Takuya Nakayama - Publications

Publications (29)

XB-PERS-2952

Publications By Takuya Nakayama

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Erratum: Best Practices for Xenopus tropicalis Husbandry., Nakayama T, Grainger RM., Cold Spring Harb Protoc. July 5, 2023; 2023 (7): pdb.err108386.
Preparation of Intact Nuclei for Single-Nucleus Omics Using Frozen Cell Suspensions from Mutant Embryos of Xenopus tropicalis., Nakayama T, Roubroeks JAY, Veenstra GJC, Grainger RM., Cold Spring Harb Protoc. December 1, 2022; 2022 (12): 641-652.
Gynogenetic Production of Embryos in Xenopus tropicalis Using a Cold Shock Procedure: Rapid Screening Method for Gene Editing Phenotypes., Nakayama T, Cox A, Howell M, Grainger RM., Cold Spring Harb Protoc. December 1, 2022; 2022 (12): 616-623.
Homology-Directed Repair by CRISPR-Cas9 Mutagenesis in Xenopus Using Long Single-Stranded Donor DNA Templates via Simple Microinjection of Embryos., Nakayama T, Grainger RM, Cha SW., Cold Spring Harb Protoc. December 1, 2022; 2022 (12): 606-615.
Best Practices for Xenopus tropicalis Husbandry., Nakayama T, Grainger RM., Cold Spring Harb Protoc. October 25, 2022;
Production of Transgenic F0 Animals and Permanent Lines by Sperm Nuclear Transplantation in Xenopus tropicalis., Nakayama T, Gray J, Grainger RM., Cold Spring Harb Protoc. October 25, 2022;
CRISPR-Cas9 Mutagenesis in Xenopus tropicalis for Phenotypic Analyses in the F0 Generation and Beyond., Blitz IL, Nakayama T., Cold Spring Harb Protoc. March 1, 2022; 2022 (3):
Simple embryo injection of long single-stranded donor templates with the CRISPR/Cas9 system leads to homology-directed repair in Xenopus tropicalis and Xenopus laevis., Nakayama T, Grainger RM, Cha SW., Genesis. June 1, 2020; 58 (6): e23366.
no privacy, a Xenopus tropicalis mutant, is a model of human Hermansky-Pudlak Syndrome and allows visualization of internal organogenesis during tadpole development., Nakayama T, Nakajima K, Cox A, Fisher M, Howell M, Fish MB, Yaoita Y, Grainger RM., Dev Biol. June 15, 2017; 426 (2): 472-486.
High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis., Michiue T, Yamamoto T, Yasuoka Y, Goto T, Ikeda T, Nagura K, Nakayama T, Taira M, Kinoshita T., Dev Biol. June 15, 2017; 426 (2): 270-290.
Genome evolution in the allotetraploid frog Xenopus laevis., Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS., Nature. October 20, 2016; 538 (7625): 336-343.
Xenopus pax6 mutants affect eye development and other organ systems, and have phenotypic similarities to human aniridia patients., Nakayama T, Fisher M, Nakajima K, Odeleye AO, Zimmerman KB, Fish MB, Yaoita Y, Chojnowski JL, Lauderdale JD, Netland PA, Grainger RM., Dev Biol. December 15, 2015; 408 (2): 328-44.
Xenopus mutant reveals necessity of rax for specifying the eye field which otherwise forms tissue with telencephalic and diencephalic character., Fish MB, Nakayama T, Fisher M, Hirsch N, Cox A, Reeder R, Carruthers S, Hall A, Stemple DL, Grainger RM., Dev Biol. November 15, 2014; 395 (2): 317-330.
Cas9-based genome editing in Xenopus tropicalis., Nakayama T, Blitz IL, Fish MB, Odeleye AO, Manohar S, Cho KW, Grainger RM., Methods Enzymol. January 1, 2014; 546 355-75.
Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis., Nakayama T, Fish MB, Fisher M, Oomen-Hajagos J, Thomsen GH, Grainger RM., Genesis. December 1, 2013; 51 (12): 835-43.
Organic small hairpin RNAs (OshR): a do-it-yourself platform for transgene-based gene silencing., Zeng M, Kuzirian MS, Harper L, Paradis S, Nakayama T, Lau NC., Methods. September 15, 2013; 63 (2): 101-9.
Simple, fast, tissue-specific bacterial artificial chromosome transgenesis in Xenopus., Fish MB, Nakayama T, Grainger RM., Genesis. March 1, 2012; 50 (3): 307-15.
Roles of ADAM13-regulated Wnt activity in early Xenopus eye development., Wei S, Xu G, Bridges LC, Williams P, Nakayama T, Shah A, Grainger RM, White JM, DeSimone DW., Dev Biol. March 1, 2012; 363 (1): 147-54.
Mutation of an upstream cleavage site in the BMP4 prodomain leads to tissue-specific loss of activity., Goldman DC, Hackenmiller R, Nakayama T, Sopory S, Wong C, Kulessa H, Christian JL., Development. May 1, 2006; 133 (10): 1933-42.
The activity and signaling range of mature BMP-4 is regulated by sequential cleavage at two sites within the prodomain of the precursor., Cui Y, Hackenmiller R, Berg L, Jean F, Nakayama T, Thomas G, Christian JL., Genes Dev. November 1, 2001; 15 (21): 2797-802.
Dissection of inhibitory Smad proteins: both N- and C-terminal domains are necessary for full activities of Xenopus Smad6 and Smad7., Nakayama T, Berg LK, Christian JL., Mech Dev. February 1, 2001; 100 (2): 251-62.
Regulation of BMP/Dpp signaling during embryonic development., Nakayama T, Cui Y, Christian JL., Cell Mol Life Sci. June 1, 2000; 57 (6): 943-56.
Post-transcriptional regulation of Xwnt-8 expression is required for normal myogenesis during vertebrate embryonic development., Tian Q, Nakayama T, Dixon MP, Christian JL., Development. August 1, 1999; 126 (15): 3371-80.
Can't get no SMADisfaction: Smad proteins as positive and negative regulators of TGF-beta family signals., Christian JL, Nakayama T., Bioessays. May 1, 1999; 21 (5): 382-90.
Physical and functional interaction of murine and Xenopus Smad7 with bone morphogenetic protein receptors and transforming growth factor-beta receptors., Souchelnytskyi S, Nakayama T, Nakao A, Morén A, Heldin CH, Christian JL, ten Dijke P., J Biol Chem. September 25, 1998; 273 (39): 25364-70.
Smad6 functions as an intracellular antagonist of some TGF-beta family members during Xenopus embryogenesis., Nakayama T, Gardner H, Berg LK, Christian JL., Genes Cells. June 1, 1998; 3 (6): 387-94.
Xenopus Smad8 acts downstream of BMP-4 to modulate its activity during vertebrate embryonic patterning., Nakayama T, Snyder MA, Grewal SS, Tsuneizumi K, Tabata T, Christian JL., Development. March 1, 1998; 125 (5): 857-67.
Identification of Smad7, a TGFbeta-inducible antagonist of TGF-beta signalling., Nakao A, Afrakhte M, Morén A, Nakayama T, Christian JL, Heuchel R, Itoh S, Kawabata M, Heldin NE, Heldin CH, ten Dijke P., Nature. October 9, 1997; 389 (6651): 631-5.
Daughters against dpp modulates dpp organizing activity in Drosophila wing development., Tsuneizumi K, Nakayama T, Kamoshida Y, Kornberg TB, Christian JL, Tabata T., Nature. October 9, 1997; 389 (6651): 627-31.

Erratum: Best Practices for Xenopus tropicalis Husbandry., Nakayama T, Grainger RM., Cold Spring Harb Protoc. July 5, 2023; 2023 (7): pdb.err108386.

Preparation of Intact Nuclei for Single-Nucleus Omics Using Frozen Cell Suspensions from Mutant Embryos of Xenopus tropicalis., Nakayama T, Roubroeks JAY, Veenstra GJC, Grainger RM., Cold Spring Harb Protoc. December 1, 2022; 2022 (12): 641-652.

Gynogenetic Production of Embryos in Xenopus tropicalis Using a Cold Shock Procedure: Rapid Screening Method for Gene Editing Phenotypes., Nakayama T, Cox A, Howell M, Grainger RM., Cold Spring Harb Protoc. December 1, 2022; 2022 (12): 616-623.

Homology-Directed Repair by CRISPR-Cas9 Mutagenesis in Xenopus Using Long Single-Stranded Donor DNA Templates via Simple Microinjection of Embryos., Nakayama T, Grainger RM, Cha SW., Cold Spring Harb Protoc. December 1, 2022; 2022 (12): 606-615.

Best Practices for Xenopus tropicalis Husbandry., Nakayama T, Grainger RM., Cold Spring Harb Protoc. October 25, 2022;

Production of Transgenic F0 Animals and Permanent Lines by Sperm Nuclear Transplantation in Xenopus tropicalis., Nakayama T, Gray J, Grainger RM., Cold Spring Harb Protoc. October 25, 2022;

CRISPR-Cas9 Mutagenesis in Xenopus tropicalis for Phenotypic Analyses in the F0 Generation and Beyond., Blitz IL, Nakayama T., Cold Spring Harb Protoc. March 1, 2022; 2022 (3):

Simple embryo injection of long single-stranded donor templates with the CRISPR/Cas9 system leads to homology-directed repair in Xenopus tropicalis and Xenopus laevis., Nakayama T, Grainger RM, Cha SW., Genesis. June 1, 2020; 58 (6): e23366.

no privacy, a Xenopus tropicalis mutant, is a model of human Hermansky-Pudlak Syndrome and allows visualization of internal organogenesis during tadpole development., Nakayama T, Nakajima K, Cox A, Fisher M, Howell M, Fish MB, Yaoita Y, Grainger RM., Dev Biol. June 15, 2017; 426 (2): 472-486.

High variability of expression profiles of homeologous genes for Wnt, Hh, Notch, and Hippo signaling pathways in Xenopus laevis., Michiue T, Yamamoto T, Yasuoka Y, Goto T, Ikeda T, Nagura K, Nakayama T, Taira M, Kinoshita T., Dev Biol. June 15, 2017; 426 (2): 270-290.

Genome evolution in the allotetraploid frog Xenopus laevis., Session AM, Uno Y, Kwon T, Chapman JA, Toyoda A, Takahashi S, Fukui A, Hikosaka A, Suzuki A, Kondo M, van Heeringen SJ, Quigley I, Heinz S, Ogino H, Ochi H, Hellsten U, Lyons JB, Simakov O, Putnam N, Stites J, Kuroki Y, Tanaka T, Michiue T, Watanabe M, Bogdanovic O, Lister R, Georgiou G, Paranjpe SS, van Kruijsbergen I, Shu S, Carlson J, Kinoshita T, Ohta Y, Mawaribuchi S, Jenkins J, Grimwood J, Schmutz J, Mitros T, Mozaffari SV, Suzuki Y, Haramoto Y, Yamamoto TS, Takagi C, Heald R, Miller K, Haudenschild C, Kitzman J, Nakayama T, Izutsu Y, Robert J, Fortriede J, Burns K, Lotay V, Karimi K, Yasuoka Y, Dichmann DS, Flajnik MF, Houston DW, Shendure J, DuPasquier L, Vize PD, Zorn AM, Ito M, Marcotte EM, Wallingford JB, Ito Y, Asashima M, Ueno N, Matsuda Y, Veenstra GJ, Fujiyama A, Harland RM, Taira M, Rokhsar DS., Nature. October 20, 2016; 538 (7625): 336-343.

Xenopus pax6 mutants affect eye development and other organ systems, and have phenotypic similarities to human aniridia patients., Nakayama T, Fisher M, Nakajima K, Odeleye AO, Zimmerman KB, Fish MB, Yaoita Y, Chojnowski JL, Lauderdale JD, Netland PA, Grainger RM., Dev Biol. December 15, 2015; 408 (2): 328-44.

Xenopus mutant reveals necessity of rax for specifying the eye field which otherwise forms tissue with telencephalic and diencephalic character., Fish MB, Nakayama T, Fisher M, Hirsch N, Cox A, Reeder R, Carruthers S, Hall A, Stemple DL, Grainger RM., Dev Biol. November 15, 2014; 395 (2): 317-330.

Cas9-based genome editing in Xenopus tropicalis., Nakayama T, Blitz IL, Fish MB, Odeleye AO, Manohar S, Cho KW, Grainger RM., Methods Enzymol. January 1, 2014; 546 355-75.

Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis., Nakayama T, Fish MB, Fisher M, Oomen-Hajagos J, Thomsen GH, Grainger RM., Genesis. December 1, 2013; 51 (12): 835-43.

Organic small hairpin RNAs (OshR): a do-it-yourself platform for transgene-based gene silencing., Zeng M, Kuzirian MS, Harper L, Paradis S, Nakayama T, Lau NC., Methods. September 15, 2013; 63 (2): 101-9.

Simple, fast, tissue-specific bacterial artificial chromosome transgenesis in Xenopus., Fish MB, Nakayama T, Grainger RM., Genesis. March 1, 2012; 50 (3): 307-15.

Roles of ADAM13-regulated Wnt activity in early Xenopus eye development., Wei S, Xu G, Bridges LC, Williams P, Nakayama T, Shah A, Grainger RM, White JM, DeSimone DW., Dev Biol. March 1, 2012; 363 (1): 147-54.

Mutation of an upstream cleavage site in the BMP4 prodomain leads to tissue-specific loss of activity., Goldman DC, Hackenmiller R, Nakayama T, Sopory S, Wong C, Kulessa H, Christian JL., Development. May 1, 2006; 133 (10): 1933-42.

The activity and signaling range of mature BMP-4 is regulated by sequential cleavage at two sites within the prodomain of the precursor., Cui Y, Hackenmiller R, Berg L, Jean F, Nakayama T, Thomas G, Christian JL., Genes Dev. November 1, 2001; 15 (21): 2797-802.

Dissection of inhibitory Smad proteins: both N- and C-terminal domains are necessary for full activities of Xenopus Smad6 and Smad7., Nakayama T, Berg LK, Christian JL., Mech Dev. February 1, 2001; 100 (2): 251-62.

Regulation of BMP/Dpp signaling during embryonic development., Nakayama T, Cui Y, Christian JL., Cell Mol Life Sci. June 1, 2000; 57 (6): 943-56.

Post-transcriptional regulation of Xwnt-8 expression is required for normal myogenesis during vertebrate embryonic development., Tian Q, Nakayama T, Dixon MP, Christian JL., Development. August 1, 1999; 126 (15): 3371-80.

Can't get no SMADisfaction: Smad proteins as positive and negative regulators of TGF-beta family signals., Christian JL, Nakayama T., Bioessays. May 1, 1999; 21 (5): 382-90.

Physical and functional interaction of murine and Xenopus Smad7 with bone morphogenetic protein receptors and transforming growth factor-beta receptors., Souchelnytskyi S, Nakayama T, Nakao A, Morén A, Heldin CH, Christian JL, ten Dijke P., J Biol Chem. September 25, 1998; 273 (39): 25364-70.

Smad6 functions as an intracellular antagonist of some TGF-beta family members during Xenopus embryogenesis., Nakayama T, Gardner H, Berg LK, Christian JL., Genes Cells. June 1, 1998; 3 (6): 387-94.

Xenopus Smad8 acts downstream of BMP-4 to modulate its activity during vertebrate embryonic patterning., Nakayama T, Snyder MA, Grewal SS, Tsuneizumi K, Tabata T, Christian JL., Development. March 1, 1998; 125 (5): 857-67.

Identification of Smad7, a TGFbeta-inducible antagonist of TGF-beta signalling., Nakao A, Afrakhte M, Morén A, Nakayama T, Christian JL, Heuchel R, Itoh S, Kawabata M, Heldin NE, Heldin CH, ten Dijke P., Nature. October 9, 1997; 389 (6651): 631-5.

Daughters against dpp modulates dpp organizing activity in Drosophila wing development., Tsuneizumi K, Nakayama T, Kamoshida Y, Kornberg TB, Christian JL, Tabata T., Nature. October 9, 1997; 389 (6651): 627-31.

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