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The immunological distances observed were used to build a tree that confirms that the squaloid and galeoid species examined belong to two separate groups and thatHeterodontus, a genus of hitherto uncertain position, belongs with the galeoids. The divergence time estimated from the transferrin comparisons is roughly 240±65 million years betweenHeterodontus and galeoids.",{"EN":164},"Evolutionary relationships of a “Primitive” shark (Heterodontus) assessed by micro-complement fixation of serum transferrin",{"VOID":166},"[\"5483209998367048125\"]",{"VOID":168},"Arnheim N, Sobel J, Canfield R (1971) Immunochemical resemblance between human leukemia and hen egg-white lysozyme and their reduced carboxymethyl derivatives. J Mol Biol 61:237–250\nArnon R, Maron E (1971) An immunological approach to the structural relationship between hen egg-white lysozyme and bovine α-lactalbumin. J Mol Biol 61:225–235\nBenjamin DC, Berzofsky JA, East IJ, Gurd FRN, Hannum C, Leach SJ, Margoliash E, Michael JG, Miller A, Prager EM, Reichlin M, Sercarz EE, Smith-Gill SJ, Todd PE, Wilson AC (1984) The antigenic structure of proteins: a reappraisal. Annu Rev Immunol 2:67–101\nBeverley SM, Wilson AC (1985) Ancient origin for Hawaiian Drosophilinae inferred from protein comparisons. Proc Natl Acad Sci USA 82:4753–4757\nBobák P, Stratil A, Valenta M (1983) Immunological comparison of transferrins of some European cyprinid fish. Biochem Syst Ecol 11:277–282\nBoettcher EW, Kistler P, Nitschmann HS (1958) Method of isolating the β1-metal-combining globulin from human blood plasma. Nature 181:490–491\nBudker P (1971) The life of sharks. Weidenfield and Nicolson, London (The world naturalist series)\nBurch SJ, Lawson R, Davies DH (1984) The relationships of cartilaginous fishes: an immunological study of serum transferrins of holocephalans and elasmobranchs. J Zool (London) 203:303–310\nChampion AB, Prager EM, Wachter D, Wilson AC (1974) Microcomplement fixation. In: Wright CA (ed) Biochemical and immunological taxonomy of animals. Academic Press, London, pp 397–416\nChampion AB, Soderberg KL, Wilson AC, Ambler RP (1975) Immunological comparison of azurins of known amino-acid sequence: dependence of cross-reactivity upon sequence resemblance. J Mol Evol 5:291–305\nCompagno LJV (1973) Interrelationships of living elasmobranchs. In: Greenwood PH, Miles RS, Patterson C (eds) Interrelationships of fishes. Academic Press, London, pp 15–61\nDessauer HC (1970) Blood chemistry of reptiles: physiological and evolutionary aspects. In: Gans C (ed) Biology of the Reptilia, vol 3. Academic Press, London, pp 1–72\nDowling HG, Highton R, Maha GC, Maxson LR (1983) Biochemical evaluation of colubrid snake phylogeny. J Zool (London) 201:309–329\nFisher WK, Thompson EOP (1979) Myolobin of the sharkHeterodontus portusjacksoni: isolation and amino acid sequence. Aust J Biol Sci 32:277–294\nFisher WK, Koureas DD, Thompson EOP (1980) Myoglobins of cartilaginous fishes. II. Isolation and amino acid sequence of myoglobin of the sharkMustelus antarcticus. Aust J Biol Sci 33:153–167\nFisher WK, Koureas DD, Thompson EOP (1981) Myoglobins of cartilaginous fishes. III. Amino acid sequence of myoglobin of the sharkGaleorhinus australis. Aust J Biol Sci 34:5–10\nFitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155:279–284\nGordon AH, Louis LN (1963) Preparation and properties of rat transferrin. Biochem J 88:409–414\nHanson JE (1984) An investigation into the phylogeny of selected teleosts using atigenic characters of isolated transferrins. MSc thesis, University of Salford, Salford, UK\nHudson BG, Ohno M, Brockway WJ, Castellino FJ (1973) Chemical and physical properties of serum transferrins from several species. Biochemistry 12:1047–1053\nKistler P, Nitschmann HS, Wyttenbach A, Studer M, Niederöst Ch, Mauerhofer M (1960) Humanes Siderophilin: Isolierung mittels Rivanol aus Blutplasma und Plasmafraktionen, analytische Bestimmung and Kristllisation. Vox Sang 5:403–415\nLøvtrup S (1977) The phylogeny of Vertebrata. Wiley, London\nMaisey JG (1984) Higher elasmobranch phylogeny and biostratigraphy. Zool J Linn Soc 82:33–54\nMao SH, Dessauer HC (1971) Selectively neutral mutations, transferrins and the evolution of natricine snakes. Comp Biochem Physiol [A] 40:669–680\nMcFarland WN, Pough FH, Cade TS, Heiser JB (1979) Vertebrate life. Macmillan, London\nMueller JO, Smithies O, Irwin MR (1962) Transferrin variation in Columbidae. Genetics 47:1385–1392\nNagler AL, Kockwa S, Wasserman LR (1962) Improved isolation of purified siderophilin from individual sera. Proc Soc Exp Biol Med 111:746–749\nNelson JS (1976) Fishes of the world. Wiley, New York, London\nOuchterlony O (1948) In vitro method for testing the toxinproducing capacity of diphtheria bacteria. Acta Pathol Microbiol Scand 25:186–191\nPalmour RM, Sutton HE (1971) Vertebrate transferrins. Molecular weights, chemical compositions, and iron-binding studies. Biochemistry 10:4026–4032\nPierson ED, Sarich VM, Lowenstein JM, Daniel MJ, Rainey WE (1986) A molecular link between the bats of New Zealand and South America. Nature 323:60–63\nPrager EM, Wilson AC (1971) The dependence of immunological cross-reactivity upon sequence resemblance among lysozymes. I. Microcomplement fixation studies. J Biol Chem 246:5978–5989\nPrager EM, Wilson AC (1975) Slow evolutionary loss of the potential for interspecific hybridization in birds: a manifestation of slow regulatory evolution. Proc Natl Acad Sci USA 72:200–204\nPrager EM, Wilson AC (1978) Construction of phylogenetic trees for proteins and nucleic acids: empirical evaluation of alternative matrix methods. J Mol Evol 11:129–142\nPrager EM, Brush AH, Nolan RA, Nakanishi M, Wilson AC (1974) Slow evolution of tansferrin and albumin in birds according to microcomplement fixation analysis. J Mol Evol 3:243–262\nPrager EM, Welling GW, Wilson AC (1978) Comparison of various immunologicalmmethods for distinguishing among mammalian pancreatic ribonucleases of known amino acid sequence. J Mol Evol 10:293–307\nRomer AS (1966) Vertebrate paleontology. University of Chicago Press, Chicago\nSage RD, Prager EM, Wake DB (1982) A Cretaceous divergence time between pelobatid frogs (Pelobates andScaphiopus): immunological studies of serum albumin. J Zool (London) 198: 481–494\nSammons DW, Adams LD, Nishizawa EE (1981) Ultrasensitive silver-based color staining of polypeptides in polyacrylamide gels. Electrophoresis 2:135–141\nSarich VM (1973) The giant panda is a bear. Nature 245:218–220\nScheidegger JJ (1955) Une micro-méthode de l'immuno-électrophorèse. Int Arch Allergy Appl Immunol 7:103–110\nWyles JS, Kunkel JG, Wilson AC (1983) Birds, behavior, and anatomical evolution. Proc Natl Acad Sci USA 80:4394–4397\nYoung JZ (1952) The life of vertebrates. Oxford University Press, Oxford, England",{"VOID":170},"10.1007\u002FBF02100043","PUBLICATION","VERIFIED","2024-05-17T00:13:56.951+00:00","Auto Verify","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002FBF02100043",[177,193,206,220],{"id":178,"sortIndex":23,"researcher":22,"roles":179,"affiliations":181,"properties":190},"9ca832d3-07fa-4707-847e-a913ba97a56d",[180],"AUTHOR",[182],{"id":183,"sortIndex":23,"affiliation":184,"properties":22},"5fd157f0-d855-4399-b273-5fd47a7825f8",{"id":183,"createTime":22,"updateTime":22,"relativeEntities":185,"slug":22,"properties":186,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":189,"statistic":22},[],{"title":187},{"VI":188},"Department of Biological Sciences, University of Salford, Salford, UK",[],{"title":191},{"VI":192},"David H. 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In mammals and birds, the OAS functions in the interferon system but it is also present in an active form in sponges, which are devoid of the interferon system. In view of these observations, we have pursued the idea that OAS genes could be present in other metazoans and in unicellular organisms as well. We have identified a number of OAS1 genes in annelids, mollusks, a cnidarian, chordates, and unicellular eukaryotes and also found a family of proteins in bacteria that contains the five OAS-specific motifs. This indicates a specific relationship to OAS. The wide distribution of the OAS genes has made it possible to suggest how the OAS1 gene could have evolved from a common ancestor to choanoflagellates and metazoans. Furthermore, we suggest that the OASL may have evolved from an ancestor of cartilaginous fishes, and that the OAS2 and the OAS3 genes evolved from a mammalian ancestor. OAS proteins function in the interferon system in mammals. This system is only found in jawed vertebrates. We therefore suggest that the original function of OAS may differ from its function in the interferon system, and that this original function of OAS is preserved even in OAS genes that code for proteins, which do not have 2′-5′-oligoadenylate synthetase activity.",{"EN":309},"Evolution of the 2′-5′-Oligoadenylate Synthetase Family in Eukaryotes and Bacteria",{"VOID":311},"[]",{"VOID":313},"Bandyopadhyay S, Ghosh A, Sarkar SN, Sen GC (1998) Production and purification of recombinant 2′-5′ oligoadenylate synthetase and its mutants using the baculovirus system. Biochemistry 37:3824–3830\nBeck G, Habicht GS (1991) Primitive cytokines: harbingers of vertebrate defense. Immunol Today 12:180–183\nBeck G, Habicht GS (1996) Characterization of an IL-6-like molecule from an echinoderm (Asterias forbesi). Cytokine 8:507–512\nBeitz E (2000) TEXshade: shading and labeling of multiple sequence alignments using LATEX2 epsilon. Bioinformatics 16:135–139\nCayley PJ, White RF, Antoniw JF, Walesby NJ, Kerr IM (1982) Distribution of the ppp(A2’p)nA-binding protein and interferon-related enzymes in animals, plants, and lower organisms. Biochem Biophys Res Commun 108:1243–1250\nEskildsen S, Justesen J, Schierup MH, Hartmann R (2003) Characterization of the 2′-5′-oligoadenylate synthetase ubiquitin-like family. Nucleic Acids Res 31:3166–3173\nFerbus D, Justesen J, Besancon F, Thang MN (1981) The 2′5′ oligoadenylate synthetase has a multifunctional 2′5′ nucleotidyl-transferase activity. Biochem Biophys Res Commun 100:847–856\nGhosh A, Desai SY, Sarkar SN, Ramaraj P, Ghosh SK, Bandyopadhyay S, Sen GC (1997a) Effects of mutating specific residues present near the amino terminus of 2′-5′-oligoadenylate synthetase. J Biol Chem 272:15452–15458\nGhosh A, Sarkar SN, Guo W, Bandyopadhyay S, Sen GC (1997b) Enzymatic activity of 2′-5′-oligoadenylate synthetase is impaired by specific mutations that affect oligomerization of the protein. J Biol Chem 272:33220–33226\nGrebenjuk VA, Kuusksalu A, Kelve M, Schutze J, Schroder HC, Muller WE (2002) Induction of (2′-5′)oligoadenylate synthetase in the marine sponges Suberites domuncula and Geodia cydonium by the bacterial endotoxin lipopolysaccharide. Eur J Biochem 269:1382–1392\nHartmann R, Justesen J, Sarkar SN, Sen GC, Yee VC (2003) Crystal structure of the 2′-specific and double-stranded RNA-activated interferon-induced antiviral protein 2′-5′-oligoadenylate synthetase. Mol Cell 12:1173–1185\nHovanessian AG, Justesen J (2007) The human 2′-5′oligoadenylate synthetase family: unique interferon-inducible enzymes catalyzing 2′-5′ instead of 3′-5′ phosphodiester bond formation. Biochimie 89:779–788\nHughes TK Jr, Smith EM, Chin R, Cadet P, Sinisterra J, Leung MK, Shipp MA, Scharrer B, Stefano GB (1990) Interaction of immunoactive monokines (interleukin 1 and tumor necrosis factor) in the bivalve mollusc Mytilus edulis. Proc Natl Acad Sci USA 87:4426–4429\nJustesen J, Hartmann R, Kjeldgaard NO (2000) Gene structure and function of the 2′-5′-oligoadenylate synthetase family. Cell Mol Life Sci 57:1593–1612\nKaiser P, Rothwell L, Avery S, Balu S (2004) Evolution of the interleukins. Dev Comp Immunol 28:375–394\nKon N, Suhadolnik RJ (1996) Identification of the ATP binding domain of recombinant human 40-kDa 2′, 5′-oligoadenylate synthetase by photoaffinity labeling with 8-azido-[alpha-32P]ATP. J Biol Chem 271:19983–19990\nKumar S, Mitnik C, Valente G, Floyd-Smith G (2000) Expansion and molecular evolution of the interferon-induced 2′-5′ oligoadenylate synthetase gene family. Mol Biol Evol 17:738–750\nKuusksalu A, Pihlak A, Muller WE, Kelve M (1995) The (2′-5′) oligoadenylate synthetase is present in the lowest multicellular organisms, the marine sponges. Demonstration of the existence and identification of its reaction products. Eur J Biochem 232:351–357\nLane KT, Beese LS (2006) Thematic review series: lipid posttranslational modifications. Structural biology of protein farnesyltransferase and geranylgeranyltransferase type I. J Lipid Res 47:681–699\nMartin G, Keller W (2007) RNA-specific ribonucleotidyl transferases. RNA 13:1834–1849\nPari M, Kuusksalu A, Lopp A, Reintamm T, Justesen J, Kelve M (2007) Expression and characterization of recombinant 2′, 5′-oligoadenylate synthetase from the marine sponge Geodia cydonium. Febs J 274:3462–3474\nPerelygin AA, Zharkikh AA, Scherbik SV, Brinton MA (2006) The mammalian 2′-5′ oligoadenylate synthetase gene family: evidence for concerted evolution of paralogous OAS1 genes in Rodentia and Artiodactyla. J Mol Evol 63:562–576\nRaftos DA, Cooper EL, Habicht GS, Beck G (1991) Invertebrate cytokines: tunicate cell proliferation stimulated by an interleukin 1-like molecule. Proc Natl Acad Sci USA 88:9518–9522\nRogozin IB, Aravind L, Koonin EV (2003) Differential action of natural selection on the N and C-terminal domains of 2′-5′ oligoadenylate synthetases and the potential nuclease function of the C-terminal domain. J Mol Biol 326:1449–1461\nSadler AJ, Williams BR (2008) Interferon-inducible antiviral effectors. Nat Rev Immunol 8:559–568\nSalzberg S, Hyman T, Turm H, Kinar Y, Schwartz Y, Nir U, Lejbkowicz F, Huberman E (1997) Ectopic expression of 2-5A synthetase in myeloid cells induces growth arrest and facilitates the appearance of a myeloid differentiation marker. Cancer Res 57:2732–2740\nSamuel CE (2001) Antiviral actions of interferons. Clin Microbiol Rev 14:778–809 table of contents\nSarkar SN, Ghosh A, Wang HW, Sung SS, Sen GC (1999) The nature of the catalytic domain of 2′-5′-oligoadenylate synthetases. J Biol Chem 274:25535–25542\nSchroder HC, Natalio F, Wiens M, Tahir MN, Shukoor MI, Tremel W, Belikov SI, Krasko A, Muller WE (2008) The 2′-5′-oligoadenylate synthetase in the lowest metazoa: isolation, cloning, expression and functional activity in the sponge Lubomirskia baicalensis. Mol Immunol 45:945–953\nSeth M, Thurlow DL, Hou YM (2002) Poly(C) synthesis by class I and class II CCA-adding enzymes. Biochemistry 41:4521–4532\nTatsumi R, Sekiya S, Nakanishi R, Mizutani M, Kojima S, Sokawa Y (2003) Function of ubiquitin-like domain of chicken 2′-5′-oligoadenylate synthetase in conformational stability. J Interferon Cytokine Res 23:667–676\nTorralba S, Sojat J, Hartmann R (2008) 2′-5′ Oligoadenylate synthetase shares active site architecture with the archaeal CCA-adding enzyme. Cell Mol Life Sci 65:2613–2620\nVenkatesh B, Kirkness EF, Loh YH, Halpern AL, Lee AP, Johnson J, Dandona N, Viswanathan LD, Tay A, Venter JC, Strausberg RL, Brenner S (2007) Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genome. PLoS Biol 5:e101\nWiens M, Kuusksalu A, Kelve M, Muller WE (1999) Origin of the interferon-inducible (2′-5′) oligoadenylate synthetases: cloning of the (2′-5′) oligoadenylate synthetase from the marine sponge Geodia cydonium. FEBS Lett 462:12–18\nWoese C (1998) The universal ancestor. Proc Natl Acad Sci USA 95:6854–6859\nYue D, Maizels N, Weiner AM (1996) CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA 2:895–908\nZimmer SL, Fei Z, Stern DB (2008) Genome-based analysis of Chlamydomonas reinhardtii exoribonucleases and poly(A) polymerases predicts unexpected organellar and exosomal features. 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is shown that the mRNA's of three periodic proteins, collagen, keratin and freezing point depressing glycoproteins show a marked degree of self-complementarity. The possible origin of this self-complementarity is discussed.",{"EN":498},"Self-complementarity of messenger RNA's of periodic proteins",{"VOID":500},"[\"13620023208325688006\"]",{"VOID":502},"Ambler, R. P.: FEBS Letters18, 351 (1971)\nDayhoff, M. O.: Atlas of protein sequence and structure, Vol. 5. National Biomedical Research Foundation. Washington, D.C.: Georgetown University Medical Center 1972\nDe Vries, A. L., Vanderheede, J., Feeney, R. E.: J. Biol. Chem.246, 305 (1971)\nElleman, T. C.: Nature New Biol. (Lond.)234, 148 (1971)\nGibbs, A. J., McIntyre, G. A.: Eur. J. Biochem.16, 1 (1970)\nLindley, H., Elleman, T. C.: Biochem. J.128, 859 (1972)\nMin Jou, W., Haegeman, G., Ysebaert, M., Fiers, W.: Nature (Lond.)237, 82 (1972)\nSobell, H. M.: Advances in Genetics17 (in press)\nSuzuki, Y., Brown, D. D.: J. mol. Biol.63, 409 (1972)\nYčas, M.: J. mol. 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sites of seven tRNA genes (Arg-2, Lys-2, Ser-2b, Ser-7, Thr-3, Thr-4, Val-3b) were studied by in situ hybridization.125I-labeled tRNA probes fromDrosophila melanogaster were hybridized to spreads of polytene chromosomes prepared from fourDrosophila species representing different evolutionary lineages (D. melanogaster, Drosophila hydei, Drosophila pseudoobscura, andDrosophila virilis). Most tRNA loci occurred on homologous chromosomal elements of all four species. In some cases the number of hybridization sites within an element varied and sites on nonhomologous elements were found. It was observed that both tRNA\n                  2\n                  Arg\n                 and tRNA\n                  2\n                  Lys\n                 hybridized to the same site on homologous elements in several species. These data suggest a limited amount of exchange among different linkage groups during the evolution ofDrosophila species.",{"EN":594},"Conservatism of sites of tRNA loci among the linkage groups of severalDrosophila species",{"VOID":596},"[\"14951457538816413686\"]",{"VOID":598},"Alexander ML (1976) The genetics ofDrosophila virilis. In: Ashburner M, Novitski E (eds) The genetics and biology ofDrosophila, vol 1c. Academic Press, London, pp 1365–1427\nAlonso C, Berendes HD (1975) The location of 5S (ribosomal) RNA genes inDrosophila hydei. Chromosoma 51:347–356\nAnaniev EV, Barsky VE (1982) A photographic map ofDrosophila hydei polytene chromosomes. Chromosoma 87:239–245\nBerendes HD (1963) The salivary gland chromosomes ofDrosophila hydei Sturtevant. Chromosoma 14:195–206\nBrock HW, Roberts DB (1983) Location of the LSP-1 genes inDrosophila species by in situ hybridization. Genetics 103:75–92\nCohen M Jr (1976) Evolution of 5S ribosomal RNA genes in the chromosomes of thevirilis group ofDrosophila. Chromosoma 55:359–371\nCommerford SL (1971) Iodination of nucleic acids in vitro. Biochemistry 10:1993–1999\nCribbs DL, Leung J, Hunter Newton C, Hayashi S, Miller RC Jr, Tener GM (1987) Extensive microheterogeneity of serine tRNA genes fromDrosophila melanogaster. J Mol Biol 197:397–404\nDunn R, Hayashi S, Gillam IC, Delaney AD, Tener GM, Grigliatti TA, Kaufman TC, Suzuki DT (1979) Genes coding for valine transfer ribonucleic acid-3b inDrosophila melanogaster. J Mol Biol 128:277–287\nGelbart WM, Irish VF, St Johnston RD, Hoffmann FM, Blackman RK, Segal D, Posakony LM, Grimaila R (1985) The decapentaplegic gene complex inDrosophila melanogaster. Cold Spring Harbor Symp Quant Biol 50:119–125\nGubenko IS, Evgen'ev MB (1984), Cytological and linkage maps ofDrosophila virilis chromosomes. Genetica 65:127–139\nHayashi S, Gillam IC, Delaney AD, Dunn R, Tener GM, Grigliatti TA, Suzuki DT (1980) Hybridization of tRNAs ofDrosophila melanogaster to polytene chromosomes. Chromosoma 76:65–84\nHayashi S, Addison WR, Gillam IC, Grigliatti TA, Tener GM (1981) Hybridization of tRNAs ofDrosophila melanogaster to the region of the 5S RNA genes of the polytene chromosomes. Chromosoma 82:385–397\nHayashi S, Gillam IC, Grigliatti TA, Tener GM (1982) Localization of tRNA genes ofDrosophila melanogaster by in situ hybridization. Chromosoma 86:279–292\nHess O (1976) Genetics ofDrosophila hydei Sturtevant. In: Ashburner M, Novitski E (eds) The genetics and biology ofDrosophila, vol 1c. Academic Press, London, pp 1343–1363\nHosbach HA, Silberklang M, McCarthy BJ (1980) Evolution of aD. melanogaster glutamate tRNA gene cluster. Cell 21:169–179\nInouye S, Saigo K, Yamada K, Kuchino Y (1986) Identification and nucleotide sequence determination of a potential primer tRNA for reverse transcription of aDrosophila retrotransposon, 297. Nucleic Acids Res 14:3031–3043\nKastritsis CD, Crumpacker DW (1966) Gene arrangements in the third chromosome ofDrosophila pseudoobscura. J. Hered 57:150–158\nLancefield DE (1922) Linkage relations of the sex-linked characters inDrosophila obscura. Genetics 7:335–384\nLefevre G Jr (1976) A photographic representation and interpretation of the polytene chromosomes ofDrosophila melanogaster salivary glands. In: Ashburner M, Novitski E (eds) The genetics and biology ofDrosophila, vol 1a. Academic Press, London, pp 31–66\nLoukas M, Kafatos FC (1986) The actin loci in the genusDrosophila: establishment of chromosomal homologies among distantly related species by in situ hybridization. Chromosoma 94:297–308\nMuller HJ (1940) Bearings ofDrosophila work on systematics. In: Huxley J (ed) The new systematics. Oxford University Press, Oxford, pp 185–268\nO'Donnell J, Mandel HC, Krauss M, Sofer W (1977) Genetic and cytogenetic analysis of theADH region inDrosophila melanogaster. Genetics 86:553–566\nPatterson JT, Stone WS (1952) Evolution in the genusDrosophila. Macmillan Company, New York\nRyseck R-P, Walldorf U, Hoffmann T, Hovemann B (1987) Heat shock loci 93D ofDrosophila melanogaster and 48B ofDrosophila hydei exhibit a common structural and transcriptional pattern. Nucleic Acids Res 15:3317–3333\nSchaeffer SW, Aquadro CF (1987) Nucleotide sequence of theAdh gene region ofDrosophila pseudoobscura: evolutionary change and evidence for an ancient gene duplication. Genetics 117:61–73\nSharp S, DeFranco D, Silberklang M, Hosbach HA, Schmidt T, Kubli E, Gergen JP, Wensink PC, Soll D (1981) The initiator tRNA genes ofDrosophila melanogaster: evidence for a tRNA pseudogene. Nucleic Acids Res 9:5867–5882\nSteinemann M (1982) Analysis of chromosomal homologies between two species of the subgenusSophophora: D. miranda andD. melanogaster using cloned DNA segments. Chromosoma 87:77–88\nStocker AJ, Kastritsis CD (1972) Developmental studies inDrosophila. III. The puffing patterns of the salivary gland chromosomes ofD. pseudoobscura. Chromosoma 37:139–176\nSturtevant AH, Novitski E (1941) The homologies of the chromosome elements in the genusDrosophila. Genetics 26:517–541\nSuter B, Kubli E (1988) tRNATyr genes ofDrosophila melanogaster: expression of single-copy genes studied by S1 mapping. Mol Cell Biol 8:3322–3331\nThrockmorton LH (1975) The phylogeny, ecology and geography ofDrosophila. In: King RC (ed) Handbook of genetics, vol 3. Plenum, New York, pp 421–469\nWeber L, Berger E (1976) Base sequence complexity of the stable RNA species ofDrosophila melanogaster. Biochemistry 15:5511–5519\nWhiting JH Jr, Pliley MD, Farmer JL, Jeffery DE (1989) In situ hybridization analysis of chromosomal homologies inDrosophila melanogaster andDrosophila virilis. Genetics 122:99–109\nWimber DE, Steffensen DM (1970) Localization of 5S RNA genes onDrosophila chromosomes by RNA-DNA hybridization. Science 170:639–641\nYen PH, Davidson N (1980) The gross anatomy of a tRNA gene cluster at region 42A of theD. melanogaster chromosome. Cell 22:137–148\nYuki S, Inouye S, Ishimaru S, Saigo K (1986) Nucleotide sequence characterization of aDrosophila retrotransposon, 412. Eur J Biochem 158:403–410",{"VOID":600},"10.1007\u002FBF02099944","2024-06-26T20:48:56.355+00:00","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002FBF02099944",[604,619,634],{"id":605,"sortIndex":23,"researcher":22,"roles":606,"affiliations":607,"properties":616},"656befe0-71df-4701-ac41-389b83ae41a3",[180],[608],{"id":609,"sortIndex":23,"affiliation":610,"properties":22},"b18fb3c9-00c6-47e8-83bc-946e68be8402",{"id":609,"createTime":22,"updateTime":22,"relativeEntities":611,"slug":22,"properties":612,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":615,"statistic":22},[],{"title":613},{"VI":614},"Department of Biology, Bucknell University, Lewisburg, USA",[],{"title":617},{"VI":618},"John Tonzetich",{"id":620,"sortIndex":102,"researcher":22,"roles":621,"affiliations":622,"properties":631},"89a6e94b-3808-4c20-9123-ec4aecd9d3f3",[180],[623],{"id":624,"sortIndex":23,"affiliation":625,"properties":22},"183cd1ab-5e2a-40ab-95a5-348c885f1e97",{"id":624,"createTime":22,"updateTime":22,"relativeEntities":626,"slug":22,"properties":627,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":630,"statistic":22},[],{"title":628},{"VI":629},"Department of Biochemistry, University of British Columbia, Vancouver, Canada",[],{"title":632},{"VI":633},"Shizu Hayashi",{"id":635,"sortIndex":208,"researcher":22,"roles":636,"affiliations":637,"properties":646},"68ab459c-4aaa-4c2d-91ec-bba516b553f9",[180],[638],{"id":639,"sortIndex":23,"affiliation":640,"properties":22},"98ffdd2a-030d-40e6-8726-4f13a1583873",{"id":639,"createTime":22,"updateTime":22,"relativeEntities":641,"slug":22,"properties":642,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":645,"statistic":22},[],{"title":643},{"VI":644},"Department of Zoology, University of British Columbia, Vancouver, Canada",[],{"title":647},{"VI":648},"T. 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Several additional and independent observations suggest that these grouping have evolutionary significance, and that successive waves of fixation of new variants occur during rodent lineage history. We have reason to believe that, in a genome, the founder sequences of different families of retroposons are in competition with regard to the amplification\u002Ffixation process.",{"EN":721},"Successive waves of fixation of B1 variants in rodent lineage history",{"VOID":723},"[\"4146886557307079972\"]",{"VOID":725},"Benzecri JP (1969) Statistical analysis as a tool to make patterns emerge from data. In: Watanabe S (ed) Methodologies of pattern recognition. Academic Press, New York, p 35\nBilofsky HS, Burks C, Fickett JW, Goad WB, Lewitter FI, Rindone WP, Swindell CD, Tang C-S (1986) The GenBank genetic sequence data bank. Nucleic Acids Res 14:1–14\nBird AP (1980) DNA methylation and the frequency of CpG in animal DNA. Nucleic Acids Res 8:1499–1504\nBritten RJ, Baron WF, Stout DB, Davidson EH (1988) Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci USA 85:4770–4774\nGoggins LW, Vass JK, Stinson MA, Lanyon WG, Paul J (1982) A B1 repetitive sequence near the mouse β-major globin gene. Gene 17:113–116\nDaniels GR, Deininger PL (1985) Integration site preferences of the Alu family and similar repetitive DNA sequences. Nucleic Acids Res 13:8939–8954\nGouy M, Milleret F, Mugnier C, Jacobzone M, Gautier C (1984) ACNUC: a nucleic acid sequence data base and analysis system. Nucleic Acids Res 12:121–127\nGouy M, Gautier C, Milleret F (1985) System analysis and nucleic acid sequence banks. Biochimie 67:433–436\nHaynes SR, Jelinek WR (1981) Low molecular weight RNAs transcribed in vitro by RNA polymerase III from Alu-type dispersed repeats in Chinese hamster DNA are also found in vivo. Proc Natl Acad Sci USA 78:6130–6134\nHiggins DG, Gouy M (1987) Interfacing similarity search software with the sequence retrieval system ACNUC. CABIOS 3:239–241\nJurka J, Smith T (1988) A fundamental division in the Alu family of repeated sequences. Proc Natl Acad Sci USA 85:4775–4778\nKalb VF, Glasser S, King D, Lingrel JB (1983) A cluster of repetitive elements within a 700 base pair region in the mouse genome. Nucleic Acids Res 11:2177–2184\nKoop BF, Miyamoto MM, Embury JE, Goodman M, Czelusniak J, Slightom JL (1986) Nucleotide sequences and evolution of the orangutan epsilon globin gene region and surrounding Alu repeats. J Mol Evol 24:94–102\nKramerov DA, Grigoryan AA, Ryskov P, Georgiev GP (1979) Long double-stranded sequences (ds RNA-B) of nuclear pre-mRNA consist of a few highly abundant classes of sequences: evidence from DNA cloning experiments. Nucleic Acids Res 6:697–713\nKrayev AS, Kramerov DA, Skryabin KG, Ryskov AP, Bayev AA, Georgiev GP (1980) The nucleotide sequence of the ubiquitous repetitive DNA sequence B1 complementary to the most abundant class of fold-back RNA. Nucleic Acids Res 8:1201–1215\nKrayev AS, Markusheva TV, Kramerov DA, Ryskov AP, Skryabin KG, Bayev AA, Georgiev GP (1982) Ubiquitous transposon-like repeats B1 and B2 of the mouse genome: B2 sequencing. Nucleic Acids Res 10:7461–7475\nMannella CA, Frank J, Delihas N (1987) Interrelatedness of 5S RNA sequences investigated by correspondence analysis. J Mol Evol 24:228–235\nQuentin Y (1988) The Alu family developed through sucessive waves of fixation closely connected with primate lineage history. J Mol Evol 27:194–202\nRogers J (1985) The origin and evolution of retroposons. Int Rev Cytol 76:67–112\nSawada I, Willard C, Shen C-KJ, Chapman B, Wilson AC, Schmid CW (1985) Evolution of Alu family repeats since the divergence of human and chimpanzee. J Mol Evol 22:316–322\nSchmid CW, Jelinek WR (1982) The Alu family of dispersed repetitive sequences. Science 216:1065–1070\nSlagel V, Flemington E, Trina-Dorge V, Bradshaw H, Deininger P (1987) Clustering and subfamily relationships of the Alu family in the human genome. Mol Biol Evol 4:19–24\nSmith TF, Waterman NS (1981) Identification of common molecular subsequences. J Mol Biol 147:195–197\nUllu E, Tschudi C (1984) Alu sequences are processed 7SL RNA genes. Nature 312:171–172\nUllu E, Weiner AM (1985) Upstream sequences modulate the internal promoter of the human 7SL RNA gene. Nature 318:371–374\nWeiner AM, Deininger PL, Efstradiatis A (1986) Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem 55:631–661\nWillard C, Nguyen HT, Schmid CW (1987) Existence of at least three distinct Alu subfamilies. J Mol Evol 26:180–186\nYoung PR, Scott RW, Hamer DH, Tilghman SM (1982) Construction and expression in vivo of an internally deleted mouse α-fetoproteine gene: presenceof a transcribed Alu-like repeat within the first intervening sequence. Nucleic Acids Res 10:3099–3116",{"VOID":727},"10.1007\u002FBF02103425","2024-05-16T13:28:58.976+00:00","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002FBF02103425",[731],{"id":732,"sortIndex":23,"researcher":22,"roles":733,"affiliations":734,"properties":743},"627aad4e-053a-4c83-92d4-b520644b774a",[180],[735],{"id":736,"sortIndex":23,"affiliation":737,"properties":22},"26a976e5-ab13-49ae-b47c-cf203e896723",{"id":736,"createTime":22,"updateTime":22,"relativeEntities":738,"slug":22,"properties":739,"entityType":22,"verifyStatus":22,"verifyTime":22,"verifyNote":22,"languages":22,"translateLanguages":22,"viewCount":22,"url":22,"parentIds":742,"statistic":22},[],{"title":740},{"VI":741},"Laboratoire de Biométrie, Génétiquet et Biologie des Populations, URA CNRS N 0066, Université Claude Bernard, Villeurbanne Cedex, France",[],{"title":744},{"VI":745},"Y. 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In evaluating the extent to which the maximum likelihood tree is a significantly better representation of the true tree, it is important to estimate the variance of the difference between log likelihood of different tree topologies. Bootstrap resampling can be used for this purpose (Hasegawa et al. 1988; Hasegawa and Kishino 1989), but it imposes a great computation burden. To overcome this difficulty, we developed a new method for estimating the variance by expressing it explicitly. The method was applied to DNA sequence data from primates in order to evaluate the maximum likelihood branching order among Hominoidea. It was shown that, although the orangutan is convincingly placed as an outgroup of a human and African apes clade, the branching order among human, chimpanzee, and gorilla cannot be determined confidently from the DNA sequence data presently available when the evolutionary rate constancy is not assumed.",{"EN":818},"Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in 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J Mol Evol 20:2–15","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002FBF02101980",{"doi":1156},"10.1007\u002FBF02101980",{"id":1158,"text":1159,"url":1160,"identifiers":1161},"46bcaebe-6e81-4a67-931e-21c7796bd044","Sibley CG, Ahlquist JE (1987) DNA hybridization evidence of hominoid phylogeny: results from an expanded data set. J Mol Evol 26:99–121","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002FBF02111285",{"doi":1162},"10.1007\u002FBF02111285",{"id":22,"text":1164,"url":22,"identifiers":1165},"Takahata N, Nei M (1985) Gene genealogy and variance of interpopulational nucleotide differences. Genetics 110:325–344",{},{"id":948,"text":1167,"url":950,"identifiers":1168},"Templeton AR (1985) The phylogeny of the hominoid primates: a statistical analysis of the DNA-DNA hybridization data. Mol Biol Evol 2:420–433",{"doi":952},{"id":948,"text":1170,"url":950,"identifiers":1171},"Templeton AR (1986) Further comments on the statistical analysis of DNA-DNA hybridization data. Mol Biol Evol 3:290–295",{"doi":952},{"id":948,"text":1173,"url":950,"identifiers":1174},"Wilson AC, Carlson SS, White TJ (1977) Biochemical evolution. Annu Rev Biochem 46:573–639",{"doi":952},{"id":1176,"createTime":1177,"updateTime":1178,"relativeEntities":1179,"slug":1180,"properties":1181,"entityType":171,"verifyStatus":172,"verifyTime":1190,"verifyNote":174,"languages":22,"translateLanguages":22,"viewCount":23,"primaryUrl":1191,"fullTextUrl":1192,"authors":1193,"publicationType":234,"publisherRelationship":1209,"citationCount":116,"citationInfo":1267,"publishDate":1271,"publishYear":1268,"citationAnalyzeStatus":943,"lastCitationAnalyze":1178,"indexDatabases":1272,"openAccess":22,"references":1273,"isForceReanalyzing":298},"68a3e7bf-3077-4d5f-8024-28003af9a0de","2023-12-09T21:28:00.542+00:00","2026-07-26T20:40:59.914+00:00",[],"Computational-Prediction-of-Genomic-Functional-Cores-Specific-to-Different-Microbes",{"abstract":1182,"title":1184,"gsPaper":1186,"doi":1188},{"EN":1183},"Computational and experimental attempts tried to characterize a universial core of genes representing the minimal set of functional needs for an organism. Based on the increasing number of available complete genomes, comparative genomics has concluded that the universal core contains < 50 genes. In contrast, experiments suggest a much larger set of essential genes (certainly more than several hundreds, even under the most restrictive hypotheses) that is dependent on the biological complexity and environmental specificity of the organism. Highly biased genes, which are generally also the most expressed in translationally biased organisms, tend to be over represented in the class of genes deemed to be essential for any given bacterial species. This association is far from perfect; nevertheless, it allows us to propose a new computational method to detect, to a certain extent, ubiquitous genes, nonorthologous genes, environment-specific genes, genes involved in the stress response, and genes with no identified function but highly likely to be essential for the cell. Most of these groups of genes cannot be identified with previously attempted computational and experimental approaches. The large variety of life-styles and the unusually detectable functional signals characterizing translationally biased organisms suggest using them as reference organisms to infer essentiality in other microbial species. The case of small parasitic genomes is discussed. Data issued by the analysis are compared with previous computational and experimental studies. Results are discussed both on methodological and biological grounds.",{"EN":1185},"Computational Prediction of Genomic Functional Cores Specific to Different 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J Mol Evol 39:306–314",{"doi":1812},"10.1007\u002FBF00160154",{"id":1814,"createTime":1815,"updateTime":1816,"relativeEntities":1817,"slug":1818,"properties":1819,"entityType":171,"verifyStatus":172,"verifyTime":1830,"verifyNote":174,"languages":22,"translateLanguages":22,"viewCount":23,"primaryUrl":1831,"fullTextUrl":22,"authors":1832,"publicationType":234,"publisherRelationship":1946,"citationCount":107,"citationInfo":2002,"publishDate":2005,"publishYear":2003,"citationAnalyzeStatus":943,"lastCitationAnalyze":2006,"indexDatabases":2007,"openAccess":22,"references":22,"isForceReanalyzing":298},"16eefc10-6248-483d-8107-9febe1ceb96b","2023-12-24T11:33:04.331+00:00","2026-07-26T10:05:07.539+00:00",[],"Evolutionary-History-of-TOPIIA-Topoisomerases-in-Animals",{"abstract":1820,"title":1822,"gsPaper":1824,"references":1826,"doi":1828},{"EN":1821},"TOPIIA topoisomerases are required for the regulation of DNA topology by DNA cleavage and re-ligation and are important targets of antibiotic and anticancer agents. Humans possess two TOPIIA paralogue genes (TOP2A and TOP2B) with high sequence and structural similarity but distinct cellular functions. Despite their functional and clinical relevance, the evolutionary history of TOPIIA is still poorly understood. Here we show that TOPIIA is highly conserved in Metazoa. We also found that TOPIIA paralogues from jawed and jawless vertebrates had different origins related with tetraploidization events. After duplication, TOP2B evolved under a stronger purifying selection than TOP2A, perhaps promoted by the more specialized role of TOP2B in postmitotic cells. We also detected genetic signatures of positive selection in the highly variable C-terminal domain (CTD), possibly associated with adaptation to cellular interactions. By comparing TOPIIA from modern and archaic humans, we found two amino acid substitutions in the TOP2A CTD, suggesting that TOP2A may have contributed to the evolution of present-day humans, as proposed for other cell cycle-related genes. Finally, we identified six residues conferring resistance to chemotherapy differing between TOP2A and TOP2B. These six residues could be targets for the development of TOP2A-specific inhibitors that would avoid the side effects caused by inhibiting TOP2B. Altogether, our findings clarify the origin, diversification and selection pressures governing the evolution of animal TOPIIA.",{"EN":1823},"Evolutionary History of TOPIIA Topoisomerases in Animals",{"VOID":1825},"[\"4735271726088550467\"]",{"VOID":1827},"Aase-Remedios ME, Ferrier DEK (2021) Improved understanding of the role of gene and genome duplications in chordate evolution with new genome and transcriptome sequences. 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J Mol Evol 53:436–446\nVan de Peer Y, Maere S, Meyer A (2009) The evolutionary significance of ancient genome duplications. Nat Rev Genet 10:725–732\nVassetzky YS, Alghisi GC, Gasser SM (1995) DNA topoisomerase II mutations and resistance to anti-tumor drugs. BioEssays 17:767–774\nWang JC (1996) DNA topoisomerases. Annu Rev Biochem 65:635–692\nWang JC (2002) Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol 3:430–440\nWatterson G (1975) On the number of segregating sites in genetical models without recombination. Theor Popul Biol 7:256–276\nWigley DB, Davies GJ, Dodson EJ, Maxwell A, Dodson G (1991) Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 351:624–629\nWu C-C et al (2011) Structural basis of type II topoisomerase inhibition by the anticancer drug etoposide. Science 333:459–462\nWu C-C, Li Y-C, Wang Y-R, Li T-K, Chan N-L (2013) On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs. Nucleic Acids Res 41:10630–10640\nXia W et al (2019) Mutations in TOP 2B cause autosomal-dominant hereditary hearing loss via inhibition of the PI 3K-Akt signalling pathway. FEBS Lett 593:2008–2018\nYang X, Li W, Prescott ED, Burden SJ, Wang JC (2000) DNA topoisomerase IIβ and neural development. Science 287:131–134\nYe J et al (2010) TRF2 and Apollo cooperate with topoisomerase 2α to protect human telomeres from replicative damage. 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The effective number of codons (ENC) values ranged from 36 to 47.8, indicating a high-to-moderate codon usage bias. The highest IBV codon adaptation index (CAI) value was 0.7, indicating a distant virus versus host synonymous codons usage. The ENC × GC3 % curve indicates that both mutational pressure and natural selection are the driving forces on codon usage pattern in S1. 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Genetics 129:897–907\nCavanagh D (2007) Coronavirus avian infectious bronchitis virus. Vet Res 38:281–297\nChacon JL, Rodrigues JN, Assayag Junior MS, Peloso C, Pedroso AC, Ferreira AJ (2011) Epidemiological survey and molecular characterization of avian infectious bronchitis virus in Brazil between 2003 and 2009. Avian Pathol 40:153–162\nComeron JM, Aguadé M (1998) An evaluation of measures of synonymous codon usage bias. J Mol Evol 47:268–274\nDe Wit JJ, Cook JK, Van der Heijden HM (2011) Infectious bronchitis virus variants: a review of the history, current situation and control measures. Avian Pathol 40:223–235\nGu W, Zhou T, Ma J, Sun X, Lu Z (2004) Analysis of synonymous codon usage in SARS Coronavirus and other viruses in the Nidovirales. Virus Res 101:155–161\nJones RC (2010) Viral respiratory diseases (ILT, aMPV infections, IB): are they ever under control? Br Poul Sci 51:1–11\nMoore KM, Jackwood MW, Hilt DA (1997) Identification of amino acids involved in a serotype and neutralization specific epitope within the S1 subunit of avian infectious bronchitis virus. Arch Virol 142:2249–2256\nRao Y, Wu G, Wang Z, Chai X, Nie Q, Zhang X (2011) Mutation bias is the driving force of codon usage in the Gallus gallus genome. DNA Res 18:499–512\nRidley M (2004) Evolution, 3rd edn. Blackwell Publishing, Oxford\nSharp PM, Li W (1987) The codon adaptation index—a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 15:1281–1295\nSwofford DL (2000) PAUP*. Phylogenetic analysis using parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland\nTamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739\nThiel V (2005) Coronaviruses molecular and cellular biology. Caster Academic Press, Norfolk\nVan Marle G, Luytjes W, Van der Most RG, Van der Straaten T, Spaan WJ (1995) Regulation of coronavirus mRNA transcription. Virology 69:7851–7856\nVetrivel U, Arunkumar V, Dorairaj S (2007) ACUA: a software tool for automated codon usage analysis. Bioinformation 2:62–63\nVillarreal LY, Sandri TL, Souza SP, Richtzenhain LJ, de Wit JJ, Brandao PE (2010) Molecular epidemiology of avian infectious bronchitis in Brazil from 2007 to 2008 in breeders, broilers, and layers. Avian Dis 54:894–898\nWinter C, Herrler G, Neumann U (2008) Infection of the tracheal epithelium by infectious bronchitis virus is sialic acid dependent. Microbes Infect 10:367–373\nWoo PC, Wong BH, Huang Y, Lau SK, Yuen KY (2007) Cytosine deamination and selection of CpG suppressed clones are the two major independent biological forces that shape codon usage bias in coronaviruses. Virology 369:431–442\nWright F (1990) The “effective number of codons” used in a gene. Gene 87:23–29\nYang A, Wei L, Zhao W, Xu Y, Rao Z (2009) Expression, crystallization and preliminary X-ray diffraction analysis of the N-terminal domain of nsp2 from avian infectious bronchitis virus. Acta Crystallogr, Sect F 65:788–790\nZhou J, Gao Z, Zhang J, Chen H, Pejsak Z, Ma L, Ding Y, Liu Y (2012) Comparative the codon usage between the three main viruses in pestivirus genus and their natural susceptible livestock. 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