Genomes and Genes
Experts and Doctors on molecular sequence data in Yokohama, Kanagawa, Japan
Locale: Yokohama, Kanagawa, Japan
Topic: molecular sequence data
Publications196 found, 100 shown here
- Miya T, Nishida H. Isolation of cDNA clones for mRNAs transcribed zygotically during cleavage in the ascidian, Halocynthia roretzi. Dev Genes Evol. 2002;212:30-7 pubmed..HrHesl1 was expressed exclusively in epidermal precursor cells during cleavage. Another gene named HrWnt-5 beta was expressed in muscle precursors. ..
- Tamada T, Feese M, Ferri S, Kato Y, Yajima R, Toguri T, et al. Substrate recognition and selectivity of plant glycerol-3-phosphate acyltransferases (GPATs) from Cucurbita moscata and Spinacea oleracea. Acta Crystallogr D Biol Crystallogr. 2004;60:13-21 pubmed..Structure analysis suggests that the size and character of the cavity that is formed from this region determines the specific recognition of acyl chains. ..
- Miyazaki Y, Jojima T, Ono T, Yamazaki T, Shishido K. A cDNA homologue of Schizosaccharomyces pombe cdc5(+) from the mushroom Lentinula edodes: characterization of the cDNA and its expressed product. Biochim Biophys Acta. 2004;1680:93-102 pubmed..cdc5 gene is most actively transcribed in primordia and small immature fruiting bodies of L. edodes, implying that Le.cdc5 may play a role in the beginning and early stage of fruiting-body formation. ..
- Nomura T, Kushiro T, Yokota T, Kamiya Y, Bishop G, Yamaguchi S. The last reaction producing brassinolide is catalyzed by cytochrome P-450s, CYP85A3 in tomato and CYP85A2 in Arabidopsis. J Biol Chem. 2005;280:17873-9 pubmed publisher..We postulate that castasterone is the major active brassinosteroid during vegetative growth in tomato, whereas brassinolide may play an organ-specific role in fruit development in this species...
- Morokuma Y, Nakamura N, Kato A, Notoya M, Yamamoto Y, Sakai Y, et al. MARCH-XI, a novel transmembrane ubiquitin ligase implicated in ubiquitin-dependent protein sorting in developing spermatids. J Biol Chem. 2007;282:24806-15 pubmed..Our data suggest that MARCH-XI acts as a ubiquitin ligase with a role in ubiquitin-mediated protein sorting in the TGN-MVB transport pathway, which may be involved in mammalian spermiogenesis. ..
- Tominaga R, Iwata M, Okada K, Wada T. Functional analysis of the epidermal-specific MYB genes CAPRICE and WEREWOLF in Arabidopsis. Plant Cell. 2007;19:2264-77 pubmed..Furthermore, we showed by gel mobility shift assays that WER chimera proteins do not bind to the GL2 promoter region. However, a CPC chimera protein, which harbors the WER R3 motif, still binds to the GL2 promoter region. ..
- Adachi M, Asakura Y, Sato Y, Tajima T, Nakajima T, Yamamoto T, et al. Novel SLC12A1 (NKCC2) mutations in two families with Bartter syndrome type 1. Endocr J. 2007;54:1003-7 pubmed..In conclusion, we found four novel SLC12A1 mutations in two BS type 1 patients. Development of effective therapy for hypercalciuria is mandatory to prevent nephrocalcinosis and resultant renal failure. ..
- Akaboshi M, Hashimoto H, Ishida H, Saijo S, Koizumi N, Sato M, et al. The crystal structure of plant-specific calcium-binding protein AtCBL2 in complex with the regulatory domain of AtCIPK14. J Mol Biol. 2008;377:246-57 pubmed publisher..Structural comparison of the two structures shows that the recognition of CBL by CIPK is performed in a similar manner, but inherent interactions confer binding affinity and specificity. ..
- Nakazawa T, Kaneko S, Miyazaki Y, Jojima T, Yamazaki T, Katsukawa S, et al. Basidiomycete Lentinula edodes CDC5 and a novel interacting protein CIPB bind to a newly isolated target gene in an unusual manner. Fungal Genet Biol. 2008;45:818-28 pubmed publisher..At least two each of the upstream and downstream sequences appear to bind CIPB in vitro. We suggest that Le.CDC5 and CIPB can cooperatively regulate the expression of ctg1. ..
- Takahashi R, Kanesashi S, Inoue T, Enomoto T, Kawano M, Tsukamoto H, et al. Presentation of functional foreign peptides on the surface of SV40 virus-like particles. J Biotechnol. 2008;135:385-92 pubmed publisher..This study demonstrates the potential usefulness of this strategy for the development of novel delivery vehicles with different cell tropisms. ..
- Piskurek O, Nishihara H, Okada N. The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis. Gene. 2009;441:111-8 pubmed publisher..The new SINEs and LINEs and other ubiquitous genomic elements characterized in the Anolis genome will prove very useful for studies in comparative genomics, phylogenetics, and functional genetics. ..
- Kakugawa K, Yasuda T, Miura I, Kobayashi A, Fukiage H, Satoh R, et al. A novel gene essential for the development of single positive thymocytes. Mol Cell Biol. 2009;29:5128-35 pubmed publisher..We generated E430004N04Rik-deficient mice, and their phenotype was virtually identical to that of the ENU mutant mice, thereby confirming that this gene is essential for the development of SP thymocytes. ..
- Maeda S, Kobayashi M, Araki S, Babazono T, Freedman B, Bostrom M, et al. A single nucleotide polymorphism within the acetyl-coenzyme A carboxylase beta gene is associated with proteinuria in patients with type 2 diabetes. PLoS Genet. 2010;6:e1000842 pubmed publisher..These results suggest that ACACB is a strong candidate for conferring susceptibility for proteinuria in patients with type 2 diabetes. ..
- Koshiba S, Li H, Motoda Y, Tomizawa T, Kasai T, Tochio N, et al. Structural basis for the recognition of nucleophosmin-anaplastic lymphoma kinase oncoprotein by the phosphotyrosine binding domain of Suc1-associated neurotrophic factor-induced tyrosine-phosphorylated target-2. J Struct Funct Genomics. 2010;11:125-41 pubmed publisher..Our results indicate that the higher binding activity of the phosphorylation-independent binding site is caused by additional hydrophobic interactions. ..
- Ehara H, Sekine S, Yokoyama S. Crystal structure of the C17/25 subcomplex from Schizosaccharomyces pombe RNA polymerase III. Protein Sci. 2011;20:1558-65 pubmed publisher..On the other hand, S. cerevisiae C17 belongs to the smallest group, with the long linker, which probably enables the subcomplex to assume the alternative conformation. ..
- Sato A, Dongak R, Hao L, Shintani S, Sato T. Organization of Mhc class II A and B genes in the tilapiine fish Oreochromis. Immunogenetics. 2012;64:679-90 pubmed publisher..The rounds established at least five monophyletic groups of genes. The founding unit of each monophyletic group might have been a pair of class II A and B loci. ..
- Takata H, Kato M, Denda K, Kitamura N. A hrs binding protein having a Src homology 3 domain is involved in intracellular degradation of growth factors and their receptors. Genes Cells. 2000;5:57-69 pubmed..Hbp is thought to be closely associated with Hrs on early endosomes. Hbp, together with Hrs may play a regulatory role in the vesicular transport of growth factor/receptor complexes through early endosomes, for their degradation. ..
- Malay A, Umehara T, Matsubara Malay K, Padmanabhan B, Yokoyama S. Crystal structures of fission yeast histone chaperone Asf1 complexed with the Hip1 B-domain or the Cac2 C terminus. J Biol Chem. 2008;283:14022-31 pubmed publisher..1/H4 in vertebrates) in a replication-dependent pathway, whereas Asf1 and HIRA/Hip1 assemble histones H3/H4 (H3.3/H4 in vertebrates) in a replication-independent pathway. ..
- Aihara T, Nakamura N, Honda S, Hirose S. A novel potential role for gametogenetin-binding protein 1 (GGNBP1) in mitochondrial morphogenesis during spermatogenesis in mice. Biol Reprod. 2009;80:762-70 pubmed publisher..These results suggest that GGNBP1 is involved in spermatogenesis by modifying mitochondrial dynamics and morphology. ..
- Fukazawa J, Nakata M, Ito T, Yamaguchi S, Takahashi Y. The transcription factor RSG regulates negative feedback of NtGA20ox1 encoding GA 20-oxidase. Plant J. 2010;62:1035-45 pubmed publisher..Furthermore, decreases in GA levels promote modifications of active histone marks in the promoter of NtGA20ox1. Our results suggest that RSG plays a role in the homeostasis of GAs through direct binding to the NtGA20ox1 promoter. ..
- Kusano S, Kukimoto Niino M, Hino N, Ohsawa N, Okuda K, Sakamoto K, et al. Structural basis for extracellular interactions between calcitonin receptor-like receptor and receptor activity-modifying protein 2 for adrenomedullin-specific binding. Protein Sci. 2012;21:199-210 pubmed publisher..Mutagenesis revealed that AM binding requires RAMP2 residues that are not conserved in RAMP1. Therefore, the differences in both the shapes and the key residues of the binding pocket are essential for the ligand specificity. ..
- Naka D, Ishii T, Yoshiyama Y, Miyazawa K, Hara H, Hishida T, et al. Activation of hepatocyte growth factor by proteolytic conversion of a single chain form to a heterodimer. J Biol Chem. 1992;267:20114-9 pubmed..From these results, we concluded that the single chain form of HGF is endoproteolytically processed by a serine-protease and that this processing is a prerequisite for the mitogenic activity of HGF. ..
- Kawaguchi T, Qin L, Shimomura T, Kondo J, Matsumoto K, Denda K, et al. Purification and cloning of hepatocyte growth factor activator inhibitor type 2, a Kunitz-type serine protease inhibitor. J Biol Chem. 1997;272:27558-64 pubmed..Because HAI-2 and HAI-1 are potent inhibitors specific for HGF activator, they may be involved in regulation of proteolytic activation of HGF in injured tissues. ..
- Naito T, Matsuura A, Ishikawa F. Circular chromosome formation in a fission yeast mutant defective in two ATM homologues. Nat Genet. 1998;20:203-6 pubmed..Upon meiosis, these derivative cells produced few viable spores. Therefore, the exclusively circular genome lacking telomeric sequences is proficient for mitotic growth, but does not permit meiosis. ..
- Nakamura T, Takeuchi K, Muraoka S, Takezoe H, Takahashi N, Mori N. A neurally enriched coronin-like protein, ClipinC, is a novel candidate for an actin cytoskeleton-cortical membrane-linking protein. J Biol Chem. 1999;274:13322-7 pubmed
- Tahirov T, Inoue Bungo T, Morii H, Fujikawa A, Sasaki M, Kimura K, et al. Structural analyses of DNA recognition by the AML1/Runx-1 Runt domain and its allosteric control by CBFbeta. Cell. 2001;104:755-67 pubmed..The point mutations of CBFalpha related to the aforementioned diseases were also mapped and their effect on DNA binding is discussed. ..
- Xin K, Urabe M, Yang J, Nomiyama K, Mizukami H, Hamajima K, et al. A novel recombinant adeno-associated virus vaccine induces a long-term humoral immune response to human immunodeficiency virus. Hum Gene Ther. 2001;12:1047-61 pubmed..These results demonstrate that AAV-HIV vector immunization may provide a novel and promising HIV vaccination strategy. ..
- Kurihara Y, Tokuriki M, Myojin R, Hori T, Kuroiwa A, Matsuda Y, et al. CPEB2, a novel putative translational regulator in mouse haploid germ cells. Biol Reprod. 2003;69:261-8 pubmed..The CPEB2 is expressed postmeiotically in mouse spermatogenesis, suggesting a possible role in translational regulation of stored mRNAs in transcriptionally inactive haploid spermatids. ..
- Shiraki T, Kondo S, Katayama S, Waki K, Kasukawa T, Kawaji H, et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A. 2003;100:15776-81 pubmed..The high-throughput nature of this technology paves the way for understanding gene networks via correlation of promoter usage and gene transcriptional factor expression. ..
- Matsui T, Hogetsu K, Akao Y, Tanaka M, Sato T, Kumasaka T, et al. Crystallization and X-ray analysis of the N-terminal core domain of a tumour-associated human DEAD-box RNA helicase, rck/p54. Acta Crystallogr D Biol Crystallogr. 2004;60:156-9 pubmed..The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 65.5, b = 73.1, c = 84.8 A, and diffracts X-rays to beyond 2.0 A resolution. ..
- Kudo H, Amizuka N, Araki K, Inohaya K, Kudo A. Zebrafish periostin is required for the adhesion of muscle fiber bundles to the myoseptum and for the differentiation of muscle fibers. Dev Biol. 2004;267:473-87 pubmed
- Nameki N, Yoneyama M, Koshiba S, Tochio N, Inoue M, Seki E, et al. Solution structure of the RWD domain of the mouse GCN2 protein. Protein Sci. 2004;13:2089-100 pubmed..Thus, it appears that the RWD domain is a novel structural domain for protein-binding that plays specific roles in individual RWD-containing proteins. ..
- Takeda M, Suzuki I, Koizumi J. Paenibacillus hodogayensis sp. nov., capable of degrading the polysaccharide produced by Sphaerotilus natans. Int J Syst Evol Microbiol. 2005;55:737-41 pubmed..It is proposed that the isolate be designated Paenibacillus hodogayensis sp. nov. The type strain is SG(T) (=JCM 12520(T)=KCTC 3919(T))...
- Miyamoto Sato E, Ishizaka M, Horisawa K, Tateyama S, Takashima H, Fuse S, et al. Cell-free cotranslation and selection using in vitro virus for high-throughput analysis of protein-protein interactions and complexes. Genome Res. 2005;15:710-7 pubmed..Thus, we consider that this simple IVV selection system based on cell-free cotranslation could be applicable to high-throughput and comprehensive analysis of PPI and complexes in large-scale settings involving parallel bait proteins. ..
- Okuda M, Horikoshi M, Nishimura Y. Structural polymorphism of chromodomains in Chd1. J Mol Biol. 2007;365:1047-62 pubmed..Chd1 is likely to have no binding affinity for any H3 MeK peptide, as found in other chromodomain proteins. ..
- Kurochkin I, Mizuno Y, Konagaya A, Sakaki Y, Schonbach C, Okazaki Y. Novel peroxisomal protease Tysnd1 processes PTS1- and PTS2-containing enzymes involved in beta-oxidation of fatty acids. EMBO J. 2007;26:835-45 pubmed..A model is proposed where the Tysnd1-mediated processing of the peroxisomal enzymes promotes their assembly into a supramolecular complex to enhance the rate of beta-oxidation. ..
- Saha S, Takeshita F, Matsuda T, Jounai N, Kobiyama K, Matsumoto T, et al. Blocking of the TLR5 activation domain hampers protective potential of flagellin DNA vaccine. J Immunol. 2007;179:1147-54 pubmed
- Yamasaki S, Ishikawa E, Sakuma M, Hara H, Ogata K, Saito T. Mincle is an ITAM-coupled activating receptor that senses damaged cells. Nat Immunol. 2008;9:1179-88 pubmed publisher..Our results suggest that Mincle is a receptor that senses nonhomeostatic cell death and thereby induces the production of inflammatory cytokines to drive the infiltration of neutrophils into damaged tissue. ..
- Sakuraba Y, Kimura T, Masuya H, Noguchi H, Sezutsu H, Takahasi K, et al. Identification and characterization of new long conserved noncoding sequences in vertebrates. Mamm Genome. 2008;19:703-12 pubmed publisher..Taken together, these results suggest that mutations occur with equal frequency in LCNS but are eliminated by natural selection during the course of evolution. ..
- Matsuda M, Tamura K, Wakui H, Maeda A, Ohsawa M, Kanaoka T, et al. Upstream stimulatory factors 1 and 2 mediate the transcription of angiotensin II binding and inhibitory protein. J Biol Chem. 2013;288:19238-49 pubmed publisher..The results also demonstrate a functional E-box-USF1/USF2 interaction in the human AGTRAP promoter, thereby suggesting that a strategy of modulating the E-box-USF1/USF2 binding has novel therapeutic potential. ..
- Hirai Y, Takebe K, Takashina M, Kobayashi S, Takeichi M. Epimorphin: a mesenchymal protein essential for epithelial morphogenesis. Cell. 1992;69:471-81 pubmed..These results indicate that this protein, termed epimorphin, plays a central role in epithelial-mesenchymal interactions. ..
- Kajita Y, Nakayama J, Aizawa M, Ishikawa F. The UUAG-specific RNA binding protein, heterogeneous nuclear ribonucleoprotein D0. Common modular structure and binding properties of the 2xRBD-Gly family. J Biol Chem. 1995;270:22167-75 pubmed..RBD is supposed to bind with RNA in general and sequence-specific manners. These two discernible binding modes are proposed to be performed by different regions of the RBD. A structural model of these two binding sites is presented. ..
- Takeuchi S, Itoh N, Uchio E, Tanaka K, Kitamura N, Kanai H, et al. Adenovirus strains of subgenus D associated with nosocomial infection as new etiological agents of epidemic keratoconjunctivitis in Japan. J Clin Microbiol. 1999;37:3392-4 pubmed..PCR followed by restriction endonuclease analysis demonstrated that they were type 8. PCR followed by sequencing revealed a high homology rate between them and type 9. ..
- Tsuchiya T, Ohta H, Okawa K, Iwamatsu A, Shimada H, Masuda T, et al. Cloning of chlorophyllase, the key enzyme in chlorophyll degradation: finding of a lipase motif and the induction by methyl jasmonate. Proc Natl Acad Sci U S A. 1999;96:15362-7 pubmed..AtCLH1 mRNA was induced rapidly by a treatment of MeJA, which is known to promote senescence and Chl degradation in plants, and a high mRNA level was maintained up to 9 h. AtCLH2, however, did not respond to MeJA. ..
- Pepin K, Momose F, Ishida N, Nagata K. Molecular cloning of horse Hsp90 cDNA and its comparative analysis with other vertebrate Hsp90 sequences. J Vet Med Sci. 2001;63:115-24 pubmed..The Hsp90 alpha isoform is apparently the result of beta gene duplication. Our results highlight the importance of organism- and isoform-specific Hsp90 functional analyses in describing the role of Hsp90 in cells. ..
- Matsuno H, Niikura K, Okahata Y. Design and characterization of asparagine- and lysine-containing alanine-based helical peptides that bind selectively to A.T base pairs of oligonucleotides immobilized on a 27 mhz quartz crystal microbalance. Biochemistry. 2001;40:3615-22 pubmed..T base pairs (K(a) = 5.9 x 10(5) M(-1)) than for G.C base pairs (K(a) = 1.2 x 10(5) M(-1)), and alpha-helices were clearly promoted by the binding to A.T base pairs from CD spectral changes. ..
- Okumura E, Fukuhara T, Yoshida H, Hanada Si S, Kozutsumi R, Mori M, et al. Akt inhibits Myt1 in the signalling pathway that leads to meiotic G2/M-phase transition. Nat Cell Biol. 2002;4:111-6 pubmed..These findings identify Myt1 as a new target of Akt, and demonstrate that Akt functions as an M-phase initiator. ..
- Miyagi Y, Yamashita T, Fukaya M, Sonoda T, Okuno T, Yamada K, et al. Delphilin: a novel PDZ and formin homology domain-containing protein that synaptically colocalizes and interacts with glutamate receptor delta 2 subunit. J Neurosci. 2002;22:803-14 pubmed..Thus, Delphilin is a postsynaptic scaffolding protein at the parallel fiber-Purkinje cell synapse, where it may serve to link GluRdelta2 with actin cytoskeleton and various signaling molecules. ..
- Kimura Y, Saeki Y, Yokosawa H, Polevoda B, Sherman F, Hirano H. N-Terminal modifications of the 19S regulatory particle subunits of the yeast proteasome. Arch Biochem Biophys. 2003;409:341-8 pubmed..These characteristics were different from those of the 20S proteasome: the chymotrypsin-like activity and accumulation level of 20S proteasome were appreciably higher from the nat1 deletion mutant than from the normal strain. ..
- Sakai H, Kajiwara S. A stearoyl-CoA-specific Delta 9 fatty acid desaturase from the basidiomycete Lentinula edodes. Biosci Biotechnol Biochem. 2003;67:2431-7 pubmed..edodes were higher than in mycelia cultivated at 18 degrees C as well as 25 degrees C. These results correlated with the increase of unsaturated fatty acids (UFAs) in total lipids during fruiting-body formation. ..
- Maeda T, Inoue M, Koshiba S, Yabuki T, Aoki M, Nunokawa E, et al. Solution structure of the SEA domain from the murine homologue of ovarian cancer antigen CA125 (MUC16). J Biol Chem. 2004;279:13174-82 pubmed..On the other hand the tissue tumor marker MUC1 has a SEA domain belonging to another subfamily, and its GSVVV motif for proteolytic cleavage is located in the short loop connecting beta2 and beta3. ..
- Yuasa K, Toyooka K, Fukuda H, Matsuoka K. Membrane-anchored prolyl hydroxylase with an export signal from the endoplasmic reticulum. Plant J. 2005;41:81-94 pubmed publisher..Analysis of this protein fused to green fluorescent protein indicated that basic amino acids in the cytoplasmic, N-terminal region of the PH play a role in its export from the ER...
- Hirota M, Kitagaki M, Itagaki H, Aiba S. Quantitative measurement of spliced XBP1 mRNA as an indicator of endoplasmic reticulum stress. J Toxicol Sci. 2006;31:149-56 pubmed..A good correlation was found between spliced XBP1 expression and BiP expression. Thus, our method may be useful for simple and quantitative evaluation of ER stress. ..
- Tsuge T, Watanabe S, Sato S, Hiraishi T, Abe H, Doi Y, et al. Variation in copolymer composition and molecular weight of polyhydroxyalkanoate generated by saturation mutagenesis of Aeromonas caviae PHA synthase. Macromol Biosci. 2007;7:846-54 pubmed..There was a strong relationship between copolymer composition and PHA synthase activity of the cells. This finding will serve as a rationale for producing tailor-made PHAs. ..
- Inamori Y, Ota M, Inoko H, Okada E, Nishizaki R, Shiota T, et al. The COL1A1 gene and high myopia susceptibility in Japanese. Hum Genet. 2007;122:151-7 pubmed..6) and associated with high myopia (P = 0.028, Pc< 0.084). Together our results provide the first evidence for COL1A1 as a gene associated with high myopia. ..
- Sano H, Narikiyo T, Kaneko S, Yamazaki T, Shishido K. Sequence analysis and expression of a blue-light photoreceptor gene, Le.phrA from the basidiomycetous mushroom Lentinula edodes. Biosci Biotechnol Biochem. 2007;71:2206-13 pubmed..phrA gene. Hymenophore-depleted pileus contained a markedly higher level of the transcript than the stipe. ..
- Nakamura N, Hirose S. Regulation of mitochondrial morphology by USP30, a deubiquitinating enzyme present in the mitochondrial outer membrane. Mol Biol Cell. 2008;19:1903-11 pubmed publisher..Our findings reveal that USP30 participates in the maintenance of mitochondrial morphology, a finding that provides new insight into the cellular function of deubiquitination. ..
- Okuda M, Tanaka A, Satoh M, Mizuta S, Takazawa M, Ohkuma Y, et al. Structural insight into the TFIIE-TFIIH interaction: TFIIE and p53 share the binding region on TFIIH. EMBO J. 2008;27:1161-71 pubmed publisher..From our in vitro studies, we demonstrate that this interaction could be a switch to replace p53 with TFIIE on TFIIH in transcription. ..
- Mizusawa K, Masuda S, Ohta H. Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana. Planta. 2008;228:553-62 pubmed publisher..These results suggest that expression of the four RSH genes is coordinately regulated and that the ppGpp-dependent plastid stringent response has certain roles in the physiology of higher plants. ..
- Izumi M, Yuasa H, Hashimoto H. Bisubstrate analogues as glycosyltransferase inhibitors. Curr Top Med Chem. 2009;9:87-105 pubmed..In this review, we describe the design and synthesis of bisubstrate analogues of glycosyltransferases as well as their inhibitory potency hoping to inform the development of potent and selective inhibitors. ..
- Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K. TriFLDB: a database of clustered full-length coding sequences from Triticeae with applications to comparative grass genomics. Plant Physiol. 2009;150:1135-46 pubmed publisher..This informative content provides an informatics gateway for Triticeae genomics and grass comparative genomics. TriFLDB is publicly available at http://TriFLDB.psc.riken.jp/. ..
- Sugiyama K, Obayashi E, Kawaguchi A, Suzuki Y, Tame J, Nagata K, et al. Structural insight into the essential PB1-PB2 subunit contact of the influenza virus RNA polymerase. EMBO J. 2009;28:1803-11 pubmed publisher..This novel interface is surprisingly small, yet, it has a crucial function in regulating the 250 kDa polymerase complex and is completely conserved among avian and human influenza viruses. ..
- Seo W, Tanaka H, Miyamoto C, Levanon D, Groner Y, Taniuchi I. Roles of VWRPY motif-mediated gene repression by Runx proteins during T-cell development. Immunol Cell Biol. 2012;90:827-30 pubmed publisher..These results indicate that Runx proteins utilize different modes to repress expression of different target genes. ..
- Yoshida H, Kawai F, Obayashi E, Akashi S, Roper D, Tame J, et al. Crystal structures of penicillin-binding protein 3 (PBP3) from methicillin-resistant Staphylococcus aureus in the apo and cefotaxime-bound forms. J Mol Biol. 2012;423:351-64 pubmed publisher..This dimer form is predicted to be highly stable in solution by the PISA server, but mass spectrometry and analytical ultracentrifugation provide unequivocal evidence that the protein is a monomer in solution. ..
- Wang Y, Yang X, Yamagata S, Yamagata T, Sato T. Involvement of Ext1 and heparanase in migration of mouse FBJ osteosarcoma cells. Mol Cell Biochem. 2013;373:63-72 pubmed publisher..Our data provide the first evidence that Ext1 regulates the expression of HPSE and also indicated that levels of Ext1 and HPSE influenced the motility of FBJ cells. ..
- Tsuganezawa K, Shinohara Y, Ogawa N, Tsuboi S, Okada N, Mori M, et al. Two-colored fluorescence correlation spectroscopy screening for LC3-P62 interaction inhibitors. J Biomol Screen. 2013;18:1103-9 pubmed publisher..The two-colored FCS-based screening was shown to be effective to screen for protein-protein interaction inhibitors. ..
- Nakamura K, Kodera H, Akita T, Shiina M, Kato M, Hoshino H, et al. De Novo mutations in GNAO1, encoding a G?o subunit of heterotrimeric G proteins, cause epileptic encephalopathy. Am J Hum Genet. 2013;93:496-505 pubmed publisher..These data suggest that aberrant G?o signaling can cause multiple neurodevelopmental phenotypes, including epileptic encephalopathy and involuntary movements. ..
- Takahashi K, Kitamura N, Shibui T, Kamizono M, Matsui R, Yoshiyama Y, et al. Cloning, sequencing and expression in Escherichia coli of cDNA for a non-A, non-B hepatitis-associated microtubular aggregates protein. J Gen Virol. 1990;71 ( Pt 9):2005-11 pubmed..Southern blot analysis revealed that p44 is a host protein in chimpanzees, and that an identical gene exists in the human genome. ..
- Fujii M, Ishii N, Joguchi A, Yasuda K, Ayusawa D. A novel superoxide dismutase gene encoding membrane-bound and extracellular isoforms by alternative splicing in Caenorhabditis elegans. DNA Res. 1998;5:25-30 pubmed..It is, therefore, indicated that SOD4-1 is an extracellular form and SOD4-2 a membrane-bound form, the latter representing a novel type of SOD. In C. elegans, SOD4-2 mRNA was found to be preferentially expressed in eggs. ..
- Tamatani T, Tezuka K, Hanzawa Higuchi N. AILIM/ICOS: a novel lymphocyte adhesion molecule. Int Immunol. 2000;12:51-5 pubmed..Furthermore, cells transfected with the AILIM gene aggregated in an AILIM-dependent manner. These results suggest a novel function for AILIM/ICOS as an adhesion molecule, which plays an important role in T cell activation. ..
- Ono R, Kobayashi S, Wagatsuma H, Aisaka K, Kohda T, Kaneko ishino T, et al. A retrotransposon-derived gene, PEG10, is a novel imprinted gene located on human chromosome 7q21. Genomics. 2001;73:232-7 pubmed..These data suggest that PEG10 is derived from a retrotransposon that was previously integrated into the mammalian genome. PEG10 is likely to be essential for understanding how exogenous genes become imprinted. ..
- Adachi N, Ishino T, Ishii Y, Takeda S, Koyama H. DNA ligase IV-deficient cells are more resistant to ionizing radiation in the absence of Ku70: Implications for DNA double-strand break repair. Proc Natl Acad Sci U S A. 2001;98:12109-13 pubmed..Our data may explain the observed severe phenotype of Lig4-deficient mice as compared with Ku-deficient mice. ..
- Sang B, Hori K, Tanji Y, Unno H. Fungal contribution to in situ biodegradation of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) film in soil. Appl Microbiol Biotechnol. 2002;58:241-7 pubmed
- Kaga N, Umitsuki G, Clark D, Nagai K, Wachi M. Extensive overproduction of the AdhE protein by rng mutations depends on mutations in the cra gene or in the Cra-box of the adhE promoter. Biochem Biophys Res Commun. 2002;295:92-7 pubmed..These results indicated that expression of the adhE gene was regulated transcriptionally by Cra and posttranscriptionally by RNase G. ..
- Ideguchi H, Ueda A, Tanaka M, Yang J, Tsuji T, Ohno S, et al. Structural and functional characterization of the USP11 deubiquitinating enzyme, which interacts with the RanGTP-associated protein RanBPM. Biochem J. 2002;367:87-95 pubmed..Finally, ubiquitin conjugation to RanBPM was inhibited in a dose-dependent manner by the addition of recombinant USP11. We conclude that RanBPM was the enzymic substrate for USP11 and was deubiquitinated specifically. ..
- Sassa H, Ushijima K, Hirano H. A pistil-specific thaumatin/PR5-like protein gene of Japanese pear (Pyrus serotina): sequence and promoter activity of the 5' region in transgenic tobacco. Plant Mol Biol. 2002;50:371-7 pubmed..Histochemical analysis localized GUS activity to stigma, transmitting tissue, anther and pollen of transgenic tobacco. ..
- Yamazaki T, Yasuda T, Miyazaki Y, Okada K, Kajiwara S, Shishido K. A promoter activity in Saccharomyces cerevisiae of the 3'-noncoding region of the basidiomycetous mushroom gene. J Gen Appl Microbiol. 2002;48:223-31 pubmed
- Ogata M, Lee J, Kim S, Ohtani H, Sekiya K, Igarashi T, et al. The prototype of sex chromosomes found in Korean populations of Rana rugosa. Cytogenet Genome Res. 2002;99:185-93 pubmed..Starting at the prototype, a whole process of morphological sex chromosome evolution was reconstructed. ..
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- Awai K, Kakimoto T, Awai C, Kaneko T, Nakamura Y, Takamiya K, et al. Comparative genomic analysis revealed a gene for monoglucosyldiacylglycerol synthase, an enzyme for photosynthetic membrane lipid synthesis in cyanobacteria. Plant Physiol. 2006;141:1120-7 pubmed..The MGlcDG synthase and the plant MGDG synthase shared low similarity, supporting the presumption that cyanobacteria and plants utilize different pathways to synthesize MGDG. ..
- Yabe S, Tazumi S, Yokoyama J, Uchiyama H. Xtbx6r, a novel T-box gene expressed in the paraxial mesoderm, has anterior neural-inducing activity. Int J Dev Biol. 2006;50:681-9 pubmed..The results of knockdown and overexpression experiments suggest that Xtbx6r is involved in some morphogenesis in the paraxial mesoderm. ..
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- Iizumi Y, Sagara H, Kabe Y, Azuma M, Kume K, Ogawa M, et al. The enteropathogenic E. coli effector EspB facilitates microvillus effacing and antiphagocytosis by inhibiting myosin function. Cell Host Microbe. 2007;2:383-92 pubmed..These results suggest that EspB inhibits myosin functions and thereby facilitates efficient infection by EPEC. ..
- Uchida Y, Ohshima T, Yamashita N, Ogawara M, Sasaki Y, Nakamura F, et al. Semaphorin3A signaling mediated by Fyn-dependent tyrosine phosphorylation of collapsin response mediator protein 2 at tyrosine 32. J Biol Chem. 2009;284:27393-401 pubmed publisher..These results suggest that Fyn-dependent phosphorylation of CRMP2 at Tyr(32) is involved in Sema3A signaling. ..
- Saitsu H, Tohyama J, Kumada T, Egawa K, Hamada K, Okada I, et al. Dominant-negative mutations in alpha-II spectrin cause West syndrome with severe cerebral hypomyelination, spastic quadriplegia, and developmental delay. Am J Hum Genet. 2010;86:881-91 pubmed publisher..These findings suggest that pathological aggregation of alpha/beta spectrin heterodimers and abnormal AIS integrity resulting from SPTAN1 mutations were involved in pathogenesis of infantile epilepsy...