Список использованной литературы
Общий
Brockman, J., The Edge, Annual Question 2005: What do you believe is true even though you cannot prove it?
Blaser, M.J., Missing Microbes (Oneworld Publications, 2014).
Chin, J. (Ed.), Control of Communicable Diseases Manual, American Public Health Association, 2000.
Crawford, D.H., Deadly Companions: How Microbes Shaped Our History (Oxford University Press, New York, 2007).
Domingo, E., Parish, C., and Holland J. (Eds.), Origin and Evolution of Viruses (Academic Press, London, 2008), p. 477.
Dyson, F.J., The Sun, the Genome and the Internet (Oxford University Press, New York, 1999).
Dyson, F.J., The Scientist as Rebel, The New York Review of Books, 2006.
Dyson, F.J., Origins of Life (Cambridge University Press, 1986).
Eigen, M., From Strange Simplicity to Complex Familiarity, A Treatise on Matter, Information, Life andThought (Oxford University Press, 2013).
Frebel, A., Auf der Suche nach den дltesten Sternen (S. Fischer Press, 2007).
Fischer, E.P., Das Genom (S. Fischer Press, 2004).
Flint, J. et al., Principles of Virology (ASM Press, 2000).
Mahy, B.W.J., The Dictionary of Virology (Academic Press, 2009).
Moelling, K., Are viruses our oldest ancestors? EMBO Reports, 2012; 13:1033.
Moelling, K., What contemporary viruses tell us about evolution – a personal view, Archives Virol. 2013; 158:1833.
Napier, J., Evolution (McGraw-Hill, 2007).
Ryan, F., Virolution (Spektrum Akademic Press, 2010).
Science special issue: HIV and TB in South Africa, Science 2013; 339:873.
Schrödinger, E., What Is Life? (Cambridge University Press, 1967).
van Regenmortel, M. and Mahy, B., Desk Encyclopedia of General Virology (Academic Press, 2009).
Villarreal, L.P., Viruses and the Evolution of Life (American Society of Microbiology Press, 2005).
Watson, J.D., The Double Helix (Norton Critical Edition, 1980; Atheneum, 1980).
Wagener, Ch., Molekulare Onkologie (G. Thieme Verlag, 1999).
Witzany, G., A perspective on natural genetic engineering and natural genome editing. Introduction, Ann. N. Y. Acad. Sci. 2009; 1178: 1–5.
Witzany, G. (Ed.), Viruses: Essential Agents of Life (Springer, 2012).
Zimmer, C., Parasite Rex: Inside the Bizarre World of Nature’s Most Dangerous Creatures (Free Press, 2000). (Циммер К. Паразит – царь природы. – М.: АНФ, 2017)
Zimmer, C., A Planet of Viruses, 2nd ed. (University of Chicago Press, 2015).
Глава 1
Katzourakis, A., Gifford, R.J. et al., Macroevolution of complex retroviruses, Science 2009; 325:1512.
Ziegler, Anna, Photograph 51, theatre play.
Maddox, B., Rosalind Franklin: The Dark Lady of DNA (HarperCollins, 2002).
Watson, J.D., and Crick, F., Molecular structure of nucleic acids: A structure for DNA. Nature, 1974; 248:765.
Crick, F., Central dogma of molecular biology, Nature 1970; 227:561.
Eigen, M., Error catastrophe and antiviral strategy, PNAS2002; 99:13374.
Patel, B.H. et al., Common origins of RNA, protein and lipid precursors in a protometabolism, Nat. Chem. 2015; 4:301.
Sweetlove, L., Number of species on Earth at 8.7 million, Nature 2011, doi:10.1038/news.2011498.
Splicing: Sharp, P.A., The discovery of split genes and RNA splicing, Trends in Biochemical Sciences 2005; 30:279.
Глава 2
Influenza: Taubenberger, J.K., Influenza viruses: Breaking all the rules, MBio. 2013; 4: p.ii: e00365–13.
Fouchier, R.A.M., Garcнa-Sastre, A., and Kawaoka, Y., H5N1 virus: Transmission studies resume for avian flu, Nature 2013; 493:609.
Vaccination: Don’t blame the CIA, Nature 2011; 265:475.
Bioterrorism: Lane, H.C., La Montagne, H.L., and Fauci, A.S., Bioterrorism: A clear and present danger, Nature Med. 2001; 7:1271.
HIV: Cohen, J., AIDS research. More woes for struggling HIV vaccine field, Science 2013; 340:667.
Naked DNA: Weber, R., Bossart, W. et al., Moelling, K., Phase I clinical trial with HIV-1 gp160 plasmid vaccine in HIV-1-infected asymptomatic subjects, Eur. J. Clin. Microbiol. Infect. Dis. 2001; 11:800.
Lowrie, D.B. et al., Moelling, K., Silva, C.L., Therapy of tuberculosis in mice by DNA vaccination, Nature 1999; 400:269.
Schlitz, J.G., Salzer, U., Mohajeri, M.H. et al., Moelling, K., Antibodies from a DNA peptide vaccination decrease the brain amyloid burden in a mouse model of Alzheimer`s disease, J. Mol. Med. 2004; 82:706.
Microbicide: Haase, A.T., Early events in sexual transmission of HIV for interventions, Annu. Rev. Med. 2011; 62:127.
Matzen, K. et al., Moelling, K., RNase H-mediated retrovirus destruction in vivo triggered by oligodeoxynucleotides, Nat. Biotechnol. 2007; 25:669; Commentary: Johnson, W.E., Assisted suicide for retroviruses, Nat. Biotech. 2007; 25:643.
Wittmer-Elzaouk, L. et al., Moelling, K., Retroviral self-inactivation in the mouse vagina, Antiviral Res. 2009; 82:22.
HIV Future: Hütter, G., Transplantation of blood stem cells for HIV/AIDS?, J. Int. AIDS Soc. 2009; 12:10.
Faria, N.R. et al., HIV eipdemiology. The early spread and ignition of HIV-1 in human, Science 2014; 346:56.
Глава 3
Reverse transcriptase: Baltimore, D., RNA-dependent DNA polymerase in virions of RNA tumour viruses, Nature 1970; 226:1209.
Temin, H.M. and Mizutani, S., RNA-dependent DNA polymerase in virions of Rous sarcoma virus, Nature 1970; 226:1211.
Mölling, K. et al., Association of viral RT with an enzyme degrading the RNA of RNA-DNA hybrids, Nat. New. Biol. 1971; 234:240.
Moelling, K., RT and RNase H: In a murine virus and in both subunits of an avian virus, CSH SyQB1975; 39:269.
Moelling, K., Targeting the RNase H by rational drug design, AIDS2012;26:1983.
Moelling, K. et al., Relationship retroviral replication and RNA interference, CSH SyQB2006; 71:365.
Simon, D.M. and Zimmerly, S., A diversity of uncharacterized RTs in bacteria, NAR2008; 36:7219.
Lampson, B.C., Inouye, M., and Inouye, S., Retrons, msDNA, bacterial genome, Cytogenet. Genome Res. 2005; 110:491.
Moelling, K. and Broecker F., The RT-RNase H: From viruses to antiviral defense, Ann. N. Y. Acad.Sci. 2015; 1341:126.
RNase H: Tisdale, M. et al., Moelling, K., Mutations in the RNase H of HIV-1 infectivity, J. Gen. Virol. 1991; 72:59.
Broecker, F., Andrae, K., and Moelling, K., Activation of HIV RNase H, suicide a novel microbicide?, ARHR2012; 28:1397.
Song, J.J. et al., Structure of Argonaute and implications for RISC slicer, Science 2004; 305:1434.
Malik, H.S. and Eickbush, T.H., RNase H suggests a late origin of LTR from TE, Genome Res. 2001; 11:1187.
Crow, Y.J. et al., Jackson, A.P., Mutations in genes encoding ribonuclease H2 subunits cause Aicardi-Goutiѐre syndrome and mimic congenital viral brain infection. Nat. Genet. 2006; 38:910.
Cerritelli, S.M. and Crouch, R.J., Ribonuclease H: The enzymes in eukaryotes, FEBS J. 2009; 276:1494.
Nowotny, M., Retroviral integrase superfamily: The structural perspective, EMBO Rep. 2009; 10:144.
Arshan Nasir, A., Sun, F.-J., Kim, K.M., and Caetano-Anolles, G., Untangling the origin of viruses and their impact on cellular evolution, Ann. N. Y. Acad. Sci. 2014; 1341:61.
Telomerase: Greider, C.W. and Blackburn, E.H., A specific telomere terminal transferase, Cell 1985; 43:405.
Skloot, R., The Immortal Life of Henrietta Lacks (Crown Publishing Group, 2010).
Nandakumar, J. and Cech, T.R., Finding the end: Recruitment of telomerase, Nat. Rev. Mol. Cell. Biol. 2013; 14:69.
Budin, I. and Szostak, J.W., Transition from primitive to modern cell membranes, PNAS2011; 108:5249.
Глава 4
Sarcoma saga: Martin, G. S., The hunting of the Src, Nat. Rev. Mol. Cell. Biol. 2001; 2:467.
Yeatman, T.J. and Roskoski, R. Jr., A renaissance for SRC, Nat. Rev. Cancer 2004; 4: 470.
Oncoproteins: Donner, P., Greiser-Wilke, I. and Moelling, K., Nuclear localization and DNA binding of Myc, Nature 1982; 296:262 and Moelling, K. et al., Nature 1984, 312:551, Myb, Cell 1985; 40:983.
Axel, R., Schlom, J., and Spiegelman, S., Presence in human breast cancer of RNA homologous to MMTV, Nature 1972; 235:32.
Raf-kinase: Moelling, K. et al., Serine–threonine PK activities of Mil/Raf, Nature 1984; 312:558.
Zimmermann, S. and Moelling, K., Phosphorylation and regulation of Raf by Akt, Science 1999; 286:1741.
Rommel, C. et al., Differentiation specific inhibition of Raf-MEK-ERK by Akt, Science 1999; 286:1738.
Zimmermann, S., Moelling K., and Radziwil, G., MEK1 mediates positive feedback on Raf, Oncogene 1997; 15:1503.
Dummer, R. and Flaherty, K.T., Resistance with tyrosine kinase inhibitors in melanoma, Curr. Opin. Oncol. 2012; 24:150.
Das Thakur, M., et al., Modelling Vemurafenib resistance in melanoma, Nature 2013; 494:251.
Holderfield, M. et al., Targeting RAF kinases for cancer therapy: BRAF-mutated melanoma and beyond, Nature Rev. Cancer 2014; 14:455.
McMahon, M., Parsing out the complexity of RAF inhibitor resistance, Pigment Cell Melanoma Res. 2011; 24:361.
Sun, C. et al., Bernards, R., Reversible resistance to BRAF(V600E) inhibition in melanoma, Nature 2014; 508:118.
Myc: Liu, J. and Levens, D., Making Myc, Curr. Top Microbiol. Immunol. 2006; 302:1.
Tumor suppressor: Gateff E: Malignant neoplasms of genetic origin in Drosophila, Science 1978; 200:1448.
Sherr, C.J. and McCormick, F., The RB and p53 pathways in cancer. Cancer Cell 2002; 2:103.
Yi, L. et al., Multiple roles of p53 in somatic and stem cell differentiation, Cancer Res. 2012; 72:563.
Wang, T. et al., Retroviruses shape the transcriptional network of p53. PNAS2007; 104:18613.
Metastases and cancer: Baumgartner, M. et al., Moelling, K., SRC-migration and invasion by PDZ, MCB2008; 28:642.
Broecker, F. et al., Moelling, K., Transcription of C-terminal metastatic c-Src mutant, FEBS J. 2016; 283:1669.
Cancer general: Vogelstein, B. et al., Cancer genome landscape, Science 2013; 339:1546.
Hanahan, D. and Weinberg, R.A., Hallmarks of cancer: The next generation, Cell 2011; 144:646.
zur Hausen, H., Papillomaviruses and cancer: From basics to clinical application, Nat. Rev. Cancer 2002; 2:342.
Cancer different: Han, Y.C. et al., Ventura, A., miR-17–92-mutant mice, Nat. Genet. 2015; 47:766–75.
Prostata: Kearney, M. et al., Coffin, J.M., Multiple sources of contamination in XMRV infection, PLoS ONE2012; 7: e30889.
Bacteria and cancer: Salama, N. et al., Life in the human stomach: Helicobacter pylori, Nat. Rev. Microbiol. 2013; 11:385.
Глава 5
Phages and microbiome: Suttle, C.A., Viruses in the sea, Nature 2005; 437:356.
Reardon, S., News: Phage therapy: Phage therapy gets revitalized, Nature 2014; 510:15.
Young, R.Y. and Gill, J.J., Phage therapy redux – What is to be done?, Science 2015; 350:1163.
Delwart, E., A roadmap to the human virome, PLoS Pathog. 2013; 9: e1003146.
Zarowiecki, M., Metagenomics with guts, Nat. Rev. Microbiol. 2012; 10:674.
Turroni, F. et al., Human gut microbiota and bifidobacteria, A. van Leeuwenhoek 2008; 94:35.
Gut: Turnbaugh, P.J. et al., Gordon, J.I., The effect of diet on human gut microbiome, Sci. Transl. Med. 2009; 1:6ra14.
Qin, J. et al., A human gut microbial gene catalogue by metagenomic sequencing, Nature 2010; 464:59.
Katsnelson, A. et al., Twin study surveys genome for cause of multiple sclerosis, Nature 2010; 464: 1259.
Mokili, J.L., Rohwer, F. and Dutilh, B.E., Metagenomics and future virus discovery, Curr. Opin. Virol. 2012; 2:63.
Cesarean section: Dominguez-Bello, et al., Microbiota of cesarean-born infants, Nat. Med. 2016; doi:10.1038/nm.4039.
Endogenous viruses: Weiss, R.A. and Stoye, J.P., Virology. Our viral inheritance, Science 2013; 340:820.
Feschotte, C. and Gilbert, C., Endogenous viruses: Viral evolution and host biology, Nature Rev. Gen. 2012; 13:283.
Plants global warming: Roossinck, M.J., The good viruses: Viral mutualistic symbioses. Nat. Rev. Microbiol. 2011; 9:99.
Roossinck, M.J., Lifestyles of plant viruses, Philos. Trans. R. Soc. Lond. B. Biol. Sci. 2010; 365:1899.
Placenta: Mi, S. et al., Syncytin – a retroviral envelope in human placenta. Nature 2000; 403:785.
Polydnavirus: Bezier, A. et al., Polydnaviruses of braconid wasps derive from an ancestral nudivirus, Science 2009; 323: 926.
Strand, M.R. and Burke, G.R., Polydnaviurses as symbionts and gene delivery systems, PLoS2012; Pathog 8: e1002757.
Prionen: Mahal, S.P. et al., Transfer of a prion strain leads to emergence of strain variants, PNAS2010; 107:22653.
Глава 6
Chlorella virus: Van Etten, J., Giant viruses; American Scientist 2011.
Van Etten, J., Lane, L.C. and Dunigan, D., DNA viruses: The really big ones (Giruses), Ann. Rev. Microbiol. 2010;64:83.
Broecker, F. et al., Viral composition in the intestine after FT, CSH Mol. Case Stud. 2016; 2: a000448.
Moelling, K. (Ed.), Nutrition and microbiome, Ann. N. Y. Acad. Sci. (2016).
Mimivirus: Boyer, M. et al., Mimivirus genome reduction after intraamoebal culture, PNAS2011; 108:10296.
Raoult, D. and Forterre, P., Redefining viruses: Lessons from mimivirus, Nat. Rev. Microbio. 2006; 6:315.
Raoult, D. et al., Claverie, J.M., The 1.2-megabase genome sequence of mimivirus, Science 2004; 306:1344.
Philippe, N. et al., Pandoraviruses: Amoeba viruses with genomes up to 2.5 Mb, Science 2013; 341:281.
La Scola, B. et al., Raoult, D., A giant virus in amoebae, Science 2003; 299:2033.
Mollivirus sibericus: Legendre, M. et al., Mollivirus sib. 30,000y giant virus in Acanthamoea, PNAS2015; 112:10795.
Sambavirus: Campos, R. K., Sambavirus: Mimivirus from rain forest, The Brazilian Amazon, Virol. J. 2014; 11:95.
Origin of giant viruses: Pennisi, E., Ever bigger viruses shake tree of life, Science 2013; 341:226.
Yutin, N., Wolf, Y.I., and Koonin, E.V., Origin of giant viruses from smaller DNA viruses, Virology 2014; 466–467:38.
Virophages, Sputnik: Yutin, N., Raoult, D. and Koonin, E., Virophages, polintons, and transpovirons: A complex evolutionary network of diverse selfish genetic elements with different reproduction strategies, Virology J. 2013; 1:15.
Fischer, M.G. and Suttle, C.A., A virophage at the origin of large DNA transposons, Science 2011; 332:231.
Forterre, P., The origin of viruses and their possible roles in major evolutionary transitions, Virus Res. 2006; 117:5.
Amoeba: Huber, H. et al., A new phylum of archaea represented by a nanosized hyperthermophilic symbiont, Nature 2002; 417:63.
Slimani, M. et al., Amoebae as battlefields for bacteria, giant viruses, and virophages. J. Virol. 2013; 87:4783.
Eyes: Yutin, N. and Koonin, E.V., Proteorhodopsin genes in giant viruses, Biology Direct 2012; 7:34.
Archaea: Stetter, K.O., A brief history of the discovery of hyperthermophilic life, Biochem. Soc. Trans. 2013; 41:416.
Podar, M. et al., A genomic analysis of the archaeal system Ignicoccus hospitalis–Nanoarchaeumequitans, Genome Biol. 2008; 9: R158.
Mochizuki, T. et al., Archaeal virus with exceptional architecture, largest ssDNA genome, PNAS2012; 109:13386.
Prangishvili, D., Forterre, P. and Garrett, R.A., Viruses of the archaea: A unifying view, Nat. Rev. Micro. 2006; 4:837.
Глава 7
Endogenous viruses: Weiss, R.A., The discovery of endogenous retroviruses, Retrovirol. 2006; 3:67.
Phoenix: Katzourakis, A. et al., Discovery of first endogenous lentivirus, PNAS2007; 10:6261.
Katzourakis, A. and Gifford, R.J., Endogenous viral elements in animal genomes, PLoS Genet. 2010: 6: e1001191.
Dewannieux, M. et al., Identification of an infectious progenitor for the HERV-K, Genome Res. 2006; 16:1548.
Koalas: Tarlinton, R.E., Meers, J., and Young, P.R., Retroviral invasion of the koala genome, Nature2006; 442:79.
Paleovirology: Belyi, V.A., Levine, A.J. and Skalka, A.M., Sequences from ancestral ssDNA viruses in vertebrate genomes: The parvoviridae and circoviridae are more than 40 to 50 mio years old, J. Virol. 2010; 84:12458.
Gifford, R.J., A transitional endogenous lentivirus from a basal primate for lentivirus evolution, PNAS2008; 105:20362.
Katzourakis, A. et al., Macroevolution of complex retroviruses, Science 2009; 32:1512.
Crippled viruses: Lander, E.S. et al., Initial sequencing and analysis of the human genome, Nature 2001; 409:860.
Cordaux, R. and Batzer, M.A., The impact of retrotransposons on human genome evolution, Nat. Rev. Genet. 2009; 10:691.
SnapSot, Transposons, Cell 2008; 135:192.
Singer, T. et al., LINE-1 retrotransposons in neuronal genomes? Trends in Neurosciences, 2010; 33:345.
Pollard, K.S. et al., RNA expressed during cortical development evolved in humans, Nature 2006; 443:167.
Finnegan, D.J., Retrotransposons, Current Biol. 2012; 22: R432–7.
McClintock, B.: Harshey, R.M., The Mu story: How a maverick phage moved the field forword, Mobile DNA 2012; 3:21.
Sander, D.M. et al., Intracisternal A-type retroviral particles in autoimmunity, Microsc. Res. Tech. 2005; 68:222.
Epigenetic Agouti mouse: Dolinoy, D.C. et al., The Agouti mouse model: An epigenetic biosensor for nutritional and environmental alterations on the fetal epigenome, Nutr. Rev. 2008, 66 Suppl. 1: S7–11.
Rassoulzadegan, M., RNA-mediated non-Mendelian inheritance of an epigenetic change in the mouse, Nature 2006; 441:469.
Sleeping beauty: Luft, F.C. et al., Sleeping Beauty jumps to new heights, Mol. Med. 2010; 88:641.
Fish: Amemiya, C.T. et al., African coelacanth genome insights into tetrapod evolution, Nature 2013; 496:311.
Platypus: Warren, W.C. et al., Genome analysis of the platypus unique evolution, Nature 2008; 453:175.
Introns: Morris, K. and Mattick, J.S., The rise of regulatory RNA, Nat. Rev. Genet. 2014; 15:423.
Chabannes, M. et al., Three infectious viral species lying in wait in the banana genome, J. Virol. 2013; 87:8624.
Bartel, D.P., MicroRNAs target recognition and regulatory functions, Cell 2009; 136:215.
Zimmerly, S. et al., GroupII intron mobility, Cell 1995; 82:545.
Beauregard, A., Curcio, M.J. and Belfort M., The take and give RT elements and hosts, Ann. Rev. Genet. 2008; 42:587.
Lambowitz, A.M. and Zimmerly S., Group II introns: Mobile ribozymes in DNA, CSH Perspect. Biol. 2011; 3: a003616.
Galej, W.P. et al., Crystal structure of Prp8 reveals active site of slicosome, Nature 2013; 493:638.
Pena, V. et al., Structure and function of an RNase H at the heart of the spliceosome, EMBO J. 2008; 27:2929.
ENCODE: Biemont, C. and Vieira, C., Junk DNA as an evolutionary force, Nature 2006; 443:521.
Venter, C., Multiple personal genomes await, Nature 2010, 464:676.
Lev, S. et al., Venter, C., The diploid genome sequence of an individual human, PLoS Biol. 2007; 5: e254.
Fukai, E. et al., Derepression of the plant Chromovirus LORE1 induces germline transposition in regenerated plants, PLoS Genet. 2010; 6(3): e1000868.
Глава 8
RNA: Eigen, M., Error catastrophe and antiviral strategy, PNAS2002; 99:13374.
Biebricher, C.K. and Eigen, M., What is a quasispecies, Curr. Top Microbiol. Immunol. 2006; 299:1.
Biebricher, C.K. and Eigen, M., The error threshold, Virus Res. 2005; 107:117.
Lincoln, T.A. and Joyce, G.F., Self-sustained replication of an RNA enzyme, Science 2009; 323:1229.
Doudna, J.A. and Szostak, J.W., RNA-catalysed synthesis of complementarystrand, RNA Nature 1989; 33:519.
Viroids: Steger, G. et al., Structure of viroid replicative intermediates of PST viroid, Nucl. Acids Res. 1986; 14:9613.
Villarreal, L.P., The widespread evolutionary significance of viruses, Viroids Cell Microbiol. 2008;10:2168.
Cech, T.R. et al., Hammerhead nailed down, Nature 1994; 372:39.
Koonin, E.V. and Dolja, V.V., A virocentric perspective on the evolution of life, Curr. Opin. Virol. 2013; 5:546.
Lambowitz, A.M. and Zimmerly, S., Mobile group II introns, Ann. Rev. Genetics 2004; 38:1.
Adamala, K., Engelhart, A.E., and Szostak, J.W., Generation of functional RNAs from inactive oligonucleotide complexes by non-enzymatic primer extension, J. Am. Chem. Soc. 2015; 137:483–489.
Forterre, P., Defining life: The virus viewpoint, Origins of Life and Evolution of Biospheres 2010; 40:51.
Moelling, K., Are viruses our oldest ancestors? EMBO Reports 2012; 13:1033.
Holmes, E.C., What does virus evolution tell us about virus origins? Journal of Virology 2011; 85:5247.
Plankton: Lescot, M. et al. and Ogata, H., Reverse transcriptase genes are highly abundant and transcriptionally active in marine plankton assemblages, ISME Journal 2015; 1–13.
Circular RNA: Memczak, S. et al., Circular RNAs with regulatory potency, Nature 2013; 495:333.
Hansen, T.B. et al., Natural RNA circles function as efficient microRNA sponges, Nature 2013; 495:384.
Hansen, T.B., Kjems, J., and Damgaard, C.K., Circular RNA and miR-7 in cancer, Cancer Res. 2013; 73:5609.
Ford, E. and Ares, M. Jr., Circular RNA using ribozymes from a T4 group I intron, PNAS1994; 12; 91:3117.
Ribozymes and ribosomes: Wilusz, J.E. and Sharp, P.A., A circuitous route to noncoding RNA. Science 2013; 340:44.
Navarro, B. et al., Viroids: Infect a host and cause disease without encoding proteins, Biochemie 2012; 94:1474.
Hammann, C. and Steger, G., Viroid-specific small RNA in plant disease, RNA Biol. 2012; 9:809.
Bartel, D.P., MicroRNAs target recognition and regulatory functions, Cell 2009; 136:215.
Eilus, J.E. and Sharp, P.A., A circuitous route to non-coding RNA, Science 2013; 340:440.
Proteins: Moore, P.B., and Steitz, T.A., The ribosome revealed, Trends in Biochemical Sciences 2005; 30:28.
Ma, B.G. et al., Zhang, H.Y., Characters of very ancient proteins, BBRC2008; 366:607.
Chaperone: Muller, G. et al., NC protein of HIV-1 for increasing catalytic activity of a ribozyme, J. Mol. Biol. 1994; 242:422.
Clover leaf: Dreher, T.W., Viral tRNAs and tRNA-like structures, Rev. RNA 2010; 1:402.
Hammond, J.A., Comparison and functional implications of viral tRNA-like structures, RNA 2009; 15:294.
Witzany, G. (Editor), Viruses: Essential Agents of Life (Springer 2012), p. 414.
Plant viruses: Eickbush, D.G., Retrotransposon ribozyme and its self-cleavage site, PLoS One 2013; 8(9): e66441.
Webb, C.H. et al., Widespread occurrence of self-cleaving ribozymes, Science 2009; 326:953.
Hammann, C. et al., The ubiquitous hammerhead ribozyme, RNA 2012; 18:871.
Hepatitis delta virus: Braza, R. and Ganem, D., The HDAg may be of human origin, Science 1996; 274:90.
Taylor, J., and Pelchat, M., Origin of hepatitis delta virus, Future Microbiol. 2010; 5:393.
Flores, R., Ruiz-Ruiz, S. and Serra, P., Viroids and hepatitis delta virus, Semin-Liver Dis. 2012; 32:201.
Retrophage: Liu, M. et al., Bordetella bacteriophages encoding RT-mediated tropism-switching, J. Bacteriol. 2004; 186:1503.
Doulatov, S. et al., Tropism switching in Bordetella bacteriophage by diversity-generating retroelements, Nature 2004; 431:476.
Tobacco viruses: Buck, K.W., Replication of tobacco mosaic virus RNA, Philos. Trans. R. Soc. Lond. B. Biol. Sci. 1999; 354:613.
Beijerinck, M.W., Contagum vivum fluidum of tobacco leaves, Phytopathol Classics No. 7, ed. Johnson, J., Am. Phyto. Soc., 1898.
Dreher, T.W., Viral tRNAs and tRNA-like structures, Rev. RNA 2010; 1:402.
Hammond, J.A. et al., 3D architectures of viral tRNA-like structures, RNA 2009; 15:294.
Apple tree: Mitrovic, J. et al., Sequences of Stolbur phytoplasma from DNA, Mol. Microbiol. Biotech. 2014; 24:1.
Georgiades, K. et al., Gene gain and loss events in Rickettsia and Orientia species, Biol. Direct 2011; 6:6.
Plants: Roossinck, M.J., Lifestyles of plant viruses, Philos. Trans. R. Soc. Lond. B. Biol. Sci. 2010; 365:1899.
Geminiviruses: Krupovic M. et al., Geminiviruses: A tale of a plasmid becoming a virus, BMC Evol. Biol. 2009; 9:112.
Tulipomania: Lesnaw, J.A. and Ghabrial, S.A., Tulip breaking: Past, present and future, Plant Disease 2000; 84:1052.
Murray, J.D., How the leopard gets its spots, Sci. Am. 1988; 3:80–87.
Глава 9
Interferon: McNab, F. et al., O’Garra, A., Type Interferons in infectious disease, Nat. Rev. Immunology 2015; 15:87–103.
siRNA: Baulcombe, D.C. and Dean, C., Epigenetic regulation in plant to the environment, CSH Pers.Biol. 2014; 6(9): a019471.
Wilson, R.C. and Doudna, J.A., Molecular mechanisms of RNA interference, Annu. Rev. Biophys. 2013; 42:217.
Moelling K., Matskevich A., and Jung J. S., Relationship between retroviral replication and RNA interference, CSH–SyQB2006; 71:365–8.
Matskevich, A. and Moelling, K., Dicer is involved in protection against influenza A virus infection, J. Gen. Virol. 2007; 88:2627–35.
Song J. J., et al., The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNA effector complexes, Nat. Struct. Biol. 2003; 10:1026–32.
Nowotny, M., Retroviral integrase superfamily: The structural perspective. EMBO Reports 2009; 19:144–151.
Nasir, A. and Caetano-Anolles, G., Origin of viruses and their impact on cellular evolution, Ann. N. Y. Acad. Sci. 2015; 1341:61.
Moelling, K. and Broecker, F., The RT-RNase H: From viruses to antiviral defense, Ann. N. Y. Acad. Sci. 2015; 1341:126–35.
Orsay virus: Sterken, M.G. et al., A heritable antiviral RNAi response limits Orsay virus infection, PLoS One 2014; 9(2).
CRISPR/Cas9: Doudna, J.A. and Charpentier, E., Genome editing. The new frontier of genome engineering with CRISPR-Cas9, Science 2014; 346 (6213):1258096.
Jinek, M. et al., Structures of Cas9 endonucleases, Science 2014; 343, 1247997.
Hsu, P.D., Lander, E.S., and Zhang, F., Development and applications of CRISPRCas9 for genome engineering, Cell 2014; 157:1262.
Barrangou, R. and Marraffini, L.A., CRISPR-Cas systems: Procaryotes to adaptive immunity, Review Mol. Cell. 2014; 54:234.
Krupovic, M. et al., Casposons: Self-synthesizing DNA transposons of CRISPR-Cas immunity, BMC Biology 2014; 12:36.
Horvath, P. and Barrangou R., CRISPR/Cas9, the immune system of bacteria and archaea, Science 2010; 327:167.
Swarts, D.C. et al., DNA-guides DNA interference by a procaryotic Argonaute, Nature 2014; 507:258.
Moelling, K. et al., Silencing of HIV by hairpin-loop DNA oligonucleotide (siDNA), FEBS Letters2006; 580:3545.
Zhou, L. et al., Transposition of hAT elements links TE and V(D)J recombination, Nature 2004; 432:995.
Bateman, A., Eddy, S.R., and Chothia, C., Members of the immunoglobulin superfamily in bacteria, Protein Sci.1996; 5:1939.
Beauregard, A., Curcio, M.J. and Belfort M., The take and give between TE, Annu. Rev. Genet. 2008; 42:587.
Antisense: Isselbacher, K.J., Retrospective: Paul C. Zamecnik (1912–2009), Science 2009; 326:1359.
Citron, M. and Schuster, H., The c4 repressors of bacteriophages P1 and P7 are antisense RNAs, Cell 1990; 62:591.
Глава 10
Reardon, S., Phage therapy gets revitalized, Nature 2014; 510:15.
Young, Ry. and Gill, J.J., Phage therapy redux – What is to be done? Science 2015; 350:1163.
Viertel, T.M., Ritter, K. and Horz, H.P., Phage therapy against MDR pathogens, J. Antimic. Chemother. 2014; 69:2326–36.
Phagoburn: EU program: The main objective of Phagoburn is to assess the safety, effectiveness and pharmacodynamics of two therapeutic phage cocktails to treat either E. coli or P. aeruginosa burn wound infections, 2013–2016.
Vanessa, K. et al., Gut microbiota from twins discordant for obesity, Science 2013; 341:1079.
Multiresistant bacteria: Nьbel, U., MRSA transmission on a neonatal intensive care unit, PLoS One. 2013;8(1): e54898.
Stower, H., Medical genetics: Narrowing down obesity genes, Nat. Med. 2014;20:349.
Lepage, P. et al., Dore, A., Metagenomic insight into our gut`s microbiome, Gut 2013; 62:146.
Smemo, S., Obesity-associated variants within FTO and with IRX3, Nature 2014; 507:371.
Blaser, M. and Bork, P. et al., The microbiome explored: Recent insights and future challenges, Nat. Rev. Microbiol. 2013;11:213.
Transgenerational epigenetics: Tobie, E.W. et al., DNA methylation to prenatal famine, Hu. Mol. Gen. 2009; 18;2:4046.
Bygren, L.O. et al., Grandmothers’ early food supply influenced mortality of female grandchildren, BMC Genet. 2014; 15:12.
Norman, J.M. et al. Alterations in the enteric virome in inflammatory bowel disease, Cell 2015;160: 447.
Grossniklaus, U. et al., Transgenerational epigenetic inheritance: How important is it?, Nat. Rev. Genet.2013; 14:228.
Pembrey, M.E. et al., Sex-specific, male-line transgenerational responses in humans, Eur. J. Hum. Genet. 2006; 14:159.
Arabidopsis Genome Initiative, Analysis of the genome sequence of Arabidopsis thaliana, Nature 2006; 441:469.
Waterland, R.A. and Jirtle, R.L., TE targets for early nutritional effects on epigenetic gene regulation. MCB2003; 23:5293.
Slotkin, R.K. and Martienssen, R., TE and the epigenetic regulation of the genome, Nat. Rev. Genet. 2007; 8:2.
Pfeifer, A. et al., Verma, I.M., Lentiviral vectors: Lack of gene silencing in embryos, PNAS2002; 99:2140.
Dutch famine: Lumey, L.H. et al., The Dutch hunger winter families study, Int. J. Epidemiol. 2007; 36:1196.
Roseboom, T., de Rooij, S. and Painter, R., The Dutch famine and consequences for adult health, EarlyHum. Dev. 2006; 82:485.
Cao-Lei, L. et al., DNA methylation triggered by prenatal stress exposure to ice storm, PLoS One 2014; 9:9(e107653).
Ost, A. et al., Paternal diet defines offspring chromatin state and intergenerational obesity, Cell 2014; 159:1352.
Phage therapy: Vandenheuvel, D., Lavigen, R. and Brьssow, H., Bacteriophage therapy, Annu. Rev.Virol. 2015; 2:599.
Gut-brain axis: Bercik, P. et al., Intestinal microbiota affect BDNF, Gastroenterology 2011; 141:599.
Obesity gene counts: Le Chatelier et al., Richness of human gut microbiome and metabolic markers, Nature 2013;500:541.
Gut microbiota: Qin, J. et al., Wang, J., A metagenome-wide study of gut microbiota in diabetes, Nature 2012; 490:55.
Cotillard, A. et al., Ehrlich, S.D., Dietary intervention impact on gut microbial gene richness, Nature 2013; 500:585.
Ackerman, D. and Gems, D., The mystery of C. elegans aging: An emerging role for fat, Bioessays 2012; 34:466.
Fecal transfer: Broecker F., Rogler, G., and Moelling, K., Intestinal microbiome of C. diff. with FT, Digestion 2013;88:243.
Reyes, A. et al., Viruses in the faecal microbiota of monozygotic twins and their mothers, Nature 2010; 466:344.
Gut virome: Norman, J.M. et al., Alterations in the enteric virome in inflammatory bowel disease, Cell 2015;160:447.
Broecker, F. et al., Bacterial and viral compositions of C. diff. patient after fecal transplant, CSH Molecular Case Stud. 2015; 2: a000448.
Elba worms: McCutcheon, J.P. and Moran, N.A., Genome reduction in symbiotic bacteria, Nat. Rev. Micr. 2012; 10:13.
Dubilier, N., Bergin, C. and Lott, C., Symbiotic diversity in marine animals, Nat. Rev. Micro. 2008; 6:725.
Глава 11
Viruses: Baltimore, D., Gene therapy. Intracellular immunization, Nature 1988; 335:39.
Ott, M.G. et al., Grez, M., Correction of X-linked chronic granulomatosis by gene therapy, Nat. Med. 2006; 12:401.
Rossi, J.J., June, C.H. and Kohn, D.B., Genetic therapies against HIV, Nat. Biotechnol. 2007; 25:144.
Pachuk, C.J. et al., Selective cleavage of bcr-abl chimeric RNAs by a ribozyme, Nucl. Acids Res. 1994; 22:301.
Lipizzan horses, malignant melanoma: Heinzerling, L. et al., IL-12 DNA into melanoma patients and white horses, Hu. Gene. Ther. 2005; 16:35, J. Mol. Med. 2001; 78:692.
Mosquito vaccination: Bian, G. et al., Wolbachia in Anopheles against plasmodium infection, Science 2013; 340:748.
Plants gene therapy: Fresco, L.O., The GMO stalemate in Europe, Science 2012; 33:883.
Pappas, K.M., Cell-cell signaling and the Agrobacterium tumefaciens Ti plasmid, Plasmid 2008; 60:89.
Thomson, H., Plant science: The chestnut resurrection, Nature 2012; 490:22–3.
Choi, G.H. and Nuss, D.L., Hypovirulence of chestnut blight fungus by an infectious viral cDNA, Science 1992; 257:800–803.
D’Hont, et al., The banana (Mus acuminata) genome and the evolution of monocotyledonous plants, Nature 2012;488:213.
Schnable, P.S. et al., The B73 maize genome: Complexity, diversity, and dynamics, Science 2009; 326:1112.
Yeast/fungi: Goffeau, A. et al., Life with 6000 genes, Science 1996; 274:546.
Goffeau, A., Genomics: Multiple moulds, Nature 2005; 438:1092.
Roossinck, M.J., The good viruses: Viral mutualistic symbiose, Nat. Rev. Microbiol. 2011; 9:99.
Márquez, L.M. et al., A virus in a fungus in a plant: Symbioses for thermal tolerance, Science 2007; 315:513.
Esteban, R. and Fujimura, T., Yeast 23S RNA narnavirus shows signals for replication, PNAS2015; 100, 5:2568.
Stem cells: Qian, L. et al., In vivo reprogramming cardiac fibroblasts into cardiomyocytes, Nature 2012; 485:593.
Hydra: Chapman, et al., The dynamic genome of hydra, Nature 2010; 464:592.
Renard, E. et al., Origin of the neuro-sensory system: In sponges, Integr. Zoolog. 2009; 4:294–308.
Smelick, C. and Ahmed S., Achieving immortality in the C. elegans germline, Ageing Res. Rev. 2005; 4:67–82.
Third tooth: Arany, P.R., Photoactivtion of TGF-b1 directs stem cell for regeneration, Sci. Transl. Med. 2014; 6(238)238.
Глава 12
Synthetic biology: Hutchinson, C.A. et al., Design and synthesis of a minimal bacterial genome, Science 2016; 351:1414.
Glass, J.I. et al., Venter C: Essential genes of a minimum bacterium, PNAS2006; 103:425.
Gil, R. et al., A determination of the core of a minimal bacterial gene set, Microbiol. Mol. Rev. 2004; 68:518.
Annaluru, N. et al., Total synthesis of a functional designer eukaryotic chromosome, Science 2014; 344:55–8.
Nystedt, B. et al., The Norway spruce genome sequence and conifer genome evolution, Nature 2013; 497:579.
Moreira, D. and Lopez-Garcia, P., Ten reasons to exclude viruses from the tree of life, Nat. Rev. Microbiol 2009; 7:306.
Lu, T. and Tauxe, W., Cocktail maker proteins and semiconductors, Nature 2015; 528: S14.
Forterre, P., The virocell concept and environmental microbiology, ISME J. 2013; 7:233.
TARA Ocean and gut: Sunagawa, S. et al., Structure and function of the global ocean microbiome, Science 2015; 348:1–9.
TARA virome: Brum, J.R. et al., Seasonal time bombs: Dominant temperate viruses, ISME J. 2016; 10:437–49.
TARA Ocean plankton: Lescot, M. et al., RT genes in marine plankton, ISME J. 2015; doi:10.1038/ismej.2015.
Moelling, K. and Broecker, F., The RT-RNase H: From viruses to antiviral defense, Ann. N. Y. Acad. Sci. 2015; 1341:126.
Retrons: Farzadfard, F. and Lu, T.K., Genomically encoded analog memory, Science 2014;346 1256272. doi: 10.1126/.
Front-runners and late-progressors: Moelling, K., Are viruses our oldest ancestors? EMBO Reports. 2012; 13:1033.
Koonin, E., Senkevich T. and Dolja, V., The ancient virus world and evolution of cells, Biology Direct 2006;1:29.
Koonin, E.V. et al., Reasons why viruses are relevant for the origin of cells, Nat. Rev. Micro. 2009; 7:615.
Villarreal, L.P., The widespread evolutionary significance of viruses, in Domingo, E., Parish, C. and Holland, J. (Eds.), Origin and Evolution of Viruses (Academic Press, 2008), pp. 477–516.
Dolja, V.V. and Koonin, E.V., Common origins and diversity of plant and animal viromes, Curr. Opin. Virol. 2011; 5:322.
Monster: Spiegelman, S. et al., Synthesis of a self-propagating and infectious NA with an enzyme, PNAS1965; 54:919.
Oehlenschläger, F. and Eigen, M., 30 years later: A new approach to Sol Spiegelman’s and Leglie Orgel’s in vitro, Origins of Life and Evolution of Biospheres, 1997; 2:437.
Kacian, D.L. et al., Replicating RNA for extracellular evolution and replication, PNAS1972; 69:3038.
Lucky: Cano, R.J. and Borucki, M.K., Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber, Science 1995; 268:1060.
Body size: Katzourakis, A. and Gifford R., Larger body size leads to lower retroviral activity, PloS Pathog. 2014, 10 (7): e100414.
Obesity and cancer: Luo, C. and Puigserver, P., Dietary fat promotes intestinal dysregulation, Nature 531,42–43.
Transgenerational inheritance: Rassoulzadegan, M. et al., Cuzin, F., RNA-mediated non-Mendelian inheritance of an epigenetic change in the mouse, Nature 2006; 441:469–74; and Essays Biochem. 2010;48(1):101–6.
Seth, M., The C. elegans CSR-1 Argonaute pathway counteracts epigenetic silencing, Cell 2013; 27:656.
Simon, M. et al., Reduced insulin/IGF-1 signaling restores germ cell immortality to C. elegans Piwi mutants, Cell Rep. 2014; 7:762.
Weick, E.M. and Miska, E., piRNAs: From biogenesis to function, Development 2014; 141:3458.
Sarkies, P., and Miska, E.A., Small RNAs break out: Mobile small RNAs, Nat. Rev. Mol. Cell. Biol. 2014; 15:525.
Shirayama, M. et al., piRNAs initiate an epigenetic memory of nonself RNA in C. elegans, Cell 2012; 150:65.
Ashe, A. et al., Miska, E.A., piRNA can trigger a multigenerational epigenetic memory, Cell 2012; 150:88.
Ng, S.Y. et al., Long ncRNAs in development and disease of CNS, Trends Genet. 2013; 29:461.
Orlando, L. and Willerslev, E., An epigenetic window into the past, Science 2014; 345:511.
Finnegan, D.J., Retrotransposon, Current Biol. 2012; 22: R432–7.
Pembrey, M. et al., Human transgenerational responses to early-life experience, J. Med. Genet. 2014;51:56.
Ost, A. et al., Paternal diet defines offspring chromatin and intergenerational obesity, Cell 2014; 159:1352.
Alleman, M., et al., An RNA-dependent RNA polymerase is required for paramutation in maize, Nature 2006; 442:295.
Lolle, S.J., Non-Mendelian inheritance of extra-genomic information in Arabidopsis, Nature 2005; 434:505.
Color patterns: Murray, J. D., How the leopard gets its spots, Sci. Am. 1988; 3: 80–87.
Honey bees: Miklos, G. L., and Maleszka, R., Epigenetic comunication in human and honey bees, Horm. Behav. 2011; 59:399.
Kohl, J. V., Nutrient dependent/pheromone evolution: A model, Socioaff. Neurosci. Psychol. 2013; 3:20553.
Ganko, E.W. et al., Contribution of LTR retrotransposons to C. elegans gene evolution, Mol. Bio. Evol. 2003; 20:1925.
