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Pane A, Wehr K, Schüpbach T. zucchini and squash encode two putative nucleases required for rasiRNA production in the Drosophila germline. Dev Cell 2007; 12:851-62. [PMID: 17543859 PMCID: PMC1945814 DOI: 10.1016/j.devcel.2007.03.022] [Citation(s) in RCA: 256] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 03/13/2007] [Accepted: 03/30/2007] [Indexed: 12/19/2022]
Abstract
RNAi is a widespread mechanism by which organisms regulate gene expression and defend their genomes against viruses and transposable elements. Here we report the identification of Drosophila zucchini (zuc) and squash (squ), which function in germline RNAi processes. Zuc and Squ contain domains with homologies to nucleases. Mutant females are sterile and show dorsoventral patterning defects during oogenesis. In addition, Oskar protein is ectopically expressed in early oocytes, where it is normally silenced by RNAi mechanisms. Zuc and Squ localize to the perinuclear nuage and interact with Aubergine, a PIWI class protein. Mutations in zuc and squ induce the upregulation of Het-A and Tart, two telomere-specific transposable elements, and the expression of Stellate protein in the Drosophila germline. We show that these defects are due to the inability of zuc and squ mutants to produce repeat-associated small interfering RNAs.
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MESH Headings
- Amino Acid Sequence
- Animals
- Blotting, Northern
- Blotting, Western
- DNA Transposable Elements/physiology
- Drosophila Proteins/genetics
- Drosophila Proteins/metabolism
- Drosophila melanogaster/enzymology
- Drosophila melanogaster/genetics
- Drosophila melanogaster/growth & development
- Embryo, Nonmammalian/metabolism
- Endonucleases/genetics
- Endonucleases/metabolism
- Endoribonucleases/genetics
- Endoribonucleases/metabolism
- Female
- Gene Expression Regulation, Fungal
- Gene Products, gag/metabolism
- Germ Cells/cytology
- Germ Cells/metabolism
- Immunoprecipitation
- Male
- Molecular Sequence Data
- Mutation
- Oocytes/cytology
- Oocytes/metabolism
- Oogenesis/physiology
- Peptide Initiation Factors/metabolism
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Small Interfering/pharmacology
- Sequence Homology, Amino Acid
- Transforming Growth Factor alpha/metabolism
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Affiliation(s)
| | | | - Trudi Schüpbach
- Corresponding author. HHMI, Department of Molecular Biology, Princeton University, Princeton, NJ 08544. Phone: 609-258-1365, Fax: 609-258-1547, E-mail address:
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52
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Theurkauf WE, Klattenhoff C, Bratu DP, McGinnis-Schultz N, Koppetsch BS, Cook HA. rasiRNAs, DNA damage, and embryonic axis specification. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2007; 71:171-80. [PMID: 17381294 DOI: 10.1101/sqb.2006.71.066] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Drosophila repeat-associated small interfering RNAs (rasiRNAs) have been implicated in retrotransposon and stellate locus silencing. However, mutations in the rasiRNA pathway genes armitage, spindle-E, and aubergine disrupt embryonic axis specification, triggering defects in microtubule organization and localization of osk and grk mRNAs during oogenesis. We show that mutations in mei-41 and mnk, which encode ATR and Chk2 kinases that function in DNA damage signal transduction, dramatically suppress the cytoskeletal and RNA localization defects associated with rasiRNA mutations. In contrast, stellate and retrotransposon silencing are not restored in mei-41 and mnk double mutants. We also find that armitage, aubergine, and spindle-E mutations lead to germ-line-specific accumulation of gamma-H2Av foci, which form at DNA double-strand breaks, and that mutations in armi lead to Chk2-dependent phosphorylation of Vasa, an RNA helicase required for axis specification. The Drosophila rasiRNA pathway thus appears to suppress DNA damage in the germ line, and mutations in this pathway block axis specification by activating an ATR/Chk2-dependent DNA damage response that disrupts microtubule polarization and RNA localization.
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Affiliation(s)
- W E Theurkauf
- Program in Molecular Medicine and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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53
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Casacuberta E, Marín FA, Pardue ML. Intracellular targeting of telomeric retrotransposon Gag proteins of distantly related Drosophila species. Proc Natl Acad Sci U S A 2007; 104:8391-6. [PMID: 17483480 PMCID: PMC1895960 DOI: 10.1073/pnas.0702566104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The retrotransposons that maintain telomeres in Drosophila melanogaster have unique features that are shared across all Drosophila species but are not found in other retrotransposons. Comparative analysis of these features provides insight into their importance for telomere maintenance in Drosophila. Gag proteins encoded by HeT-A(mel) and TART(mel) are efficiently and cooperatively targeted to telomeres in interphase nuclei, a behavior that may facilitate telomere-specific transposition. Drosophila virilis, separated from D. melanogaster by 60 MY, has telomeres maintained by HeT-A(vir) and TART(vir). The Gag proteins from HeT-A(mel) and HeT-A(vir) have only 16% amino acid identity, yet several of their functional features are conserved. Using transient transfection of cultured cells from both species, we show that the telomere association of HeT-A(vir) Gag is indistinguishable from that of HeT-A(mel) Gag. Deletion derivatives show that organization of localization signals within the two proteins is strikingly similar. Gag proteins of TART(mel) and TART(vir) are only 13% identical. In contrast to HeT-A, surprisingly, TART(vir) Gag does not localize to the nucleus, although TART(vir) is a major component of D. virilis telomeres, and localization signals in the protein have much the same organization as in TART(mel) Gag. Thus, the mechanism of telomere targeting of TART(vir) differs, at least in a minor way, from that of TART(mel). Our findings suggest that, despite dramatic rates of protein evolution, protein and cellular determinants that correctly localize these Gag proteins have been conserved throughout the 60 MY separating these species.
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Affiliation(s)
- Elena Casacuberta
- *Institute of Molecular Biology of Barcelona, Consejo Superior de Investigaciones Científicas and Institute for Research on Biomedicine of Barcelona (IRB), 08028 Barcelona, Spain; and
| | - Fernando Azorín Marín
- *Institute of Molecular Biology of Barcelona, Consejo Superior de Investigaciones Científicas and Institute for Research on Biomedicine of Barcelona (IRB), 08028 Barcelona, Spain; and
| | - Mary-Lou Pardue
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139
- To whom correspondence should be addressed at: Biology Department, 68–670, Massachusetts Institute of Technology, Cambridge, MA 02139. E-mail:
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54
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Abstract
Overlapping epigenetic mechanisms have evolved in eukaryotic cells to silence the expression and mobility of transposable elements (TEs). Owing to their ability to recruit the silencing machinery, TEs have served as building blocks for epigenetic phenomena, both at the level of single genes and across larger chromosomal regions. Important progress has been made recently in understanding these silencing mechanisms. In addition, new insights have been gained into how this silencing has been co-opted to serve essential functions in 'host' cells, highlighting the importance of TEs in the epigenetic regulation of the genome.
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Affiliation(s)
- R Keith Slotkin
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
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55
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Frydrychova RC, Biessmann H, Konev AY, Golubovsky MD, Johnson J, Archer TK, Mason JM. Transcriptional activity of the telomeric retrotransposon HeT-A in Drosophila melanogaster is stimulated as a consequence of subterminal deficiencies at homologous and nonhomologous telomeres. Mol Cell Biol 2007; 27:4991-5001. [PMID: 17470550 PMCID: PMC1951507 DOI: 10.1128/mcb.00515-07] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Drosophila melanogaster telomeres have two DNA domains: a terminal array of retrotransposons and a subterminal repetitive telomere-associated sequence (TAS), a source of telomere position effect (TPE). We reported previously that deletion of the 2L TAS array leads to dominant suppression of TPE by stimulating in trans expression of a telomeric transgene. Here, we compared the transcript activities of a w transgene inserted between the retrotransposon and TAS arrays at the 2L telomere in genotypes with different lengths of the 2L TAS. In contrast to individuals bearing a wild-type 2L homologue, flies with a TAS deficiency showed a significant increase in the level of telomeric w transcript during development, especially in pupae. Moreover, we identified a read-through w transcript initiated from a retrotransposon promoter in the terminal array. Read-through transcript levels also significantly increased with the presence of a 2L TAS deficiency in trans, indicating a stimulating force of the TAS deficiency on retrotransposon promoter activity. The read-through transcript contributes to total w transcript, although most w transcript originates at the w promoter. While silencing of transgenes in nonhomologous telomeres is suppressed by 2L TAS deficiencies, suggesting a global effect, the overall level of HeT-A transcripts is not increased under similar conditions.
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Affiliation(s)
- Radmila Capkova Frydrychova
- Laboratory of Molecular Genetics, D3-01, P.O. Box 12233, 111 T. W. Alexander Drive, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709-2233, USA
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56
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Riha K, Heacock ML, Shippen DE. The role of the nonhomologous end-joining DNA double-strand break repair pathway in telomere biology. Annu Rev Genet 2007; 40:237-77. [PMID: 16822175 DOI: 10.1146/annurev.genet.39.110304.095755] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Double-strand breaks are a cataclysmic threat to genome integrity. In higher eukaryotes the predominant recourse is the nonhomologous end-joining (NHEJ) double-strand break repair pathway. NHEJ is a versatile mechanism employing the Ku heterodimer, ligase IV/XRCC4 and a host of other proteins that juxtapose two free DNA ends for ligation. A critical function of telomeres is their ability to distinguish the ends of linear chromosomes from double-strand breaks, and avoid NHEJ. Telomeres accomplish this feat by forming a unique higher order nucleoprotein structure. Paradoxically, key components of NHEJ associate with normal telomeres and are required for proper length regulation and end protection. Here we review the biochemical mechanism of NHEJ in double-strand break repair, and in the response to dysfunctional telomeres. We discuss the ways in which NHEJ proteins contribute to telomere biology, and highlight how the NHEJ machinery and the telomere complex are evolving to maintain genome stability.
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Affiliation(s)
- Karel Riha
- Gregor Mendel Institute of Plant Molecular Biology, Austrian Academy of Sciences, A-1030 Vienna, Austria.
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57
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Klattenhoff C, Bratu DP, McGinnis-Schultz N, Koppetsch BS, Cook HA, Theurkauf WE. Drosophila rasiRNA pathway mutations disrupt embryonic axis specification through activation of an ATR/Chk2 DNA damage response. Dev Cell 2007; 12:45-55. [PMID: 17199040 DOI: 10.1016/j.devcel.2006.12.001] [Citation(s) in RCA: 235] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2006] [Revised: 11/10/2006] [Accepted: 12/02/2006] [Indexed: 11/20/2022]
Abstract
Small repeat-associated siRNAs (rasiRNAs) mediate silencing of retrotransposons and the Stellate locus. Mutations in the Drosophila rasiRNA pathway genes armitage and aubergine disrupt embryonic axis specification, triggering defects in microtubule polarization as well as asymmetric localization of mRNA and protein determinants in the developing oocyte. Mutations in the ATR/Chk2 DNA damage signal transduction pathway dramatically suppress these axis specification defects, but do not restore retrotransposon or Stellate silencing. Furthermore, rasiRNA pathway mutations lead to germline-specific accumulation of gamma-H2Av foci characteristic of DNA damage. We conclude that rasiRNA-based gene silencing is not required for axis specification, and that the critical developmental function for this pathway is to suppress DNA damage signaling in the germline.
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Affiliation(s)
- Carla Klattenhoff
- Program in Molecular Medicine and Program in Cell Dynamics, University of Massachusetts Medical School, Worcester, MA 01605, USA
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58
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Walter MF, Biessmann MR, Benitez C, Török T, Mason JM, Biessmann H. Effects of telomere length in Drosophila melanogaster on life span, fecundity, and fertility. Chromosoma 2006; 116:41-51. [PMID: 17089138 PMCID: PMC2254661 DOI: 10.1007/s00412-006-0081-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2006] [Revised: 07/29/2006] [Accepted: 08/28/2006] [Indexed: 11/28/2022]
Abstract
Chromosome length in Drosophila is maintained by targeted transposition of three non-long terminal repeat retrotransposons, HeT-A, TART, and TAHRE, to the chromosome ends. The length and composition of these retrotransposon arrays can vary significantly between chromosome tips and between fly stocks, but the significance and consequences of these length differences are not understood. A dominant genetic factor, Tel, has been described, which causes a severalfold elongation of the retrotransposon arrays at all telomeres. We used this strain to assess possible affects of extended telomeres on the organism. While we found no effect on life span of the adults, we could demonstrate a correlation between long telomeres and reduced fertility and fecundity in individual females, which is also reflected in abnormal oocyte development.
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Affiliation(s)
- Marika F. Walter
- Developmental Biology Center, University of California, Irvine, CA 92697, USA
| | - Max R. Biessmann
- Developmental Biology Center, University of California, Irvine, CA 92697, USA
| | - Cecil Benitez
- Developmental Biology Center, University of California, Irvine, CA 92697, USA
| | - Tibor Török
- Department of Genetics and Molecular Biology, University of Szeged, Szeged, Hungary
| | - James M. Mason
- Laboratory of Molecular Genetics, NIEHS, Research Triangle Park, NC 27709, USA
| | - Harald Biessmann
- Developmental Biology Center, University of California, Irvine, CA 92697, USA
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59
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George JA, DeBaryshe PG, Traverse KL, Celniker SE, Pardue ML. Genomic organization of the Drosophila telomere retrotransposable elements. Genome Res 2006; 16:1231-40. [PMID: 16963706 PMCID: PMC1581432 DOI: 10.1101/gr.5348806] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The emerging sequence of the heterochromatic portion of the Drosophila melanogaster genome, with the most recent update of euchromatic sequence, gives the first genome-wide view of the chromosomal distribution of the telomeric retrotransposons, HeT-A, TART, and Tahre. As expected, these elements are entirely excluded from euchromatin, although sequence fragments of HeT-A and TART 3 untranslated regions are found in nontelomeric heterochromatin on the Y chromosome. The proximal ends of HeT-A/TART arrays appear to be a transition zone because only here do other transposable elements mix in the array. The sharp distinction between the distribution of telomeric elements and that of other transposable elements suggests that chromatin structure is important in telomere element localization. Measurements reported here show (1) D. melanogaster telomeres are very long, in the size range reported for inbred mouse strains (averaging 46 kb per chromosome end in Drosophila stock 2057). As in organisms with telomerase, their length varies depending on genotype. There is also slight under-replication in polytene nuclei. (2) Surprisingly, the relationship between the number of HeT-A and TART elements is not stochastic but is strongly correlated across stocks, supporting the idea that the two elements are interdependent. Although currently assembled portions of the HeT-A/TART arrays are from the most-proximal part of long arrays, approximately 61% of the total HeT-A sequence in these regions consists of intact, potentially active elements with little evidence of sequence decay, making it likely that the content of the telomere arrays turns over more extensively than has been thought.
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Affiliation(s)
- Janet A. George
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - P. Gregory DeBaryshe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Karen L. Traverse
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Susan E. Celniker
- Berkeley Drosophila Genome Project, Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Mary-Lou Pardue
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Corresponding author.E-mail ; fax (617) 253-8699
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60
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Díez JL, Vilariño VR, Medina FJ, Morcillo G. Nucleolar localization of a reverse transcriptase related to telomere maintenance in Chironomus (Diptera). Histochem Cell Biol 2006; 126:445-52. [PMID: 16607537 DOI: 10.1007/s00418-006-0179-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2006] [Indexed: 10/24/2022]
Abstract
A growing number of cellular processes originally thought not to involve the nucleolus now seem to be associated with this organelle. In recent years, a variety of RNAs and proteins with no apparent function in ribosome genesis have been discovered in this nuclear compartment. This paper reports the presence in the nucleolus of a reverse transcriptase (RT) previously found to be associated with telomeres in Chironomus. Immunofluorescence detection using a specific antibody against conserved domains shared by RTs showed a distinct pattern of staining in the giant nucleoli of polytenized cells. This nucleolar localization was confirmed in a number of larval tissues and embryonic cells of Chironomus thummi and C. pallidivitatus; its distribution showed a definite necklace pattern that did not completely colocalize with fibrillarin or nucleolin and appeared to be different to that of typical nucleolar components. There is evidence that both telomerase RT and RNA template subunits are present in the nucleoli of mammalian and yeast cells. However, chironomids do not have typical telomeres or telomerase. As in other Diptera, telomeres lack the short, simple repeats maintained by telomerase and instead have more complex sequences in the range of hundreds of nucleotides. It has been suggested that the RT associated with these telomeres might be involved in their maintenance, perhaps involving a mechanism similar to that of telomerase retrotranscription and retrotransposition in Drosophila. The present results indicate that the putative Chironomus telomere elongation machinery and telomerase share a nucleolar localization. This reinforces the idea that nucleoli are functionally linked to telomere maintenance irrespective of the differences in their molecular organization and therefore in the strategy adopted for their elongation.
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Affiliation(s)
- José Luis Díez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040, Madrid, Spain.
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61
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Fujiwara H, Osanai M, Matsumoto T, Kojima KK. Telomere-specific non-LTR retrotransposons and telomere maintenance in the silkworm, Bombyx mori. Chromosome Res 2005; 13:455-67. [PMID: 16132811 DOI: 10.1007/s10577-005-0990-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Most insects have telomeres that consist of pentanucleotide (TTAGG) telomeric repeats, which are synthesized by telomerase. However, all species in Diptera so far examined and several species in other orders of insect have lost the (TTAGG)n repeats, suggesting that some of them recruit telomerase-independent telomere maintenance. The silkworm, Bombyx mori, retains the TTAGG motifs in the chromosomal ends but expresses quite a low level of telomerase activity in all stages of various tissues. Just proximal to a 6-8-kb stretch of the TTAGG repeats in B. mori, more than 1000 copies of non-LTR retrotransposons, designated TRAS and SART families, occur among the telomeric repeats and accumulate. TRAS and SART are abundantly transcribed and actively retrotransposed into TTAGG telomeric repeats in a highly sequence-specific manner. They have three possible mechanisms to ensure specific integration into the telomeric repeats. This article focuses on the telomere structure and telomere-specific non-LTR retrotransposons in B. mori and discusses the mechanisms for telomere maintenance in this insect.
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Affiliation(s)
- Haruhiko Fujiwara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Bioscience Building 501, Kashiwano-ha, 277-8562 Kashiwa, Japan.
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