Search Results - "Pukkila, Patricia J."

Strand-Specific RNA-Seq Analyses of Fruiting Body Development in Coprinopsis cinerea by Muraguchi, Hajime, Umezawa, Kiwamu, Niikura, Mai, Yoshida, Makoto, Kozaki, Toshinori, Ishii, Kazuo, Sakai, Kiyota, Shimizu, Motoyuki, Nakahori, Kiyoshi, Sakamoto, Yuichi, Choi, Cindy, Ngan, Chew Yee, Lindquist, Eika, Lipzen, Anna, Tritt, Andrew, Haridas, Sajeet, Barry, Kerrie, Grigoriev, Igor V, Pukkila, Patricia J

“…The basidiomycete fungus Coprinopsis cinerea is an important model system for multicellular development. Fruiting bodies of C. cinerea are typical mushrooms,…”
Get full text

Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes by Iyer, Lakshminarayan M., Zhang, Dapeng, de Souza, Robson F., Pukkila, Patricia J., Rao, Anjana, Aravind, L.

“…TET/JBP dioxygenases oxidize methylpyrimidines in nucleic acids and are implicated in generation of epigenetic marks and potential intermediates for DNA…”
Get full text

5'-Serial Analysis of Gene Expression studies reveal a transcriptomic switch during fruiting body development in Coprinopsis cinerea by Cheng, Chi Keung, Au, Chun Hang, Wilke, Sarah K, Stajich, Jason E, Zolan, Miriam E, Pukkila, Patricia J, Kwan, Hoi Shan

“…The transition from the vegetative mycelium to the primordium during fruiting body development is the most complex and critical developmental event in the life…”
Get full text

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea by Chavez, Lukas, Huang, Yun, Luong, Khai, Agarwal, Suneet, Iyer, Lakshminarayan M, Pastor, William A, Hench, Virginia K, Frazier-Bowers, Sylvia A, Korol, Evgenia, Liu, Shuo, Tahiliani, Mamta, Wang, Yinsheng, Clark, Tyson A, Korlach, Jonas, Pukkila, Patricia J, Aravind, L, Rao, Anjana

“…Significance A prominent epigenetic mechanism for gene regulation is methylation of cytosine bases in DNA. TET enzymes facilitate DNA demethylation by…”
Get full text

Analysis of the Basidiomycete Coprinopsis cinerea reveals conservation of the core meiotic expression program over half a billion years of evolution by Burns, Claire, Stajich, Jason E, Rechtsteiner, Andreas, Casselton, Lorna, Hanlon, Sean E, Wilke, Sarah K, Savytskyy, Oleksandr P, Gathman, Allen C, Lilly, Walt W, Lieb, Jason D, Zolan, Miriam E, Pukkila, Patricia J

“…Coprinopsis cinerea (also known as Coprinus cinereus) is a multicellular basidiomycete mushroom particularly suited to the study of meiosis due to its…”
Get full text

Coprinopsis cinerea by Pukkila, Patricia J.

Get full text

Novel proteins required for meiotic silencing by unpaired DNA and siRNA generation in Neurospora crassa by Hammond, Thomas M, Xiao, Hua, Boone, Erin C, Decker, Logan M, Lee, Seung A, Perdue, Tony D, Pukkila, Patricia J, Shiu, Patrick K T

“…During meiosis in the filamentous fungus Neurospora crassa, unpaired genes are identified and silenced by a process known as meiotic silencing by unpaired DNA…”
Get full text

QIP, a protein that converts duplex siRNA into single strands, is required for meiotic silencing by unpaired DNA by Xiao, Hua, Alexander, William G, Hammond, Thomas M, Boone, Erin C, Perdue, Tony D, Pukkila, Patricia J, Shiu, Patrick K T

“…RNA interference (RNAi) depends on the production of small RNA to regulate gene expression in eukaryotes. Two RNAi systems exist to control repetitive selfish…”
Get full text

SAD-3, a Putative Helicase Required for Meiotic Silencing by Unpaired DNA, Interacts with Other Components of the Silencing Machinery by Hammond, Thomas M, Xiao, Hua, Boone, Erin C, Perdue, Tony D, Pukkila, Patricia J, Shiu, Patrick K T

“…In Neurospora crassa, genes lacking a pairing partner during meiosis are suppressed by a process known as meiotic silencing by unpaired DNA (MSUD). To identify…”
Get full text

DCL-1 colocalizes with other components of the MSUD machinery and is required for silencing by Alexander, William G., Raju, Namboori B., Xiao, Hua, Hammond, Thomas M., Perdue, Tony D., Metzenberg, Robert L., Pukkila, Patricia J., Shiu, Patrick K.T.

“…In Neurospora, a gene present in an abnormal number of copies is usually a red flag for mischief. One way to deal with these potential intruders is by…”
Get full text

Fluorescent and bimolecular-fluorescent protein tagging of genes at their native loci in Neurospora crassa using specialized double-joint PCR plasmids by Hammond, Thomas M., Xiao, Hua, Rehard, David G., Boone, Erin C., Perdue, Tony D., Pukkila, Patricia J., Shiu, Patrick K.T.

“…► Novel plasmids created for targeted genome integration in Neurospora crassa. ► Designed for GFP, RFP, and split-YFP (BiFC) tagging. ► Customized construction…”
Get full text

Introducing student inquiry in large introductory genetics classes by Pukkila, Patricia J

“…An appreciation of genetic principles depends upon understanding the individual curiosity that sparked particular investigations, the creativity involved in…”
Get full text

Characterization of Interactions Between and Among Components of the Meiotic Silencing by Unpaired DNA Machinery in Neurospora crassa Using Bimolecular Fluorescence Complementation by Bardiya, N, Alexander, W.G, Perdue, T.D, Barry, E.G, Metzenberg, R.L, Pukkila, P.J, Shiu, P.K.T

“…Bimolecular fluorescence complementation (BiFC) is based on the complementation between two nonfluorescent fragments of the yellow fluorescent protein (YFP)…”
Get full text

Meiotic cytogenetics in Coprinus cinereus by Zolan, Miriam E, Pukkila, Patricia J

“…The basidiomycete fungus Coprinus cinereus has naturally synchronous meiosis and is amenable to analysis using an array of well-developed genetic and molecular…”
Get more information

EFFECTS OF HIGH LEVELS OF DNA ADENINE METHYLATION ON METHYL-DIRECTED MISMATCH REPAIR IN ESCHERICHIA COLI by Pukkila, Patricia J, Peterson, Janet, Herman, Gail, Modrich, Paul, Meselson, Matthew

“…Two methods were used in an attempt to increase the efficiency and strand selectivity of methyl-directed mismatch repair of bacteriophage lambda heteroduplexes…”
Get full text

Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus) by Stajich, Jason E., Wilke, Sarah K., Ahrén, Dag, Au, Chun Hang, Birren, Bruce W., Borodovsky, Mark, Burns, Claire, Canbäck, Björn, Casselton, Lorna A., Cheng, C.K., Deng, Jixin, Dietrich, Fred S., Fargo, David C., Farman, Mark L., Gathman, Allen C., Goldberg, Jonathan, Guigó, Roderic, Hoegger, Patrick J., Hooker, James B., Huggins, Ashleigh, James, Timothy Y., Kamada, Takashi, Kilaru, Sreedhar, Kodira, Chinnapa, Kües, Ursula, Kupfer, Doris, Kwan, H.S., Lomsadze, Alexandre, Li, Weixi, Lilly, Walt W., Ma, Li-Jun, Mackey, Aaron J., Manning, Gerard, Martin, Francis, Muraguchi, Hajime, Natvig, Donald O., Palmerini, Heather, Ramesh, Marilee A., Rehmeyer, Cathy J., Roe, Bruce A., Shenoy, Narmada, Stanke, Mario, Ter-Hovhannisyan, Vardges, Tunlid, Anders, Velagapudi, Rajesh, Vision, Todd J., Zeng, Qiandong, Zolan, Miriam E., Pukkila, Patricia J., Bennett, Joan Wennstrom

“…The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life…”
Get full text

Variation in ribosomal DNA among biological species of Armillaria, a genus of root-infecting fungi by Anderson, J.B. (University of Toronto, Mississauga, Ontario, Canada), Bailey, S.S, Pukkila, P.J

“…Armillaria is a genus of root-infecting fungi composed of several biological species in North America and Europe. To examine relatedness among biological…”
Get full text

Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in Coprinopsis cinerea by Chavez, Lukas, Huang, Yun, Luong, Khai, Agarwal, Suneet, Iyer, Lakshminaraya M., Pastor, William A., Hench, Virginia K., Frazier-Bowers, Sylvia A., Korol, Evgenia, Liu, Shuo, Tahiliani, Mamta, Wang, Yinsheng, Clark, Tyson A., Korlach, Jonas, Pukkila, Patricia J., Aravind, L., Rao, Anjana

Get full text

An expanded family of fungalysin extracellular metallopeptidases of Coprinopsis cinerea by Lilly, Walt W., Stajich, Jason E., Pukkila, Patricia J., Wilke, Sarah K., Inoguchi, Noriko, Gathman, Allen C.

“…Proteolytic enzymes, particularly secreted proteases of fungal origin, are among the most important of industrial enzymes, yet the biochemical properties and…”
Get full text

Analysis of the Basidiomycete Coprinopsis cinerea Reveals Conservation of the Core Meiotic Expression Program over Half a Billion Years of Evolution: e1001135 by Burns, Claire, Stajich, Jason E, Rechtsteiner, Andreas, Casselton, Lorna, Hanlon, Sean E, Wilke, Sarah K, Savytskyy, Oleksandr P, Gathman, Allen C, Lilly, Walt W, Lieb, Jason D, Zolan, Miriam E, Pukkila, Patricia J

“…Coprinopsis cinerea (also known as Coprinus cinereus) is a multicellular basidiomycete mushroom particularly suited to the study of meiosis due to its…”
Get full text