Experts and Doctors on phylogeny in Japan

Summary

Locale: Japan
Topic: phylogeny

Top Publications

  1. Fukunaga M, Koreki Y. The flagellin gene of Borrelia miyamotoi sp. nov. and its phylogenetic relationship among Borrelia species. FEMS Microbiol Lett. 1995;134:255-8 pubmed
    ..This finding indicates that a phylogenetic analysis using flagellin gene sequences might be useful for classification of Borrelia strains...
  2. Bessho Y, Tamura S, Hori H, Tanaka H, Ohama T, Osawa S. Planarian mitochondria sequence heterogeneity: relationships between the type of cytochrome c oxidase subunit I gene sequence, karyotype and genital organ. Mol Ecol. 1997;6:129-36 pubmed
    ..These lineages are assumed to be asexual. The heterogeneity of COI gene sequences in the presumed asexual lineages would have resulted from an accumulation of mutations by repeated asexual reproduction. ..
  3. Katagiri T, Takahashi S, Shinozaki K. Involvement of a novel Arabidopsis phospholipase D, AtPLDdelta, in dehydration-inducible accumulation of phosphatidic acid in stress signalling. Plant J. 2001;26:595-605 pubmed
    ..The accumulation of PtdOH in response to dehydration was significantly suppressed in AtPLDdelta antisense transgenic plants. These results suggest that AtPLDdelta may be involved in PtdOH accumulation in the dehydration stress response. ..
  4. Katoh M, Katoh M. Characterization of human FOXN4 gene in silico. Int J Mol Med. 2004;14:949-53 pubmed
    ..This is the first report on comprehensive characterization of the human FOXN4 gene as well as on identification of the FN14 domain. ..
  5. Djais A, Nakazawa F, Sato M, Sato N, Sundqvist G, Hoshino E. Asaccharolytic anaerobic gram-negative coccobacilli (AAGNC) isolated from infected root canals and periodontal pockets. Oral Microbiol Immunol. 2006;21:28-31 pubmed
    ..The last isolate revealed 35 mol% G + C content, but had higher 16S rDNA sequence similarity with D. invisus than with D. pneumosintes. The group of oral AAGNC isolates need to be reclassified. ..
  6. Tsumura Y, Kado T, Takahashi T, Tani N, Ujino Ihara T, Iwata H. Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica. Genetics. 2007;176:2393-403 pubmed
  7. Okamoto H. History of discoveries and pathogenicity of TT viruses. Curr Top Microbiol Immunol. 2009;331:1-20 pubmed
  8. Kakumura K, Watanabe S, Bell J, Donald J, Toop T, Kaneko T, et al. Multiple urea transporter proteins in the kidney of holocephalan elephant fish (Callorhinchus milii). Comp Biochem Physiol B Biochem Mol Biol. 2009;154:239-47 pubmed publisher
    ..The present finding of multiple UTs in elephant fish provides a key to understanding the molecular mechanisms of urea reabsorption system in the cartilaginous fish kidney. ..
  9. Yamada T, Satoh S, Ishikawa H, Fujiwara A, Kawasaki T, Fujie M, et al. A jumbo phage infecting the phytopathogen Ralstonia solanacearum defines a new lineage of the Myoviridae family. Virology. 2010;398:135-47 pubmed publisher
    ..We identified six of them including a tail sheath protein and a topoisomerase IB by N-terminal sequencing. Based on a DNA microarray analysis, we identified two transcription patterns...

More Information

Publications307 found, 100 shown here

  1. Yamashita T, Yokoyama H, Kanafusa S, Ogino A, Ishida M, Osada T, et al. Nitrate-removal activity of a biofilm attached to a perlite carrier under continuous aeration conditions. Biosci Biotechnol Biochem. 2011;75:578-81 pubmed
    ..4 mg-N/kg-perlite/h from wastewater containing cow milk and manure. In a clone library analysis of the biofilm, bacteria showing high similarity to the denitrifying bacteria Thauera spp. were detected...
  2. Ikeda H, Carlsen T, Fujii N, Brochmann C, Setoguchi H. Pleistocene climatic oscillations and the speciation history of an alpine endemic and a widespread arctic-alpine plant. New Phytol. 2012;194:583-94 pubmed publisher
    ..nipponica. Our results suggest that even currently allopatric species may not have diverged solely under geographic isolation, and that their evolutionary history may have been influenced by Pleistocene range dynamics...
  3. Ozutsumi Y, Tajima K, Takenaka A, Itabashi H. McrA gene and 16S rRNA gene in the phylogenetic analysis of methanogens in the rumen of faunated and unfaunated cattle. Anim Sci J. 2012;83:727-34 pubmed publisher
    ..001). It was suggested that the presence of protozoa strongly affected the composition of rumen methanogens...
  4. Kato Y, Salter Cid L, Flajnik M, Kasahara M, Namikawa C, Sasaki M, et al. Isolation of the Xenopus complement factor B complementary DNA and linkage of the gene to the frog MHC. J Immunol. 1994;153:4546-54 pubmed
  5. Harada Y, Shoguchi E, Taguchi S, Okai N, Humphreys T, Tagawa K, et al. Conserved expression pattern of BMP-2/4 in hemichordate acorn worm and echinoderm sea cucumber embryos. Zoolog Sci. 2002;19:1113-21 pubmed
    ..This is in agreement with the homology between their basic larval body plans with respect to coelomogenesis and allows us to discuss the evolutionary counterparts of the coelomopore complex in chordates. ..
  6. Park C, Kurobe T, Hirono I, Aoki T. Cloning and characterization of cDNAs for two distinct tumor necrosis factor receptor superfamily genes from Japanese flounder Paralichthys olivaceus. Dev Comp Immunol. 2003;27:365-75 pubmed
    ..35 microg/ml) for 3 h. The different expression patterns of the two distinct TNFR homologues may be critical in determining whether binding with TNF-alpha or TNF-beta have activating, proliferative, or apoptotic effects on target cells. ..
  7. Tsatsralt Od B, Takahashi M, Nishizawa T, Inoue J, Ulaankhuu D, Okamoto H. High prevalence of hepatitis B, C and delta virus infections among blood donors in Mongolia. Arch Virol. 2005;150:2513-28 pubmed
  8. Yap Y, Kodama Y, Waller F, Chung K, Ueda H, Nakamura K, et al. Activation of a novel transcription factor through phosphorylation by WIPK, a wound-induced mitogen-activated protein kinase in tobacco plants. Plant Physiol. 2005;139:127-37 pubmed publisher
    ..These results suggest that NtWIF is a transcription factor that is directly phosphorylated by WIPK, thereby being activated for transcription of target gene(s) involved in wound and pathogen responses...
  9. Tzeh Gung A, Kondo H, Aoki T, Hirono I. Growth differentiation factor 15, a novel acute phase response gene in Japanese flounder, Paralichthys olivaceus. Fish Shellfish Immunol. 2009;26:230-4 pubmed publisher
    ..The transcripts were highly up-regulated in liver at 6h post-injection with formalin-killed E. tarda. Moreover, up-regulation of the transcripts was also observed at 12h post-injection with formalin-killed Streptococcus iniae. ..
  10. An K, Kiyuna T, Kigawa R, Sano C, Miura S, Sugiyama J. The identity of Penicillium sp. 1, a major contaminant of the stone chambers in the Takamatsuzuka and Kitora Tumuli in Japan, is Penicillium paneum. Antonie Van Leeuwenhoek. 2009;96:579-92 pubmed publisher
    ..Therefore, this is the first report of P. paneum isolation from samples relating to the biodeteriorated cultural properties such as mural paintings on plaster walls. ..
  11. Kokuho T, Yasukochi Y, Watanabe S, Inumaru S. Molecular cloning and expression profile analysis of a novel beta-D-N-acetylhexosaminidase of domestic silkworm (Bombyx mori). Genes Cells. 2010;15:525-36 pubmed publisher
    ..e. ovary, fat bodies, mid-intestine, skin), but not in pupae, suggesting its unique function in the carbohydrate metabolism of juvenile silkworm. ..
  12. Noda H, Munderloh U, Kurtti T. Endosymbionts of ticks and their relationship to Wolbachia spp. and tick-borne pathogens of humans and animals. Appl Environ Microbiol. 1997;63:3926-32 pubmed
    ..The two symbionts that live in the Malpighian tubules, one closely related to C. burnetii and the other closely related to F. tularensis, appear to be of ancient origin and be widely distributed in ticks. ..
  13. Suzuki T, Kawasaki Y, Furukohri T, Ellington W. Evolution of phosphagen kinase. VI. Isolation, characterization and cDNA-derived amino acid sequence of lombricine kinase from the earthworm Eisenia foetida, and identification of a possible candidate for the guanidine substrate recognition site. Biochim Biophys Acta. 1997;1343:152-9 pubmed
    ..A phylogenetic analysis using amino acid sequences of all four phosphagen kinases indicates that CK, GK and LK probably evolved from a common immediate ancestor protein. ..
  14. Tokita H, Okamoto H, Iizuka H, Kishimoto J, Tsuda F, Miyakawa Y, et al. The entire nucleotide sequences of three hepatitis C virus isolates in genetic groups 7-9 and comparison with those in the other eight genetic groups. J Gen Virol. 1998;79 ( Pt 8):1847-57 pubmed publisher
    ..7 vs 4-7%). These results indicate that HCV might not have evolved in the two-tiered fashion, at least in a strict sense...
  15. Imada T, Yamaguchi S, Mase M, Tsukamoto K, Kubo M, Morooka A. Avian nephritis virus (ANV) as a new member of the family Astroviridae and construction of infectious ANV cDNA. J Virol. 2000;74:8487-93 pubmed
    ..These observations suggested that the ANV (G-4260 strain) is a new genus of the family Astroviridae...
  16. Shiotani M, Miura R, Fujita K, Wakasa C, Uema M, Kai C. Molecular properties of the matrixprotein(M) gene of the lapinized rinderpest virus. J Vet Med Sci. 2001;63:801-5 pubmed
    ..In the present study, all coding regions of the RPV-L strain have been determined. ..
  17. Kajikawa M, Yamato K, Kohzu Y, Shoji S, Matsui K, Tanaka Y, et al. A front-end desaturase from Chlamydomonas reinhardtii produces pinolenic and coniferonic acids by omega13 desaturation in methylotrophic yeast and tobacco. Plant Cell Physiol. 2006;47:64-73 pubmed
    ..PA and CA accumulated in the leaves of transgenic plants. The highest combined yield of PA and CA was 44.7% of total fatty acids, suggesting that PA and CA can be produced in higher plants on a large scale. ..
  18. Taroura S, Shimada Y, Sakata Y, Miyama T, Hiraoka H, Watanabe M, et al. Detection of DNA of 'Candidatus Mycoplasma haemominutum' and Spiroplasma sp. in unfed ticks collected from vegetation in Japan. J Vet Med Sci. 2005;67:1277-9 pubmed
    ..Mycoplasma haemominutum'. Spiroplasma DNA was also detected from unfed I. ovatus in Hokkaido, Fukushima and Yamaguchi Prefectures. The analysis of nucleotides sequence suggested that this Spiroplasma was distinct from registered species...
  19. Mano H, Ogasawara F, Sato K, Higo H, Minobe Y. Isolation of a regulatory gene of anthocyanin biosynthesis in tuberous roots of purple-fleshed sweet potato. Plant Physiol. 2007;143:1252-68 pubmed
  20. Kosaka T, Nakayama S, Nakaya K, Yoshino S, Furukawa K. Characterization of the sol operon in butanol-hyperproducing Clostridium saccharoperbutylacetonicum strain N1-4 and its degeneration mechanism. Biosci Biotechnol Biochem. 2007;71:58-68 pubmed
    ..These results suggest that the degeneration is caused by the incompetence of the induction mechanism of the sol operon, and that transcription might be under the control of a quorum-sensing mechanism. ..
  21. Ushizawa K, Takahashi T, Hosoe M, Ohkoshi K, Hashizume K. Expression and characterization of novel ovine orthologs of bovine placental prolactin-related proteins. BMC Mol Biol. 2007;8:95 pubmed
    ..We investigated placental PRP in sheep in order to gain a comprehensive understanding of the function and evolution of these molecules. We also examined the sequence properties, expression and lactogenic activation of the cloned genes...
  22. Suzuki Y. Positive selection operates continuously on hemagglutinin during evolution of H3N2 human influenza A virus. Gene. 2008;427:111-6 pubmed publisher
  23. Takano R, Nidom C, Kiso M, Muramoto Y, Yamada S, Shinya K, et al. A comparison of the pathogenicity of avian and swine H5N1 influenza viruses in Indonesia. Arch Virol. 2009;154:677-81 pubmed publisher
    ..We found that swine isolates were less virulent to mice than avian isolates, suggesting that the viruses became attenuated during their replication in pigs. Continuous surveillance of H5N1 viruses among pigs is clearly warranted. ..
  24. Kamikawa R, Yabuki A, Nakayama T, Ishida K, Hashimoto T, Inagaki Y. Cercozoa comprises both EF-1?-containing and EFL-containing members. Eur J Protistol. 2011;47:24-8 pubmed publisher
    ..Based on the results, we postulate that cercozoan EF-1? genes have been vertically inherited, and the current EFL-containing species may have secondarily lost their EF-1? genes. ..
  25. Harada J, Takaku S, Watanabe K. An on-demand metalloprotease from psychro-tolerant Exiguobacterium undae Su-1, the activity and stability of which are controlled by the Ca2+ concentration. Biosci Biotechnol Biochem. 2012;76:986-92 pubmed
    ..On the other hand, its flexibility was enhanced when one Ca2+ binding site was lost and by replacement for proline and isoleucine residues. ..
  26. Konno U, Kouduka M, Komatsu D, Ishii K, Fukuda A, Tsunogai U, et al. Novel microbial populations in deep granitic groundwater from Grimsel Test Site, Switzerland. Microb Ecol. 2013;65:626-37 pubmed publisher
  27. Mase M, CHUUJOU M, Inoue T, Nakamura K, Yamaguchi S, Imada T. Genetic characterization of fowl adenoviruses isolated from chickens with hydropericardium syndrome in Japan. J Vet Med Sci. 2009;71:1455-8 pubmed
    ..This suggested that FAdV-4 from the HPS chickens in India and Pakistan was derived from a common ancestor, but the origin of the FAdV-4 from the HPS chickens in Japan was completely different. ..
  28. Fukunaga M, Hamase A, Okada K, Inoue H, Tsuruta Y, Miyamoto K, et al. Characterization of spirochetes isolated from ticks (Ixodes tanuki, Ixodes turdus, and Ixodes columnae) and comparison of the sequences with those of Borrelia burgdorferi sensu lato strains. Appl Environ Microbiol. 1996;62:2338-44 pubmed
    ..The results of 16S rRNA gene sequence comparison suggest that the strain Am501 from I. columnae is related to group Hk501, although its level of DNA relatedness is less than 70%. ..
  29. Tagawa M, Shirasawa T, Yahagi Y, Tomoda T, Kuroyanagi H, Fujimura S, et al. Identification of a receptor-type protein tyrosine phosphatase expressed in postmitotic maturing neurons: its structure and expression in the central nervous system. Biochem J. 1997;321 ( Pt 3):865-71 pubmed
    ..Because the expression of RPTP-BK in the developing neocortex is correlated with the stage of axonogenesis in cortical neurons, RPTP-BK might be crucial in neural cell development of the mammalian central nervous system. ..
  30. Sato N, Tachikawa T, Wada A, Tanaka A. Temperature-dependent regulation of the ribosomal small-subunit protein S21 in the cyanobacterium Anabaena variabilis M3. J Bacteriol. 1997;179:7063-71 pubmed
    ..These results suggest that S21 is involved in the adaptation to changes in temperature in cyanobacteria. ..
  31. Endo Y, Takahashi M, Nakao M, Saiga H, Sekine H, Matsushita M, et al. Two lineages of mannose-binding lectin-associated serine protease (MASP) in vertebrates. J Immunol. 1998;161:4924-30 pubmed
    ..Furthermore, the presence of MASP or MASP-like sequences in most vertebrate species suggests that the lectin pathway functions extensively in vertebrates and that its origin is traced back to the invertebrate stage...
  32. Hayward C, Iwashita M, Crane J, Ogawa K. First report of the invasive eel pest Pseudodactylogyrus bini in North America and in wild American eels. Dis Aquat Organ. 2001;44:53-60 pubmed
    ..crassus) are likely to continue to colonise other regions of the world. ..
  33. Inoshima Y, Murakami K, Yokoyama T, Sentsui H. Genetic heterogeneity among parapoxviruses isolated from sheep, cattle and Japanese serows (Capricornis crispus). J Gen Virol. 2001;82:1215-20 pubmed
    ..The methods presented here are useful for genetic characterization and classification of parapoxviruses...
  34. Yamazaki M, Yamagishi E, Gong Z, Fukuchi Mizutani M, Fukui Y, Tanaka Y, et al. Two flavonoid glucosyltransferases from Petunia hybrida: molecular cloning, biochemical properties and developmentally regulated expression. Plant Mol Biol. 2002;48:401-11 pubmed
    ..Southern blotting analysis of genomic DNA indicates that both 3-GT and 5-GT genes exist in two copies in P. hybrida, respectively. The results are discussed in relation to the molecular evolution of flavonoid glycosyltransferases. ..
  35. Suzuki T, Yamasaki K, Fujita S, Oda K, Iseki M, Yoshida K, et al. Archaeal-type rhodopsins in Chlamydomonas: model structure and intracellular localization. Biochem Biophys Res Commun. 2003;301:711-7 pubmed
    ..A. Sineshchekov, K.H. Jung, J.H. Spudich, Proc. Natl. Sci. USA 99 (2002) 8689; G. Nagel, D. Olig, M. Fuhrmann, S. Kateriya, A.M. Musti, E. Bamberg, P. Hegemann, Science 296 (2002) 2395]. ..
  36. Hayano A, Amano M, Miyazaki N. Phylogeography and population structure of the Dall's porpoise, Phocoenoides dalli, in Japanese waters revealed by mitochondrial DNA. Genes Genet Syst. 2003;78:81-91 pubmed
  37. Ishikura M, Ando S, Shinagawa Y, Matsuura K, Hasegawa S, Nakayama T, et al. Phylogenetic analysis of spotted fever group rickettsiae based on gltA, 17-kDa, and rOmpA genes amplified by nested PCR from ticks in Japan. Microbiol Immunol. 2003;47:823-32 pubmed
    ..ovatus and I. persulcatus were identical with R. helvetica. Genotype IX detected from I. nipponensis was genetically close to the strains IRS3, IRS4, and IrR/Munich isolated from I. ricinus in Slovakia and German...
  38. Hosoi M, Ito M, Yagura T, Adams R, Honda G. cDNA isolation and functional expression of myrcene synthase from Perilla frutescens. Biol Pharm Bull. 2004;27:1979-85 pubmed
    ..9% sabinene, 19.8% linalool and 5.5% limonene. As for the extraction of reaction products, we performed SPME (solid phase micro extraction) as well as conventional solvent extraction, and compared these two extraction methods...
  39. Hayashi K, Kawaide H, Notomi M, Sakigi Y, Matsuo A, Nozaki H. Identification and functional analysis of bifunctional ent-kaurene synthase from the moss Physcomitrella patens. FEBS Lett. 2006;580:6175-81 pubmed publisher
    ..The mutational analysis of two conserved motifs in PpCPS/KS indicated that the DVDD motif is responsible for CPS activity (GGDP to CDP) and the DDYFD motif for KS activity (CDP to ent-kaurene and ent-16alpha-hydroxykaurene)...
  40. Hoshino K, Isawa H, Tsuda Y, Yano K, Sasaki T, Yuda M, et al. Genetic characterization of a new insect flavivirus isolated from Culex pipiens mosquito in Japan. Virology. 2007;359:405-14 pubmed publisher
    ..The 3' UTR of CxFV contains four tandem repeats, which have sequence similarities to the two direct repeats in the CFA and KRV 3' UTRs. These results suggest that CxFV may be a new group of insect flaviviruses...
  41. Hatayama K, Shoun H, Ueda Y, Nakamura A. Tuberibacillus calidus gen. nov., sp. nov., isolated from a compost pile and reclassification of Bacillus naganoensis Tomimura et al. 1990 as Pullulanibacillus naganoensis gen. nov., comb. nov. and Bacillus laevolacticus Andersch et al. 1994 as Sporo. Int J Syst Evol Microbiol. 2006;56:2545-51 pubmed
    ..Based on these results, it is proposed that B. naganoensis and B. laevolacticus should be transferred to Pullulanibacillus naganoensis gen. nov., comb. nov. and Sporolactobacillus laevolacticus comb. nov., respectively...
  42. Ninomiya M, Nishizawa T, Takahashi M, Lorenzo F, Shimosegawa T, Okamoto H. Identification and genomic characterization of a novel human torque teno virus of 3.2 kb. J Gen Virol. 2007;88:1939-44 pubmed publisher
    ..These results suggest that SAVs are deletion mutants of the novel virus with intermediate genomic length between those of TTV and TTMV and that the novel virus can be classified into a third group of the genus Anellovirus...
  43. Akagami M, Shibahara T, Yoshiga T, Tanaka N, Yaguchi Y, Onuki T, et al. Granulomatous nephritis and meningoencephalomyelitis caused by Halicephalobus gingivalis in a pony gelding. J Vet Med Sci. 2007;69:1187-90 pubmed
    ..gingivalis. The present results indicated that H. gingivalis caused granulomatous nephritis and meningoencephalomyelitis in this pony gelding...
  44. Tamura T, Asakura T, Uemura T, Ueda T, Terauchi K, Misaka T, et al. Signal peptide peptidase and its homologs in Arabidopsis thaliana--plant tissue-specific expression and distinct subcellular localization. FEBS J. 2008;275:34-43 pubmed
    ..These results suggest that AtSPP mediates the cleavage of signal peptide in the ER membrane as well as HsSPP does, and also that AtSPPL1 and AtSPPL2 located in the endosomes have distinct roles in cells. ..
  45. Liu J, Ban Y, Wen X, Nakajima I, Moriguchi T. Molecular cloning and expression analysis of an arginine decarboxylase gene from peach (Prunus persica). Gene. 2009;429:10-7 pubmed publisher
    ..All of these, taken together, suggest that PpADC is a stress-responsive gene and can be considered as a potential target that is genetically manipulated so as to create novel germplasms with enhanced stress tolerance in the future. ..
  46. Hirayama J, Sekizuka T, Tazumi A, Taneike I, Moore J, Millar B, et al. Structural analysis of the full-length gene encoding a fibronectin-binding-like protein (CadF) and its adjacent genetic loci within Campylobacter lari. BMC Microbiol. 2009;9:192 pubmed publisher
    ..Probable consensus sequence at the -35 and -10 regions were identified in all C. lari isolates, as a promoter...
  47. Masubuchi K, Wakatsuki A, Iwamoto K, Takahashi T, Kokubu T, Shimizu M. Immunological and genetic characterization of feline caliciviruses used in the development of a new trivalent inactivated vaccine in Japan. J Vet Med Sci. 2010;72:1189-94 pubmed
  48. Bando T, Hamada Y, Kurita K, Nakamura T, Mito T, Ohuchi H, et al. Lowfat, a mammalian Lix1 homologue, regulates leg size and growth under the Dachsous/Fat signaling pathway during tissue regeneration. Dev Dyn. 2011;240:1440-53 pubmed publisher
  49. Murakami Y, Otsuka S, Senoo K. Abundance and community structure of sphingomonads in leaf residues and nearby bulk soil. Microbes Environ. 2010;25:183-9 pubmed
    ..The results show that particular sphingomonad populations accumulate in leaf residues compared to the surrounding bulk soil under field conditions. ..
  50. Xue Q, Shimizu K, Sakharkar M, Utsumi M, Cao G, Li M, et al. Geosmin degradation by seasonal biofilm from a biological treatment facility. Environ Sci Pollut Res Int. 2012;19:700-7 pubmed publisher
    ..Here, for the first time, we evaluated the biodegradation of geosmin by microorganisms in biofilm from biological treatment unit of actual potable water treatment plant...
  51. Sakamoto M, Ohkuma M. Bacteroides reticulotermitis sp. nov., isolated from the gut of a subterranean termite (Reticulitermes speratus). Int J Syst Evol Microbiol. 2013;63:691-5 pubmed publisher
    ..9 mol%. Based on these data, strain Rs-03(T) represents a novel species in the genus Bacteroides, for which the name Bacteroides reticulotermitis sp. nov. is proposed. The type strain is Rs-03(T) (?=?JCM 10512(T)?=?CCUG 62153(T))...
  52. Konishi M, Watsuji T, Nakagawa S, Hatada Y, Takai K, Toyofuku T. Effects of hydrogen sulfide on bacterial communities on the surface of galatheid crab, Shinkaia crosnieri, and in a bacterial mat cultured in rearing tanks. Microbes Environ. 2013;28:25-32 pubmed
    ..Interestingly, major clones were related to symbionts of Alviniconcha sp. type 2 and to endosymbionts of Osedax mucofloris, in Epsilonproteobacteria...
  53. Ishii S, Ashida N, Ohno H, Segawa T, Yabe S, Otsuka S, et al. Noviherbaspirillum denitrificans sp. nov., a denitrifying bacterium isolated from rice paddy soil and Noviherbaspirillum autotrophicum sp. nov., a denitrifying, facultatively autotrophic bacterium isolated from rice paddy soil and proposal to reclass. Int J Syst Evol Microbiol. 2017;67:1841-1848 pubmed publisher
    ..nov. and Noviherbaspirillum autotrophicum sp. nov. are proposed, respectively. We also propose the reclassification of Herbaspirillum massiliense as Noviherbaspirillum massiliense comb. nov...
  54. 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. ..
  55. Kawano T, Imada M, Chamavit P, Kobayashi S, Hashimoto T, Nozaki T. Genetic diversity of Entamoeba: Novel ribosomal lineages from cockroaches. PLoS ONE. 2017;12:e0185233 pubmed publisher
    ..This is the first report of the diversity of SSU rDNA sequences from Entamoeba in non-vertebrate host species, and should help to understand the genetic diversity of the genus Entamoeba...
  56. Shimizu N, Takeuchi Y, Naruse T, Inagaki M, Moriyama E, Gojobori T, et al. Six strains of human immunodeficiency virus type 1 isolated in Japan and their molecular phylogeny. J Mol Evol. 1992;35:329-36 pubmed
    ..In particular, GUN-1 and GUN-2 isolates were on the branch of a San Francisco isolate, ARV2, while GUN-5 and GUN-6 isolates were on the branch of HTLV-IIIB-related isolates. ..
  57. Komoto N, Yukuhiro K, Tamura T. Structure and expression of tandemly duplicated xanthine dehydrogenase genes of the silkworm (Bombyx mori). Insect Mol Biol. 1999;8:73-83 pubmed
    ..Phylogenetic analysis indicates that BmXDH gene duplication occurred after the divergence of the silkworm and dipteran species. Intron insertion site comparison shows that some introns were lost during insect XDH gene evolution. ..
  58. Todo T. Functional diversity of the DNA photolyase/blue light receptor family. Mutat Res. 1999;434:89-97 pubmed
  59. Hirano M, Nakamura S, Mitsunaga F, Okada M, Shirahama S, Eberle R. One-step PCR to distinguish B virus from related primate alphaherpesviruses. Clin Diagn Lab Immunol. 2002;9:716-9 pubmed
    ..Thus, this PCR method is useful to discriminate BV from other closely related primate alphaherpesviruses. ..
  60. Ohsako T, Yamane K, Ohnishi O. Two new Fagopyrum (Polygonaceae) species, F. gracilipedoides and F. jinshaense from Yunnan, China. Genes Genet Syst. 2002;77:399-408 pubmed
    ..gilesii. In the clade of F. capillatum, F. gracilipes, F. gracilipedoides and F. rubifolium, the breakdown of self-incompatibility accompanying genome duplication seems to have occurred twice independently...
  61. Utsumi M, Belova S, King G, Uchiyama H. Phylogenetic comparison of methanogen diversity in different wetland soils. J Gen Appl Microbiol. 2003;49:75-83 pubmed
    ..In terms of the Shannon-Weaver diversity index, the archaeal community diversity in Okefenokee Swamp was greater than that of the other wetlands. ..
  62. Uchiyama Y, Kimura S, Yamamoto T, Ishibashi T, Sakaguchi K. Plant DNA polymerase lambda, a DNA repair enzyme that functions in plant meristematic and meiotic tissues. Eur J Biochem. 2004;271:2799-807 pubmed publisher
    ..These properties suggest that plant Pol lambda is a DNA repair enzyme which functions in plant meristematic and meiotic tissues, and that it can substitute for Pol beta and terminal deoxyribonucleotidyl transferase...
  63. Takaishi M, Makino T, Morohashi M, Huh N. Identification of human hornerin and its expression in regenerating and psoriatic skin. J Biol Chem. 2005;280:4696-703 pubmed
    ..Hornerin protein was detected in the proximal epidermis (but not in the distal epidermis) at 15 days after wounding. These results indicate that hornerin has a function similar to but distinct from that of filaggrin in cornification. ..
  64. Sakagami H, Aoki J, Natori Y, Nishikawa K, Kakehi Y, Natori Y, et al. Biochemical and molecular characterization of a novel choline-specific glycerophosphodiester phosphodiesterase belonging to the nucleotide pyrophosphatase/phosphodiesterase family. J Biol Chem. 2005;280:23084-93 pubmed
    ..The present results suggest that NPP6 has a specific role through the hydrolysis of polyunsaturated LPC, glycerophosphorylcholine, or sphingosylphosphorylcholine in these organs. ..
  65. Nishibori M, Shimogiri T, Hayashi T, Yasue H. Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Anim Genet. 2005;36:367-75 pubmed
    ..Alternative clustering of RJF and chicken alleles were also observed. These findings taken together strongly indicate that inter-species hybridizations have occurred between GyJF and RJF/chicken and between GyJF and CJF...
  66. Odbileg R, Konnai S, Ohashi K, Onuma M. Molecular cloning and phylogenetic analysis of inflammatory cytokines of Camelidae (llama and camel). J Vet Med Sci. 2005;67:921-5 pubmed
    ..Phylogenetic analyses based on nucleic acid sequences showed that llama IL-1alpha, IL-1beta, IL-6 and TNF-alpha were more closely related to those of camel, pig, cattle, sheep and horse than to those of human, dog, cat, mouse and rat. ..
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    ..Elimination of susceptibility to poliovirus infection in simians may be difficult, because it also requires elimination of advantageous effects that have been exerted by CD155. ..
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    ..Amyloid deposition was observed in the Disse space of the liver, splenic sinus, and lamina propria of the bronchiolar, bronchial, and tracheal areas. Amyloidosis could be one factor inducing the fowlpox infection in vaccinated chickens...
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    ..The possible modes of action of NSL1 protein in negative regulation of cell death programs and defense responses are discussed. ..
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    ..These results suggest the requirement for LjnsRING in rhizobial infection and the subsequent nodule formation process...
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    ..A comparison of the amino acid sequences between M11 and its parental isolate IbG, and analysis of recombinant infectious clones between M11 and IbG revealed that an amino acid at position 314 was involved in the attenuation of BYMV. ..
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    ..To improve chytridiomycosis risk management, we must consider the risk of B. dendrobatidis changing hosts as a result of anthropogenic disturbance of the host-specific distribution of the fungus...
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    ..These results suggest that xTRAIL1 can cause apoptosis, probably mediated through xDR-Ms, in larval RBCs, but may not kill adult RBCs, presumably owing to PKC activation, as part of the mechanism for RBC switching. ..
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    ..These geomicrobiological results suggest that deep granitic groundwater has been stably colonized by Thauera spp. probably owing to the limitation of O(2), NO(3)(-), and organic acids...
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    ..nov. is proposed for the strain. The type strain is S582(T) (=NBRC 104112(T) =BCC 28624(T))...
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    ..The presence of three covalent linkages might explain why both OsGBSSI-CD structures adopted only the closed domain arrangement. ..
  79. Kato S, Krepski S, Chan C, Itoh T, Ohkuma M. Ferriphaselus amnicola gen. nov., sp. nov., a neutrophilic, stalk-forming, iron-oxidizing bacterium isolated from an iron-rich groundwater seep. Int J Syst Evol Microbiol. 2014;64:921-5 pubmed publisher
    ..nov., sp. nov. is proposed; the type strain of Ferriphaselus amnicola is OYT1(T) (?=?JCM 18545(T)?=?DSM 26810(T)). ..
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    ..Hence we conclude that KIF4 is a novel microtubule-associated anterograde motor protein for membranous organelles, the expression of which is regulated developmentally. ..
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    ..The order of the genes in H. halobium essentially agreed with that of the corresponding genes of E. coli (S10-operon), except for certain deletions or insertions of additional protein genes. ..
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    ..4) also have a free-standing ORF in loop 1 and loop 2, respectively. These results show that these group-I introns and the intronic ORFs have evolved from the same ancestral origin, but that these ORFs have been propagated independently. ..
  83. Nakazawa F, Poco S, Ikeda T, Sato M, Kalfas S, Sundqvist G, et al. Cryptobacterium curtum gen. nov., sp. nov., a new genus of gram-positive anaerobic rod isolated from human oral cavities. Int J Syst Bacteriol. 1999;49 Pt 3:1193-200 pubmed
    ..nov., sp. nov. is proposed. The type strain of Cryptobacterium curtum is 12-3T (= ATCC 700683T). ..
  84. Harasawa R, Hotzel H, Sachse K. Comparison of the 16S-23S rRNA intergenic spacer regions among strains of the Mycoplasma mycoides cluster, and reassessment of the taxonomic position of Mycoplasma sp. bovine group 7. Int J Syst Evol Microbiol. 2000;50 Pt 3:1325-9 pubmed
    ..The data also provided evidence in favour of a reclassification of Mycoplasma sp. bovine group 7 as another subspecies of M. capricolum. ..
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    ..Stimulation of CAS activity and protein accumulation by ethylene without the concomitant increase of its mRNA suggested that ethylene induces CAS protein accumulation at the post-transcriptional level...
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    ..Based on the evolutionary conservation of the CCND1-ORAOV1-FGF19-FGF4 locus from zebrafish to human, it was concluded that Fgf15 gene is the rodent ortholog of human FGF19 gene. ..
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    ..Several routes or sources are conceivable for APV to invade into Japan...
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    ..All six symbiotic sequences obtained here (approximately 4000-bp sequences of 18S rDNA, ITS1, 5.8S rDNA, and ITS2) were completely identical in each, strongly suggesting a common origin. ..
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    ..These results suggest that MVC together with BPV can possibly be classified into a new clade in the Parvovirinae subfamily. ..
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    ..Homologs are widely found in mammals and higher plants. The data suggest that DmGEN belongs to a new class of RAD2 nuclease. ..
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    ..The results of the real time PCR analysis approximately agree with those of the clone analysis. These results indicate that real-time PCR analysis is useful for quantitatively describing methanogenic communities. ..
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    ..FAT4 mRNA was expressed in fetal brain, infant brain, brain tumor and colorectal cancer. FAT family members were revealed to be targets of systems medicine in the fields of oncology and neurology. ..