Genomes and Genes
Experts and Doctors on phylogeny in Yokohama, Kanagawa, Japan
Locale: Yokohama, Kanagawa, Japan
Publications118 found, 100 shown here
- Nakamura S, Hondo K, Kawara T, Okazaki Y, Saito K, Kobayashi K, et al. Conferring high-temperature tolerance to nontransgenic tomato scions using graft transmission of RNA silencing of the fatty acid desaturase gene. Plant Biotechnol J. 2016;14:783-90 pubmed publisher..Thus, it was shown that high-temperature tolerance was conferred in the nontransgenic scions after grafting onto the silenced rootstocks. ..
- Nag K, Kato A, Nakada T, Hoshijima K, Mistry A, Takei Y, et al. Molecular and functional characterization of adrenomedullin receptors in pufferfish. Am J Physiol Regul Integr Comp Physiol. 2006;290:R467-78 pubmed
- Maruyama Nakashita A, Nakamura Y, Tohge T, Saito K, Takahashi H. Arabidopsis SLIM1 is a central transcriptional regulator of plant sulfur response and metabolism. Plant Cell. 2006;18:3235-51 pubmed
- 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. ..
- Okazaki Y, Shimojima M, Sawada Y, Toyooka K, Narisawa T, Mochida K, et al. A chloroplastic UDP-glucose pyrophosphorylase from Arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis. Plant Cell. 2009;21:892-909 pubmed publisher..A comparative genomics study on UGP3 homologs across different plant species suggested the structural and functional conservation of the proteins and, thus, a committing role for UGP3 in sulfolipid synthesis. ..
- Kawahara K, Tanaka A, Yoon J, Yokota A. Reclassification of a parathione-degrading Flavobacterium sp. ATCC 27551 as Sphingobium fuliginis. J Gen Appl Microbiol. 2010;56:249-55 pubmed..3%). The strain showed similar physiological characteristics and a moderate value of DNA-DNA relatedness to S. fuliginis. These data suggested it reasonable to conclude that strain ATCC 27551 was identified as S. fuliginis...
- Konishi S, Sasakuma T, Sasanuma T. Identification of novel Mlo family members in wheat and their genetic characterization. Genes Genet Syst. 2010;85:167-75 pubmed..This result suggested that the organ specific expression of individual Mlo members occurred relatively recently in their evolution...
- Prakash T, Oshima K, Morita H, Fukuda S, Imaoka A, Kumar N, et al. Complete genome sequences of rat and mouse segmented filamentous bacteria, a potent inducer of th17 cell differentiation. Cell Host Microbe. 2011;10:273-84 pubmed publisher..However, SFB lack most of the clostridial virulence-related genes. Comparative analysis with clostridial genomes suggested possible mechanisms for host responses and specific adaptations in the intestine. ..
- Takamiya S, Hashimoto M, Mita T, Yokota T, Nakajima Y, Yamakura F, et al. Bioinformatic identification of cytochrome b5 homologues from the parasitic nematode Ascaris suum and the free-living nematode Caenorhabditis elegans highlights the crucial role of A. suum adult-specific secretory cytochrome bâ‚… in parasitic adaptatio. Parasitol Int. 2016;65:113-20 pubmed publisher..These results suggest that this free-living nematode does not need a haemoprotein such as the A. suum cytochrome b5 and highlight the crucial function of this A. suum adult-specific secretory cytochrome b5 in parasitic adaptation. ..
- Dinesh B, Lau N, Furusawa G, Kim S, Taylor T, Foong S, et al. Comparative genome analyses of novel Mangrovimonas-like strains isolated from estuarine mangrove sediments reveal xylan and arabinan utilization genes. Mar Genomics. 2016;25:115-121 pubmed publisher..In contrast, these carbohydrate metabolism genes were not found in the genome sequence of LY01. In addition, TPBH4(T) and ST2L12(T) show capability to degrade xylan using qualitative plate assay method. ..
- Sato T. Sensory and endocrine characteristics of the avian pineal organ. Microsc Res Tech. 2001;53:2-11 pubmed..The demonstration of melatonin receptors in a variety of avian peripheral tissues suggest a possible direct action of melatonin on the physiological functions of different organ systems in response to internal and external stimuli. ..
- Awai K, Mar chal E, Block M, Brun D, Masuda T, Shimada H, et al. Two types of MGDG synthase genes, found widely in both 16:3 and 18:3 plants, differentially mediate galactolipid syntheses in photosynthetic and nonphotosynthetic tissues in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2001;98:10960-5 pubmed publisher..e., in inflorescence (atMGD2) and roots (atMGD3), where they conceivably influence the eukaryotic structure prominence in MGDG. In addition, their expression of type B enzymes is enhanced under phosphate deprivation...
- 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. ..
- Islam M, Kawase O, Hase S, Hoshi M, Matsumoto M. PKA activation in concert with ARIS and asterosap induces the acrosome reaction in starfish. Zygote. 2006;14:329-40 pubmed..To investigate this, we have cloned a gene that encodes a regulatory subunit of PKA that had been identified in starfish spermatozoa...
- 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. ..
- Tominaga R, Iwata M, Sano R, Inoue K, Okada K, Wada T. Arabidopsis CAPRICE-LIKE MYB 3 (CPL3) controls endoreduplication and flowering development in addition to trichome and root hair formation. Development. 2008;135:1335-45 pubmed publisher..Notably, the CPL3 gene has pleiotropic effects on flowering development, epidermal cell size and trichome branching through the regulation of endoreduplication. ..
- Kuroha T, Tokunaga H, Kojima M, Ueda N, Ishida T, Nagawa S, et al. Functional analyses of LONELY GUY cytokinin-activating enzymes reveal the importance of the direct activation pathway in Arabidopsis. Plant Cell. 2009;21:3152-69 pubmed publisher..Our results strongly suggest that the direct activation pathway via LOGs plays a pivotal role in regulating cytokinin activity during normal growth and development in Arabidopsis. ..
- Mochida K, Uehara Yamaguchi Y, Yoshida T, Sakurai T, Shinozaki K. Global landscape of a co-expressed gene network in barley and its application to gene discovery in Triticeae crops. Plant Cell Physiol. 2011;52:785-803 pubmed publisher..Furthermore, the insights obtained should be transferable to investigations of Triticeae plants. The associated data set generated in this analysis is publicly accessible at http://coexpression.psc.riken.jp/barley/. ..
- Morlighem J, Aoki S, Kishima M, Hanami M, Ogawa C, Jalloh A, et al. Mutation analysis of 2009 pandemic influenza A(H1N1) viruses collected in Japan during the peak phase of the pandemic. PLoS ONE. 2011;6:e18956 pubmed publisher..Among them, 12 were new micro-clades, while two were previously reported. Oseltamivir resistance-related mutations, i.e., NA-H275Y and NA-N295S, were also detected in sporadic cases in Osaka and Tokyo...
- Fujitsuka A, Tsukagoshi H, Arakawa M, Goto Sugai K, Ryo A, Okayama Y, et al. A molecular epidemiological study of respiratory viruses detected in Japanese children with acute wheezing illness. BMC Infect Dis. 2011;11:168 pubmed publisher..The results suggested that these genetically diverse respiratory viruses, especially RSV and HRV, might be associated with wheezing in Japanese children. ..
- Masuda S, Harada J, Yokono M, Yuzawa Y, Shimojima M, Murofushi K, et al. A monogalactosyldiacylglycerol synthase found in the green sulfur bacterium Chlorobaculum tepidum reveals important roles for galactolipids in photosynthesis. Plant Cell. 2011;23:2644-58 pubmed publisher..These observations provide new insights regarding the importance of regulated MGDG synthesis in the physiology of higher plants...
- Yoshida K, Terai Y, Mizoiri S, Aibara M, Nishihara H, Watanabe M, et al. B chromosomes have a functional effect on female sex determination in Lake Victoria cichlid fishes. PLoS Genet. 2011;7:e1002203 pubmed publisher..Because some sex chromosomes in amphibians and arthropods are thought to be derived from B chromosomes, the B chromosomes in Lake Victoria cichlids may represent an evolutionary transition toward the generation of sex chromosomes. ..
- Date Y, Iikura T, Yamazawa A, Moriya S, Kikuchi J. Metabolic sequences of anaerobic fermentation on glucose-based feeding substrates based on correlation analyses of microbial and metabolite profiling. J Proteome Res. 2012;11:5602-10 pubmed publisher..This is the first report to visualize the entire metabolic dynamic in an anaerobic fermentation ecosystem as metabolic sequences. ..
- Kawasaki K, Mikami M, Nakatomi M, Braasch I, Batzel P, H Postlethwait J, et al. SCPP Genes and Their Relatives in Gar: Rapid Expansion of Mineralization Genes in Osteichthyans. J Exp Zool B Mol Dev Evol. 2017;328:645-665 pubmed publisher..Furthermore, the absence of acidic SCPP genes in chondrichthyans might be explained by the secondary loss of earliest acidic genes. It appears that many SCPP genes expanded rapidly in stem osteichthyans and in basal actinopterygians. ..
- Miyazawa K, Wang Y, Minoshima S, Shimizu N, Kitamura N. Structural organization and chromosomal localization of the human hepatocyte growth factor activator gene--phylogenetic and functional relationship with blood coagulation factor XII, urokinase, and tissue-type plasminogen activator. Eur J Biochem. 1998;258:355-61 pubmed..The phylogenetic and functional relationships between HGFA and FXII as well as urokinase and tissue-type plasminogen activator are discussed. ..
- Abe J, Suzuki H, Notoya M, Yamamoto T, Hirose S. Ig-hepta, a novel member of the G protein-coupled hepta-helical receptor (GPCR) family that has immunoglobulin-like repeats in a long N-terminal extracellular domain and defines a new subfamily of GPCRs. J Biol Chem. 1999;274:19957-64 pubmed..Ig-Hepta defines a new subfamily of GPCRs. ..
- Piskurek O, Okada N. Poxviruses as possible vectors for horizontal transfer of retroposons from reptiles to mammals. Proc Natl Acad Sci U S A. 2007;104:12046-51 pubmed
- Nagai H, Terai Y, Sugawara T, Imai H, Nishihara H, Hori M, et al. Reverse evolution in RH1 for adaptation of cichlids to water depth in Lake Tanganyika. Mol Biol Evol. 2011;28:1769-76 pubmed publisher..The latter parallelism represents the complete reverse evolution from the derived to the ancestral state, following back adaptive mutation with reversal of the RH1 pigment function accompanied by reversal of the species habitat shift. ..
- Nikaido M, Cao Y, Okada N, Hasegawa M. The phylogenetic relationships of insectivores with special reference to the lesser hedgehog tenrec as inferred from the complete sequence of their mitochondrial genome. Genes Genet Syst. 2003;78:107-12 pubmed
- Manji S, Ishihara A. Screening of tetrachlorodibenzo- p-dioxin-degrading fungi capable of producing extracellular peroxidases under various conditions. Appl Microbiol Biotechnol. 2004;63:438-44 pubmed..strain MS325 on a practical scale in the environment has several advantages over many white rot fungi, which produce extracellular peroxidases only under specific conditions such as nutrient limitation. ..
- Ojima N, Yamashita M. Cloning and characterization of two distinct isoforms of rainbow trout heat shock factor 1. Evidence for heterotrimer formation. Eur J Biochem. 2004;271:703-12 pubmed
- Ojima N, Yamashita M, Watabe S. Comparative expression analysis of two paralogous Hsp70s in rainbow trout cells exposed to heat stress. Biochim Biophys Acta. 2005;1681:99-106 pubmed..These results suggest that the comprehensive identification of duplicated genes is a prerequisite to examining the gene expression profiles for tetraploid species such as rainbow trout. ..
- Yamashita A, Ohnishi T, Kashima I, Taya Y, Ohno S. Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay. Genes Dev. 2001;15:2215-28 pubmed..Taken together, we conclude that hSMG-1 plays a critical role in NMD through the direct phosphorylation of hUPF1/SMG-2 in the evolutionally conserved mRNA surveillance complex. ..
- Hirose N, Makita N, Yamaya T, Sakakibara H. Functional characterization and expression analysis of a gene, OsENT2, encoding an equilibrative nucleoside transporter in rice suggest a function in cytokinin transport. Plant Physiol. 2005;138:196-206 pubmed
- Watanabe M, Kato Y, Togami K, Yamanaka M, Wakabayashi K, Ogawa H, et al. [Evaluation of gene index for identification of Byssochlamys spp]. Shokuhin Eiseigaku Zasshi. 2008;49:82-7 pubmed..Re-classification will be necessary, based on detailed morphological observations...
- Hanada K, Hase T, Toyoda T, Shinozaki K, Okamoto M. Origin and evolution of genes related to ABA metabolism and its signaling pathways. J Plant Res. 2011;124:455-65 pubmed publisher..Taken together, these results suggest that expansion of the gene families related to ABA signaling pathways may have contributed to the sophisticated stress tolerance mechanisms of higher land plants...
- 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. ..
- 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. ..
- Goroncy A, Koshiba S, Tochio N, Tomizawa T, Sato M, Inoue M, et al. NMR solution structures of actin depolymerizing factor homology domains. Protein Sci. 2009;18:2384-92 pubmed publisher..The G-actin binding site of the ADF-H domain of human HIP-55-drebrin-like protein is absent and distorted in mouse GMF beta and GMF gamma. ..
- Mawaribuchi S, Ito M, Ogata M, Oota H, Katsumura T, Takamatsu N, et al. Meiotic recombination counteracts male-biased mutation (male-driven evolution). Proc Biol Sci. 2016;283: pubmed publisher..Intriguingly, the Î²- and Î³-values were larger and smaller than 1, respectively, indicating that meiotic recombination might reduce male-biased mutations. ..
- 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. ..
- Nikaido M, Suzuki H, Toyoda A, Fujiyama A, Hagino Yamagishi K, Kocher T, et al. Lineage-specific expansion of vomeronasal type 2 receptor-like (OlfC) genes in cichlids may contribute to diversification of amino acid detection systems. Genome Biol Evol. 2013;5:711-22 pubmed publisher..This study implies that cichlids have developed a potent capacity to detect a variety of amino acids (and their derivatives) through OlfCs, which may have contributed to the extraordinary diversity of their feeding habitats...
- Léran S, Varala K, Boyer J, Chiurazzi M, Crawford N, Daniel Vedele F, et al. A unified nomenclature of NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family members in plants. Trends Plant Sci. 2014;19:5-9 pubmed publisher..We propose that the members should be named accordingly: NPFX.Y, where X denotes the subfamily and Y the individual member within the species. ..
- 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))...
- 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. ..
- Kawai K, Nikaido M, Harada M, Matsumura S, Lin L, Wu Y, et al. Intra- and interfamily relationships of Vespertilionidae inferred by various molecular markers including SINE insertion data. J Mol Evol. 2002;55:284-301 pubmed publisher..Our study represents the most comprehensive phylogenetic model of Vespertilionidae to date...
- Sasaki T, Takahashi K, Nikaido M, Miura S, Yasukawa Y, Okada N. First application of the SINE (short interspersed repetitive element) method to infer phylogenetic relationships in reptiles: an example from the turtle superfamily Testudinoidea. Mol Biol Evol. 2004;21:705-15 pubmed..This information may be applied to the phylogenetic resolution of relevant turtle lineages. ..
- Ukitsu H, Kuromori T, Toyooka K, Goto Y, Matsuoka K, Sakuradani E, et al. Cytological and biochemical analysis of COF1, an Arabidopsis mutant of an ABC transporter gene. Plant Cell Physiol. 2007;48:1524-33 pubmed..Pollen observation showed that mutant pollen grains were irregularly shaped. The function of COF1/WBC11 in lipid transport for the construction of cuticle layers and pollen coats for normal organ formation is discussed. ..
- He F, Saito K, Kobayashi N, Harada T, Watanabe S, Kigawa T, et al. Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway. J Mol Biol. 2009;393:478-95 pubmed publisher..The present structural study will shed light on the role of the Neur NHR1 domain in the Notch signaling pathway. ..
- Ohkubo M, Aranishi F, Shimizu A. Molecular cloning and brain distribution of three types of gonadotropin-releasing hormone from mummichog Fundulus heteroclitus. J Fish Biol. 2010;76:379-94 pubmed publisher..These results suggest that the mdGnRH is involved in the stimulation of gonadotrophs in the pituitary, whereas cGnRH-II and sGnRH are involved in neurotransmission and neuromodulation. ..
- Fukui Y, Kobayashi M, Saito H, Oikawa H, Yano Y, Satomi M. Algimonas ampicilliniresistens sp. nov., isolated from the red alga Porphyra yezoensis, and emended description of the genus Algimonas. Int J Syst Evol Microbiol. 2013;63:4407-12 pubmed publisher..nov. is proposed. The type strain is 14A-2-7(T) (?=?LMG 26421(T)?=?NBRC 108219(T)). An emended description of the genus Algimonas is also proposed. ..
- Yoshida S, Hiraga K, Takehana T, Taniguchi I, Yamaji H, Maeda Y, et al. A bacterium that degrades and assimilates poly(ethylene terephthalate). Science. 2016;351:1196-9 pubmed publisher..Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol. ..
- Suzuki T, Inoki Y, Yamagishi A, Iwasaki T, Wakagi T, Oshima T. Molecular and phylogenetic characterization of isopropylmalate dehydrogenase of a thermoacidophilic archaeon, Sulfolobus sp. strain 7. J Bacteriol. 1997;179:1174-9 pubmed..These results suggested that the present enzyme is the most primitive among isopropylmalate dehydrogenases belonging in the decarboxylating dehydrogenase family. ..
- Nikaido M, Kawai K, Cao Y, Harada M, Tomita S, Okada N, et al. Maximum likelihood analysis of the complete mitochondrial genomes of eutherians and a reevaluation of the phylogeny of bats and insectivores. J Mol Evol. 2001;53:508-16 pubmed..Recent phylogenetic controversy over the polyphyly of microbats, the monophyly of rodents, and the position of hedgehogs is also examined...
- Munemura T, Saikusa M, Kawakami C, Shimizu H, Oseto M, Hagiwara A, et al. Genetic diversity of enterovirus 71 isolated from cases of hand, foot and mouth disease in Yokohama City between 1982 and 2000. Arch Virol. 2003;148:253-63 pubmed..However, the genetic diversity of EV71 in Yokohama City was not directly correlated with the severity of HFMD. The results confirmed the circulation of two distinct genotypes of EV71 over the past 20 years in Japan...
- Ohshima K, Okada N. SINEs and LINEs: symbionts of eukaryotic genomes with a common tail. Cytogenet Genome Res. 2005;110:475-90 pubmed..We also use several biological examples to discuss the impact and significance of SINEs and LINEs in the evolution of vertebrate genomes. ..
- Kato A, Doi H, Nakada T, Sakai H, Hirose S. Takifugu obscurus is a euryhaline fugu species very close to Takifugu rubripes and suitable for studying osmoregulation. BMC Physiol. 2005;5:18 pubmed..These properties make "mefugu", which has drawn little attention from animal physiologists until this study, a useful model animal for studying the molecular mechanism of maintaining body fluid homeostasis. ..
- Todaka N, Inoue T, Saita K, Ohkuma M, Nalepa C, Lenz M, et al. Phylogenetic analysis of cellulolytic enzyme genes from representative lineages of termites and a related cockroach. PLoS ONE. 2010;5:e8636 pubmed publisher..This gives us a fresh perspective from which to understand the evolutionary dynamics of symbiosis. ..
- Mori H, Maruyama F, Kurokawa K. VITCOMIC: visualization tool for taxonomic compositions of microbial communities based on 16S rRNA gene sequences. BMC Bioinformatics. 2010;11:332 pubmed publisher..VITCOMIC is freely available at http://mg.bio.titech.ac.jp/vitcomic/. ..
- Kato A, Muro T, Kimura Y, Li S, Islam Z, Ogoshi M, et al. Differential expression of Na+-Cl- cotransporter and Na+-K+-Cl- cotransporter 2 in the distal nephrons of euryhaline and seawater pufferfishes. Am J Physiol Regul Integr Comp Physiol. 2011;300:R284-97 pubmed publisher..These results suggest that NaCl reabsorption in the distal nephron of the fish kidney is mediated by NCC and NKCC2 in freshwater and by NKCC2 in seawater. ..
- Nikaido M, Noguchi H, Nishihara H, Toyoda A, Suzuki Y, Kajitani R, et al. Coelacanth genomes reveal signatures for evolutionary transition from water to land. Genome Res. 2013;23:1740-8 pubmed publisher..These coelacanth genomes will provide a cornerstone for studies to elucidate how ancestral aquatic vertebrates evolved into terrestrial animals. ..
- Nikaido M, Matsuno F, Hamilton H, Brownell R, Cao Y, Ding W, et al. Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins. Proc Natl Acad Sci U S A. 2001;98:7384-9 pubmed..The combination of SINE and flanking sequence analysis suggests a topology and set of divergence times for odontocete relationships, offering alternative explanations for several long-standing problems in cetacean evolution...
- Nikaido M, Matsuno F, Abe H, Shimamura M, Hamilton H, Matsubayashi H, et al. Evolution of CHR-2 SINEs in cetartiodactyl genomes: possible evidence for the monophyletic origin of toothed whales. Mamm Genome. 2001;12:909-15 pubmed..We reconstruct the evolutionary history of the CHR-2 SINEs during evolution of cetartiodactyl genomes. ..
- 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. ..
- Nakamura Y, Tsuchiya M, Ohta H. Plastidic phosphatidic acid phosphatases identified in a distinct subfamily of lipid phosphate phosphatases with prokaryotic origin. J Biol Chem. 2007;282:29013-21 pubmed..Thus, in Arabidopsis, there are three isoforms of plastidic PAP that belong to a distinct subfamily of LPP, and LPP gamma may be the primary plastidic PAP. ..
- Sugano Y. DyP-type peroxidases comprise a novel heme peroxidase family. Cell Mol Life Sci. 2009;66:1387-403 pubmed publisher..In this review, firstly, an outline of the characteristics of DyP from T. cucumeris is presented and then interesting characteristics of the DyP-type peroxidase family are discussed. ..
- Nagatoshi Y, Nakamura T. Arabidopsis HARMLESS TO OZONE LAYER protein methylates a glucosinolate breakdown product and functions in resistance to Pseudomonas syringae pv. maculicola. J Biol Chem. 2009;284:19301-9 pubmed publisher..maculicola. Here we propose that AtHOL1 is involved in glucosinolate metabolism and defense against phytopathogens. Moreover, CH(3)Cl synthesized by AtHOL1 could be considered a byproduct of NCS(-) metabolism. ..
- Matsuyama T, Yasuike M, Fujiwara A, Nakamura Y, Takano T, Takeuchi T, et al. A Spirochaete is suggested as the causative agent of Akoya oyster disease by metagenomic analysis. PLoS ONE. 2017;12:e0182280 pubmed publisher..We propose 'Candidatus Maribrachyspira akoyae' gen. nov, sp nov., for this bacterium. ..
- Nakayama M, Masuda T, Sato N, Yamagata H, Bowler C, Ohta H, et al. Cloning, subcellular localization and expression of CHL1, a subunit of magnesium-chelatase in soybean. Biochem Biophys Res Commun. 1995;215:422-8 pubmed publisher..CHLI was localized in the soluble fraction in soybean chloroplasts, suggesting that it was a stromal subunit of Mg-chelatase. chlI mRNA in cell culture (SB-P) of soybean was reversibly induced by light...
- Nakajima Y, Fujiwara T, Fukumori Y. Purification and characterization of a [3Fe-4S][4Fe-4S] type ferredoxin from hyperthermophilic archaeon, Pyrobaculum islandicum. J Biochem. 1998;123:521-7 pubmed..Furthermore, the amino acid sequence of the P. islandicum ferredoxin was compared with those of several other bacterial ferredoxins...
- Naito T, Saito Y, Yamamoto J, Nozaki Y, Tomura K, Hazama M, et al. Putative pheromone receptors related to the Ca2+-sensing receptor in Fugu. Proc Natl Acad Sci U S A. 1998;95:5178-81 pubmed..These genes appear to be the homologues of the vomeronasal pheromone receptors recently described in rodents. The Fugu genes are expressed in the tissues of the nose, suggesting that they may have a similar physiological role...
- Oguchi S, Sassa H, Hirano H. OsPAA2, a distinct alpha 1 subunit gene for the 20S proteasome in rice (Oryza sativa L.). Gene. 2001;272:19-23 pubmed..The expression pattern of the OsPAA2 gene was different from that of another alpha1 gene, OsPAA1. These data suggest that OsPAA2 might play a distinct role from that of OsPAA1 in the 20S proteasome complex. ..
- Nikaido M, Cao Y, Harada M, Okada N, Hasegawa M. Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla. Mol Phylogenet Evol. 2003;28:276-84 pubmed..However, this conclusion depends on species sampling in Erinaceoidea, demonstrating the importance of both species sampling and use of an appropriate substitution model when inferring phylogenetic relationships...
- 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
- Hayashi N, Arai R, Tada S, Taguchi H, Ogawa Y. Detection and identification of Brettanomyces/Dekkera sp. yeasts with a loop-mediated isothermal amplification method. Food Microbiol. 2007;24:778-85 pubmed..This LAMP method with primer sets for the identification of Brettanomyces/Dekkera yeasts is advantageous in terms of specificity, sensitivity and ease of operation compared with standard PCR methods. ..
- Okamoto M, Benno Y, Leung K, Maeda N. Bifidobacterium tsurumiense sp. nov., from hamster dental plaque. Int J Syst Evol Microbiol. 2008;58:144-8 pubmed publisher..nov. is proposed. The type strain is OMB115(T) (=JCM 13495(T) =DSM 17777(T))...
- Kato A, Rooney A, Furutani Y, Hirose S. Evolution of trappin genes in mammals. BMC Evol Biol. 2010;10:31 pubmed publisher..These results suggest that trappin is an eutherian-specific molecule and eutherian genomes have the potential to form trappin multigenes. ..
- Kuromori T, Sugimoto E, Shinozaki K. Arabidopsis mutants of AtABCG22, an ABC transporter gene, increase water transpiration and drought susceptibility. Plant J. 2011;67:885-94 pubmed publisher..Also, the atabcg22 mutation enhanced the phenotype of nced3 mutants, which were defective in ABA biosynthesis. Accordingly, the additive roles of AtABCG22 functions in ABA signalling and ABA biosynthesis are discussed...
- Fukushima E, Seki H, Ohyama K, Ono E, Umemoto N, Mizutani M, et al. CYP716A subfamily members are multifunctional oxidases in triterpenoid biosynthesis. Plant Cell Physiol. 2011;52:2050-61 pubmed publisher..These findings will be useful in the heterologous production of pharmacologically and industrially important triterpenoids, including oleanolic acid, ursolic acid and betulinic acid...
- Nakamura Y, Sasaki N, Kobayashi M, Ojima N, Yasuike M, Shigenobu Y, et al. The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). PLoS ONE. 2013;8:e57122 pubmed publisher..These findings shed light on unexplained features of macroalgal genes and genomes, and suggest that the genome of P. yezoensis is a promising model genome of marine red algae. ..
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