To be or not to be alive: How recent discoveries challenge the traditional definitions of viruses and life
Tóm tắt
Từ khóa
Tài liệu tham khảo
Abrescia, 2012, Structure unifies the viral universe, Annual Review of Biochemistry, 81, 795, 10.1146/annurev-biochem-060910-095130
Akita, 2007, The crystal structure of a virus-like particle from the hyperthermophilic archaeon Pyrococcus furiosus provides insight into the evolution of viruses, Journal of Molecular Biology, 368, 1469, 10.1016/j.jmb.2007.02.075
Baltimore, 1971, Expression of animal virus genomes, Bacteriological Reviews, 35, 235, 10.1128/MMBR.35.3.235-241.1971
Bamford, 2003, Do viruses form lineages across different domains of life?, Research in Microbiology, 154, 231, 10.1016/S0923-2508(03)00065-2
Bandea, 1983, A new theory on the origin and the nature of viruses, The Journal of Theoretical Biology, 105, 591, 10.1016/0022-5193(83)90221-7
Bandea, 2009, The origin and evolution of viruses as molecular organisms, Nature Precedings, 10.1038/npre.2009.3886.1
Bos, 1999, Beijerinck's work on tobacco mosaic virus: historical context and legacy, Philosophical Transactions of the Royal Society B: Biological Sciences, 354, 675, 10.1098/rstb.1999.0420
Bos, 2000, 100 years of virology: from vitalism via molecular biology to genetic engineering, Trends in Microbiology, 8, 82, 10.1016/S0966-842X(99)01678-9
Boyer, 2010, Phylogenetic and phyletic studies of informational genes in genomes highlight existence of a 4 domain of life including giant viruses, PLoS One, 5, e15530, 10.1371/journal.pone.0015530
Brüssow, 2009, The not so universal tree of life or the place of viruses in the living world, Philosophical Transactions of the Royal Society B: Biological Sciences, 364, 2263, 10.1098/rstb.2009.0036
Cello, 2002, Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template, Science, 297, 1016, 10.1126/science.1072266
Chauvier, 2008, Particuliers, individus et individuation, 11
Claverie, 2006, Viruses take center stage in cellular evolution, Genome Biology, 7, 110, 10.1186/gb-2006-7-6-110
Claverie, 2013, Open questions about giant viruses, Advances in Virus Research, 85, 25, 10.1016/B978-0-12-408116-1.00002-1
Claverie, 2016, Giant Viruses: The Difficult Breaking of Multiple Epistemological Barriers, Studies in History and Philosophy of Biological and Biomedical Sciences, 59, 89, 10.1016/j.shpsc.2016.02.015
Comeau, 2005, War is peace–dispatches from the bacterial and phage killing fields, Current Opinion in Microbiology, 8, 488, 10.1016/j.mib.2005.06.004
Cortez, 2009, A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes, Genome Biology, 10, R65, 10.1186/gb-2009-10-6-r65
Daubin, 2004, Start-up entities in the origin of new genes, Current Opinion in Genetics and Development, 14, 616, 10.1016/j.gde.2004.09.004
Dolja, 2012
Dupre, 2009, Variety of living things: life at the intersection of lineages and metabolism, Philosophy and Theory in Biology, 1, e003, 10.3998/ptb.6959004.0001.003
Dupré, 2016, Viruses as Living Processes, Studies in History and Philosophy of Biological and Biomedical Sciences, 59, 109, 10.1016/j.shpsc.2016.02.010
Dyall, 2000, Origins of hydrogenosomes and mitochondria: evolution and organelle biogenesis, Current Opinion in Microbiology, 3, 404, 10.1016/S1369-5274(00)00112-0
Engels, 2006, 1
Feschotte, 2002, Plant transposable elements: where genetics meets genomics, Nature Reviews Genetics, 3, 329, 10.1038/nrg793
Filée, 2013, Route of NCLDV evolution: the genomic accordion, Current Opinion in Virology, 3, 595, 10.1016/j.coviro.2013.07.003
Fischer, 2010, Giant virus with a remarkable complement of genes infects marine zooplankton, Proceedings of the National Academy of Sciences of the United States of America, 107, 19508, 10.1073/pnas.1007615107
Forterre, 1992, New hypotheses about the origins of viruses, prokaryotes and eukaryotes, 221
Forterre, 2002, The origin of DNA genomes and DNA replication proteins, Current Opinion in Microbiology, 5, 525, 10.1016/S1369-5274(02)00360-0
Forterre, 2005, The two ages of the RNA world, and the transition to the DNA world: a story of viruses and cells, Biochimie, 87, 793, 10.1016/j.biochi.2005.03.015
Forterre, 2006, The origin of viruses and their possible roles in major evolutionary transitions, Virus Research, 117, 5, 10.1016/j.virusres.2006.01.010
Forterre, 2006, Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain, Proceedings of the National Academy of Sciences of United States of America, 103, 10.1073/pnas.0510333103
Forterre, 2011, Manipulation of cellular syntheses and the nature of viruses: the virocell concept, Comptes Rendus Chimie, 4, 392, 10.1016/j.crci.2010.06.007
Forterre, 2010, Giant viruses: conflicts in revisiting the virus concept, Intervirology, 53, 362, 10.1159/000312921
Forterre, 2012, Darwin's goldmine is still open: variation and selection run the world, Frontiers in Cellular and Infection Microbiology, 2, 106, 10.3389/fcimb.2012.00106
Forterre, 2012
Forterre, 2013, The virocell concept and environmental microbiology, The ISME Journal, 7, 233, 10.1038/ismej.2012.110
Forterre, 2015, The universal tree of life: an update, Frontiers in Microbiology, 6, 717, 10.3389/fmicb.2015.00717
Forterre, 2012, The origin of virions and virocells: the escape hypothesis revisited
Forterre, 2014, Cellular domains and viral lineages, Trends in Microbiology, 22, 554, 10.1016/j.tim.2014.07.004
Forterre, 2009, The great billion-year war between ribosome- and capsid-encoding organisms (cells and viruses) as the major source of evolutionary novelties, Annals of the New York Academy of Sciences, 1178, 65, 10.1111/j.1749-6632.2009.04993.x
Forterre, 2009, The origin of viruses, Research In Microbiology, 160, 466, 10.1016/j.resmic.2009.07.008
Forterre, 2013, The major role of viruses in cellular evolution: facts and hypotheses, Current Opinion in Virology, 3, 558, 10.1016/j.coviro.2013.06.013
Gaudin, 2014, Extracellular membrane vesicles harbouring viral genomes, Environmental Microbiology, 16, 1167, 10.1111/1462-2920.12235
Helvoort, 1994, History of virus research in the twentieth century: the problem of conceptual continuity, History of Science, 32, 185, 10.1177/007327539403200204
Hulo de Castro, 2011, ViralZone: a knowledge resource to understand virus diver- sity, Nucleic Acids Research, 39, D576, 10.1093/nar/gkq901
Jalasvuori, 2008, Structural co-evolution of viruses and cells in the primordial world, Origins of Life and Evolution of the Biosphere, 38, 165, 10.1007/s11084-008-9121-x
Jalasvuori, 2015, Classification of prokaryotic genetic replicators: between selfishness and altruism, Annals of the New York Academy of Sciences, 1341, 96, 10.1111/nyas.12696
Koonin, 2013, A virocentric perspective on the evolution of life, Current Opinion in Virology, 3, 546, 10.1016/j.coviro.2013.06.008
Koonin, 2014, Virus world as an evolutionary network of viruses and capsidless selfish elements, Microbiology and Molecular Biology Reviews, 78, 278, 10.1128/MMBR.00049-13
Koonin, 2006, The ancient virus world and evolution of cells, Biology Direct, 2006, 29, 10.1186/1745-6150-1-29
Koonin, 2016, Are Viruses Alive? The Replicator Paradigm Sheds Decisive Light on an Old but Misguided Question, Studies in History and Philosophy of Biological and Biomedical Sciences, 59, 125, 10.1016/j.shpsc.2016.02.016
Koonin, 2012, Evolution of microbes and viruses: a paradigm shift in evolutionary biology?, Frontiers in Cellular and Infection Microbiology, 13, 119
Kostyrka, 2016, What Roles for Viruses in Origin of Life Scenarios?, Studies in History and Philosophy of Biological and Biomedical Sciences, 59, 135, 10.1016/j.shpsc.2016.02.014
Kristensen, 2010, New dimensions of the virus world discovered through metagenomics, Trends in Microbiology, 18, 11, 10.1016/j.tim.2009.11.003
Krupovic, 2013, Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses, Current Opinion in Virology, 3, 578, 10.1016/j.coviro.2013.06.010
López-García, 2012, The place of viruses in biology in light of the metabolism- versus-replication-first debate, History and Philosophy of the Life Sciences, 34, 391
Lopez-Garcia, 2012, Viruses in biology, Evolution: Education & Outreach, 5, 389
Lwoff, 1957, The concept of virus, Journal of General Microbiology, 17, 239
Lwoff, 1966, Interaction among virus, cell, and organism, Science, 152, 1216, 10.1126/science.152.3726.1216
Makarova, 2013, Comparative genomics of defense systems in archaea and bacteria, Nucleic Acids Research, 41, 4360, 10.1093/nar/gkt157
Méthot, 2016, Writing the History of Virology in the Twentieth Century: Discovery, Disciplines, and Conceptual Change, Studies in History and Philosophy of Biological and Biomedical Sciences, 59, 145, 10.1016/j.shpsc.2016.02.011
Moliner, 2010, Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution, FEMS Microbiology Reviews, 34, 281, 10.1111/j.1574-6976.2009.00209.x
Morange, 2011, Problems raised by the definition of life, 3
Moreira, 2009, Ten reasons to exclude viruses from the tree of life, Nature Reviews Microbiology, 7, 306, 10.1038/nrmicro2108
Nakabachi, 2006, The 160-kilobase genome of the bacterial endosymbiont Carsonella, Science, 314, 267, 10.1126/science.1134196
Nasir, 2014, The distribution and impact of viral lineages in domains of life, Frontiers in Microbiology, 5, 194, 10.3389/fmicb.2014.00194
Nasir, 2012, Viral evolution: primordial cellular origins and late adaptation to parasitism, Mobile Genetic Elements, 2, 247, 10.4161/mge.22797
Ogata, 2007, Unique genes in giant viruses: regular substitution pattern and anomalously short size, Genome Research, 17, 1353, 10.1101/gr.6358607
Philippe, 2013, Pandoraviruses: amoeba viruses with genomes up to 2.5 Mb reaching that of parasitic eukaryotes, Science, 341, 281, 10.1126/science.1239181
Pradeu, 2010, What is an organism? an immunological answer, History & Philosophy of the Life Sciences, 32, 247
Pradeu, 2016, Mutualistic Viruses and the Heteronomy of Life, Studies in History and Philosophy of Biological and Biomedical Sciences, 59, 80, 10.1016/j.shpsc.2016.02.007
Prangishvili, 2013, The wonderful world of archaeal viruses, Annual Review of Microbiology, 67, 565, 10.1146/annurev-micro-092412-155633
Prangishvili, 2006, Evolutionary genomics of archaeal viruses: unique viral genomes in the third domain of life, Virus Research, 117, 52, 10.1016/j.virusres.2006.01.007
Quax, 2013, Massive activation of archaeal defense genes during viral infection, The Journal of Virology, 87, 8419, 10.1128/JVI.01020-13
Rancurel, 2009, Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation, The Journal of Virology, 83, 10719, 10.1128/JVI.00595-09
Raoult, 2004, The 1.2-megabase genome sequence of Mimivirus, Science, 306, 1344, 10.1126/science.1101485
Raoult, 2008, Redefining viruses: lessons from Mimivirus, Nature Reviews Microbiology, 6, 315, 10.1038/nrmicro1858
Ryan, 2007, Viruses as symbionts, Symbiosis, 44, 11
Ryan, 2009
Sapp, 2005, The prokaryote-eukaryote dichotomy: meanings and mythology, Microbiology and Molecular Biology Reviews, 69, 292, 10.1128/MMBR.69.2.292-305.2005
Spang, 2015, Complex archaea that bridge the gap between prokaryotes and eukaryotes, Nature, 521, 173, 10.1038/nature14447
Stern, 2011, The phage-host arms race: shaping the evolution of microbes, Bioessays, 33, 43, 10.1002/bies.201000071
Suttle, 2013, Viruses: unlocking the greatest biodiversity on Earth, Genome, 56, 542, 10.1139/gen-2013-0152
Temin, 1971, The protovirus hypothesis: speculations on the significance of RNA-directed DNA synthesis for normal development and for carcinogenesis, The Journal of the National Cancer Institute, 46, 3
Thompson, 2011, Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism, Proceedings of the National Academy of Sciences of the United States of America, 27, 757, 10.1073/pnas.1102164108
Van Regenmortel, 2003, Viruses are real, virus species are man-made, taxonomic constructions, Archives of Virology, 148, 2481, 10.1007/s00705-003-0246-y
Van Regenmortel, 2010, Logical puzzles and scientific controversies: the nature of species, viruses and living organisms, Systematic and Applied Microbiology, 33, 1, 10.1016/j.syapm.2009.11.001
van Regenmortel, 2016, The Metaphor that Viruses are Living is Alive and Well, but it is No More than a Metaphor, Studies in History and Philosophy of Biological and Biomedical Sciences, 59, 117, 10.1016/j.shpsc.2016.02.017
Villarreal, 2007, Virus-host symbiosis mediated by persistence, Symbiosis, 44, 1
Villarreal, 2010, Viruses are essential agents within the roots and stem of the tree of life, Journal of Theoretical Biology, 262, 698, 10.1016/j.jtbi.2009.10.014
Wimmer, 2006, The test-tube synthesis of a chemical called poliovirus, EMBO Reports, 7, 53, 10.1038/sj.embor.7400728
Witzany, 2012
Woese, 1990, Towards a natural system of organisms: proposal for the domains archaea, bacteria, and eucarya, Proceedings of the National Academy of Sciences of the United States of America, 87, 4576, 10.1073/pnas.87.12.4576
Yin, 2008, Identification and investigation of ORF-ans in the viral world, BMC Genomics, 9, 24, 10.1186/1471-2164-9-24