 Dothideomycetes genomes: A test case for predicting lifestyles and emergence of pathogens

Author

Sub Molecular Microbiology, Molecular Microbiology, Haridas, S., Albert, R., Binder, M., Bloem, J., LaButti, K., Salamov, A., Andreopoulos, B., Baker, S. E., Barry, K., Bills, G., Bluhm, B. H., Cannon, C., Castanera, R., Culley, D. E., Daum, C., Ezra, D., González, J. B., Henrissat, B., Kuo, A., Liang, C., Lipzen, A., Lutzoni, F., Magnuson, J., Mondo, S. J., Nolan, M., Ohm, R. A., Pangilinan, J., Park, H. J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L. H., Turgeon, B. G., Goodwin, S. B., Spatafora, J. W., Crous, P. W., Grigoriev, I. V., Sub Molecular Microbiology, Molecular Microbiology, Haridas, S., Albert, R., Binder, M., Bloem, J., LaButti, K., Salamov, A., Andreopoulos, B., Baker, S. E., Barry, K., Bills, G., Bluhm, B. H., Cannon, C., Castanera, R., Culley, D. E., Daum, C., Ezra, D., González, J. B., Henrissat, B., Kuo, A., Liang, C., Lipzen, A., Lutzoni, F., Magnuson, J., Mondo, S. J., Nolan, M., Ohm, R. A., Pangilinan, J., Park, H. J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L. H., Turgeon, B. G., Goodwin, S. B., Spatafora, J. W., Crous, P. W., and Grigoriev, I. V.

Published
2020

22. Investigation of properties of stacked-type interface-treated Josephson junctions fabricated with PrGaO[subscript 3] doping process

Author

Yoshinaga, Y., Izawa, S., Wakita, K., Kito, T., Inoue, M., Fujimaki, A., and Hayakawa, H.

Subjects
Josephson junction -- Research, Superconductive devices -- Research, Business, Electronics, Electronics and electrical industries
Abstract

The relationship between the surface morphology and the properties of stacked-type interface-treated junctions with the PGO doping processes is examined and reported.

Published
2003

39. Study on fabrication conditions of the interface-treated trilayer junctions

Author

Maruyama, M, Yoshida, K., Kito, T., Furutani, T., Yoshinaga, Y., Horibe, M., Inoue, M., Fujimaki, A., and Hayakawa, H.

Subjects
Josephson junction -- Research, Business, Electronics, Electronics and electrical industries
Abstract

The effects of fabrication conditions on interface-treated trilayer Josephson junctions are reported.

Published
2001

45. Draft Genome Sequence of the White-Rot Fungus Obba rivulosa 3A-2

Author

Haridas, S., Albert, R., Binder, M., Bloem, J., Labutti, Kurt, Salamov, A., Andreopoulos, B., Baker, S.E., Barry, Kerrie, Bills, G., Bluhm, B.H., Cannon, C., Castanera, R., Culley, D.E., Daum, C., Ezra, D., González, J.B., Henrissat, Bernard, Kuo, A., Liang, C., Lipzen, Anna, Lutzoni, F., Magnuson, J., Mondo, S.J., Nolan, M., Ohm, R.A., Pangilinan, J., Park, H.-J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L.-H., Turgeon, B.G., Goodwin, S.B., Spatafora, J.W., Crous, P.W., Grigoriev, I.V., Ulaganathan, ThirumalaiSelvi, Shi, Rong, Yao, Deqiang, Gu, Ruo-Xu, Garron, Marie-Line, Cherney, Maia, Tieleman, D Peter, Sterner, Eric, Li, Guoyun, Li, Lingyun, Linhardt, Robert, Cygler, Miroslaw, Van Wyk, Niël, Drancourt, Michel, Kremer, Laurent, Miettinen, Otto, Riley, Robert, Cullen, Dan, De Vries, Ronald, Hainaut, Matthieu, Hatakka, Annele, Hildén, Kristiina, Kuo, Rita, Mäkelä, Miia, Sandor, Laura, Spatafora, Joseph, Grigoriev, Igor, Hibbett, David, CBS-KNAW Fungal Biodiversity Centre, US Department of Energy Joint Genome Institute, U.S Department of Energy, U.S. Department of Energy [Washington] (DOE)-U.S. Department of Energy [Washington] (DOE), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), United States Department of Energy, Architecture et fonction des macromolécules biologiques (AFMB), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Finnish Museum of Natural History, Botany, Department of Food and Nutrition, Resarch Group of Annele Hatakka, and Fungal Genetics and Biotechnology

Subjects
0301 basic medicine, MESH: Mycobacterium tuberculosis, Eukaryotes, substrate specificity, Aulographales Crous, MESH: Carbohydrate Metabolism, [SDV]Life Sciences [q-bio], Rpfs, Genome, MESH: Protein Conformation, Coniosporiaceae Crous, Polyporales, glycoside hydrolase, MESH: Conserved Sequence, biology, MESH: beta-Glucans, 1184 Genetics, developmental biology, physiology, Basidiomycota, 030108 mycology & parasitology, active site, CAZy database, protein dynamics, Eremomycetales Crous, Coniosporiales Crous, MESH: Hydrolysis, crystal structure, CAZy, Obba rivulosa, Lineolatales Crous, Fungus, Microbiology, complex mixtures, 03 medical and health sciences, MESH: Cell Wall, New taxa, Polypore, Botany, Journal Article, Genetics, MESH: Glycoside Hydrolases, MESH: Protein Binding, Spatafora, Molecular Biology, Machine-learning, Rhizodiscinaceae Crous, MESH: Glycoconjugates, trehalose, heparin lyase, Whole genome sequencing, MESH: Humans, Human Genome, technology, industry, and agriculture, Mycobacterium tuberculosis, biology.organism_classification, Genome-based prediction, Haridas & Grigoriev, 030104 developmental biology, MESH: Polysaccharides, Fungal evolution, MESH: Substrate Specificity, Biochemistry and Cell Biology, Lineolataceae Crous
Abstract

We report here the first genome sequence of the white-rot fungus Obba rivulosa (Polyporales, Basidiomycota), a polypore known for its lignin-decomposing ability. The genome is based on the homokaryon 3A-2 originating in Finland. The genome is typical in size and carbohydrate active enzyme (CAZy) content for wood-decomposing basidiomycetes.

Published
2016

49. 101 Dothideomycetesgenomes: A test case for predicting lifestyles and emergence of pathogens

Author

Haridas, S., Albert, R., Binder, M., Bloem, J., LaButti, K., Salamov, A., Andreopoulos, B., Baker, S.E., Barry, K., Bills, G., Bluhm, B.H., Cannon, C., Castanera, R., Culley, D.E., Daum, C., Ezra, D., González, J.B., Henrissat, B., Kuo, A., Liang, C., Lipzen, A., Lutzoni, F., Magnuson, J., Mondo, S.J., Nolan, M., Ohm, R.A., Pangilinan, J., Park, H.-J., Ramírez, L., Alfaro, M., Sun, H., Tritt, A., Yoshinaga, Y., Zwiers, L.-H., Turgeon, B.G., Goodwin, S.B., Spatafora, J.W., Crous, P.W., and Grigoriev, I.V.

Abstract

Dothideomycetesis the largest class of kingdom Fungi and comprises an incredible diversity of lifestyles, many of which have evolved multiple times. Plant pathogens represent a major ecological niche of the class Dothideomycetesand they are known to infect most major food crops and feedstocks for biomass and biofuel production. Studying the ecology and evolution of Dothideomyceteshas significant implications for our fundamental understanding of fungal evolution, their adaptation to stress and host specificity, and practical implications with regard to the effects of climate change and on the food, feed, and livestock elements of the agro-economy. In this study, we present the first large-scale, whole-genome comparison of 101 Dothideomycetesintroducing 55 newly sequenced species. The availability of whole-genome data produced a high-confidence phylogeny leading to reclassification of 25 organisms, provided a clearer picture of the relationships among the various families, and indicated that pathogenicity evolved multiple times within this class. We also identified gene family expansions and contractions across the Dothideomycetesphylogeny linked to ecological niches providing insights into genome evolution and adaptation across this group. Using machine-learning methods we classified fungi into lifestyle classes with >95 % accuracy and identified a small number of gene families that positively correlated with these distinctions. This can become a valuable tool for genome-based prediction of species lifestyle, especially for rarely seen and poorly studied species.

Published
2020
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results