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eMicrobevol SIGNED

Early Microbial Evolution

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EC-Contrib. €

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Project "eMicrobevol" data sheet

The following table provides information about the project.

Coordinator
HEINRICH-HEINE-UNIVERSITAET DUESSELDORF 

Organization address
address: UNIVERSITAETSSTRASSE 1
city: DUSSELDORF
postcode: 40225
website: www.uni-duesseldorf.de

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Germany [DE]
 Project website http://www.molevol.hhu.de
 Total cost 2˙393˙447 €
 EC max contribution 2˙393˙447 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2014-ADG
 Funding Scheme ERC-ADG
 Starting year 2015
 Duration (year-month-day) from 2015-11-01   to  2020-10-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    HEINRICH-HEINE-UNIVERSITAET DUESSELDORF DE (DUSSELDORF) coordinator 2˙393˙447.00

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 Project objective

From the primordial emergence of the earliest cells to the ongoing diversification of modern microbiota, the mechanisms that underlie the origin of major prokaryotic groups are still poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms — ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions. Because eukaryotes started out as a prokaryote lineage, the same holds true at the prokaryote-eukaryote transition. Prokaryotic higher taxa are currently circumscribed by phylogenomic studies encompassing 30-40 proteins for information processing that are universal to all genomes, or nearly so. The core is useful in taxonomy but comprises only about 1% of an average genome. It does not predict gene content in the remaining 99% of the genome, because of the role of lateral gene transfer (LGT) in generating diversity within and between prokaryotic groups. Especially in groups with large pangenomes or broad ecological diversity, the core itself does not reveal which gene innovations underlie the origin of major groups, but gene distributions might. This proposal aims to harness all the evolutionary data that genomes have to offer — gene trees, gene distributions, and split distributions across sets of trees — to chart the history of the 99% component of microbial genome evolution and the role of LGT in the origin of higher microbial taxa. The focus is on three important questions: i) What are the quantitative and lineage specific relative contributions of gene transfer from endosymbionts vs. gene transfers from other prokaryotes during eukaryotic genome evolution, ii) Are there significant differences in verticality in comparisons of genome evolution in prokaryotes vs. eukaryotes and how can we statistically better quantify them, and iii) What was the biological nature of the earliest prokaryotes.

 Publications

year authors and title journal last update
List of publications.
2019 S. B. Gould, S. G. Garg, M. Handrich, S. Nelson-Sathi, N. Gruenheit, A. G. M. Tielens, W. F. Martin
Adaptation to life on land at high O 2 via transition from ferredoxin-to NADH-dependent redox balance
published pages: 20191491, ISSN: 0962-8452, DOI: 10.1098/rspb.2019.1491
Proceedings of the Royal Society B: Biological Sciences 286/1909 2019-11-28
2019 John F. Allen, Brenda Thake, William F. Martin
Nitrogenase Inhibition Limited Oxygenation of Earth’s Proterozoic Atmosphere
published pages: 1022-1031, ISSN: 1360-1385, DOI: 10.1016/j.tplants.2019.07.007
Trends in Plant Science 24/11 2019-11-28
2019 Tanita Wein, Devani Romero Picazo, Frances Blow, Christian Woehle, Elie Jami, Thorsten B.H. Reusch, William F. Martin, Tal Dagan
Currency, Exchange, and Inheritance in the Evolution of Symbiosis
published pages: 836-849, ISSN: 0966-842X, DOI: 10.1016/j.tim.2019.05.010
Trends in Microbiology 27/10 2019-11-28
2019 Joana C. Xavier, William F. Martin
Sediment, methane and energy
published pages: 547-549, ISSN: 2058-5276, DOI: 10.1038/s41564-019-0417-6
Nature Microbiology 4/4 2019-11-28
2019 Mauro Degli Esposti, Marek Mentel, William Martin, Filipa L. Sousa
Oxygen Reductases in Alphaproteobacterial Genomes: Physiological Evolution From Low to High Oxygen Environments
published pages: , ISSN: 1664-302X, DOI: 10.3389/fmicb.2019.00499
Frontiers in Microbiology 10 2019-11-28
2019 Martina Preiner, Joana C. Xavier, Andrey do Nascimento Vieira, Karl Kleinermanns, John F. Allen, William F. Martin
Catalysts, autocatalysis and the origin of metabolism
published pages: 20190072, ISSN: 2042-8898, DOI: 10.1098/rsfs.2019.0072
Interface Focus 9/6 2019-11-28
2019 Verena Zimorski, Marek Mentel, Aloysius G.M. Tielens, William F. Martin
Energy metabolism in anaerobic eukaryotes and Earth\'s late oxygenation
published pages: 279-294, ISSN: 0891-5849, DOI: 10.1016/j.freeradbiomed.2019.03.030
Free Radical Biology and Medicine 140 2019-11-28
2019 Edi Sudianto, Chung-Shien Wu, Lars Leonhard, William F. Martin, Shu-Miaw Chaw
Enlarged and highly repetitive plastome of Lagarostrobos and plastid phylogenomics of Podocarpaceae
published pages: 24-32, ISSN: 1055-7903, DOI: 10.1016/j.ympev.2018.12.012
Molecular Phylogenetics and Evolution 133 2019-11-28
2019 Clifford F. Brunk, William F. Martin
Archaeal Histone Contributions to the Origin of Eukaryotes
published pages: 703-714, ISSN: 0966-842X, DOI: 10.1016/j.tim.2019.04.002
Trends in Microbiology 27/8 2019-11-28
2019 William F. Martin
Carbon–Metal Bonds: Rare and Primordial in Metabolism
published pages: 807-818, ISSN: 0968-0004, DOI: 10.1016/j.tibs.2019.04.010
Trends in Biochemical Sciences 44/9 2019-11-28
2018 Shir Portugez, William F. Martin, Einat Hazkani-Covo
Mosaic mitochondrial-plastid insertions into the nuclear genome show evidence of both non-homologous end joining and homologous recombination
published pages: , ISSN: 1471-2148, DOI: 10.1186/s12862-018-1279-x
BMC Evolutionary Biology 18/1 2019-11-28
2018 Sriram G. Garg, William F. Martin
Asking endosymbionts to do an enzyme’s job
published pages: E4543-E4544, ISSN: 0027-8424, DOI: 10.1073/pnas.1804397115
Proceedings of the National Academy of Sciences 115/20 2019-07-02
2017 William F. Martin
Going back in genes
published pages: 20-23, ISSN: 0006-3347, DOI:
The Biologist 64 2019-07-02
2018 Nils Kapust, Shijulal Nelson-Sathi, Barbara Schönfeld, Einat Hazkani-Covo, David Bryant, Peter J Lockhart, Mayo Röttger, Joana C Xavier, William F Martin
Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication
published pages: 1198-1209, ISSN: 1759-6653, DOI: 10.1093/gbe/evy080
Genome Biology and Evolution 10/5 2019-07-02
2017 William F. Martin
Too Much Eukaryote LGT
published pages: 1700115, ISSN: 0265-9247, DOI: 10.1002/bies.201700115
BioEssays 39/12 2019-07-02
2016 Gerda Horneck, Nicolas Walter, Frances Westall, John Lee Grenfell, William F. Martin, Felipe Gomez, Stefan Leuko, Natuschka Lee, Silvano Onofri, Kleomenis Tsiganis, Raffaele Saladino, Elke Pilat-Lohinger, Ernesto Palomba, Jesse Harrison, Fernando Rull, Christian Muller, Giovanni Strazzulla, John R. Brucato, Petra Rettberg, Maria Teresa Capria
AstRoMap European Astrobiology Roadmap
published pages: 201-243, ISSN: 1531-1074, DOI: 10.1089/ast.2015.1441
Astrobiology 16/3 2019-07-02
2016 John F. Allen, William F. Martin
Why Have Organelles Retained Genomes?
published pages: 70-72, ISSN: 2405-4712, DOI: 10.1016/j.cels.2016.02.007
Cell Systems 2/2 2019-07-02
2016 Marek Mentel, Aloysius G. M. Tielens, William F. Martin
Animals, anoxic environments, and reasons to go deep
published pages: , ISSN: 1741-7007, DOI: 10.1186/s12915-016-0266-1
BMC Biology 14/1 2019-07-02
2015 Nives Rajević, Goran Kovačević, Mirjana Kalafatić, Sven B. Gould, William F. Martin, Damjan Franjević
Algal endosymbionts in European Hydra strains reflect multiple origins of the zoochlorella symbiosis
published pages: 55-62, ISSN: 1055-7903, DOI: 10.1016/j.ympev.2015.07.014
Molecular Phylogenetics and Evolution 93 2019-07-02
2017 Cessa Rauch, Peter Jahns, Aloysius G. M. Tielens, Sven B. Gould, William F. Martin
On Being the Right Size as an Animal with Plastids
published pages: 1402, ISSN: 1664-462X, DOI: 10.3389/fpls.2017.01402
Frontiers in Plant Science 8 2019-07-02
2015 Shijulal Nelson-Sathi, William F. Martin
The Origin of a Killer Revealed by Bronze Age Yersinia Genomes
published pages: 513-514, ISSN: 1931-3128, DOI: 10.1016/j.chom.2015.10.016
Cell Host & Microbe 18/5 2019-07-02
2016 Madeline C. Weiss, Sinje Neukirchen, Mayo Roettger, Natalia Mrnjavac, Shijulal Nelson-Sathi, William F. Martin, Filipa L. Sousa
Reply to ‘Is LUCA a thermophilic progenote?’
published pages: 16230, ISSN: 2058-5276, DOI: 10.1038/nmicrobiol.2016.230
Nature Microbiology 1/12 2019-07-02
2018 William F. Martin
Eukaryote lateral gene transfer is Lamarckian
published pages: 754-754, ISSN: 2397-334X, DOI: 10.1038/s41559-018-0521-7
Nature Ecology & Evolution 2/5 2019-07-02
2017 William F. Martin, Verena Zimorski, Madeline C. Weiss
Wo lebten die ersten Zellen - und wovon?
published pages: 186-192, ISSN: 0045-205X, DOI: 10.1002/biuz.201710622
Biologie in unserer Zeit 47/3 2019-07-02
2015 William F. Martin, Sinje Neukirchen, Filipa L. Sousa
Early Life
published pages: 171-184, ISSN: , DOI: 10.1515/9783110340716.171
Microbial Evolution under Extreme Conditions 2019-07-02
2015 Filipa L Sousa, Wim Hordijk, Mike Steel, William F Martin
Autocatalytic sets in E. coli metabolism
published pages: , ISSN: 1759-2208, DOI: 10.1186/s13322-015-0009-7
Journal of Systems Chemistry 6/1 2019-07-02
2017 Einat Hazkani-Covo, William F. Martin
Quantifying the number of independent organelle DNA insertions in genome evolution and human health
published pages: 1190–1203, ISSN: 1759-6653, DOI: 10.1093/gbe/evx078
Genome Biology and Evolution 9 2019-07-02
2016 Bill Martin
Bill Martin
published pages: R515-R517, ISSN: 0960-9822, DOI: 10.1016/j.cub.2016.05.010
Current Biology 26/13 2019-07-02
2016 S. Garg, V. Zimorski, W.F. Martin
Endosymbiotic Theory
published pages: 511-517, ISSN: , DOI: 10.1016/b978-0-12-800049-6.00191-8
The Encyclopedia of Evolutionary Biology, Vol. 1 2019-07-02
2015 Chuan Ku, Shijulal Nelson-Sathi, Mayo Roettger, Sriram Garg, Einat Hazkani-Covo, William F. Martin
Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes
published pages: 10139-10146, ISSN: 0027-8424, DOI: 10.1073/pnas.1421385112
Proceedings of the National Academy of Sciences 112/33 2019-07-02
2017 William F Martin, Donald A Bryant, J Thomas Beatty
A physiological perspective on the origin and evolution of photosynthesis
published pages: 205-231, ISSN: 1574-6976, DOI: 10.1093/femsre/fux056
FEMS Microbiology Reviews 42/2 2019-07-02
2018 Filipa L Sousa, Martina Preiner, William F Martin
Native metals, electron bifurcation, and CO 2 reduction in early biochemical evolution
published pages: 77-83, ISSN: 1369-5274, DOI: 10.1016/j.mib.2017.12.010
Current Opinion in Microbiology 43 2019-07-02
2016 Xi Chen, Karoline Schreiber, Jens Appel, Alexander Makowka, Berit Fähnrich, Mayo Roettger, Mohammad R. Hajirezaei, Frank D. Sönnichsen, Peter Schönheit, William F. Martin, Kirstin Gutekunst
The Entner–Doudoroff pathway is an overlooked glycolytic route in cyanobacteria and plants
published pages: 5441-5446, ISSN: 0027-8424, DOI: 10.1073/pnas.1521916113
Proceedings of the National Academy of Sciences 113/19 2019-07-02
2016 Peter Schönheit, Wolfgang Buckel, William F. Martin
On the Origin of Heterotrophy
published pages: 12-25, ISSN: 0966-842X, DOI: 10.1016/j.tim.2015.10.003
Trends in Microbiology 24/1 2019-07-02
2015 Sven B. Gould, Uwe-G. Maier, William F. Martin
Protein Import and the Origin of Red Complex Plastids
published pages: R515-R521, ISSN: 0960-9822, DOI: 10.1016/j.cub.2015.04.033
Current Biology 25/12 2019-07-02
2015 Sriram Garg, Jan Stölting, Verena Zimorski, Petr Rada, Jan Tachezy, William F. Martin, Sven B. Gould
Conservation of Transit Peptide-Independent Protein Import into the Mitochondrial and Hydrogenosomal Matrix
published pages: 2716-2726, ISSN: 1759-6653, DOI: 10.1093/gbe/evv175
Genome Biology and Evolution 7/9 2019-07-02
2017 William F. Martin, Rudolf K. Thauer
Energy in Ancient Metabolism
published pages: 953-955, ISSN: 0092-8674, DOI: 10.1016/j.cell.2017.02.032
Cell 168/6 2019-07-02
2015 William F. Martin, Sriram Garg, Verena Zimorski
Endosymbiotic theories for eukaryote origin
published pages: 20140330, ISSN: 0962-8436, DOI: 10.1098/rstb.2014.0330
Philosophical Transactions of the Royal Society B: Biological Sciences 370/1678 2019-07-02
2017 William F. Martin, Helmut Sies
Physiological evolution: Genomic redox footprints
published pages: 17071, ISSN: 2055-0278, DOI: 10.1038/nplants.2017.71
Nature Plants 3/6 2019-07-02
2015 Nick Lane, William F. Martin
Eukaryotes really are special, and mitochondria are why
published pages: E4823-E4823, ISSN: 0027-8424, DOI: 10.1073/pnas.1509237112
Proceedings of the National Academy of Sciences 112/35 2019-07-02
2016 Re-Young Yu, William F. Martin
Symbiotic associations: all about chemistry
published pages: 3-11, ISSN: , DOI: 10.1007/978-3-319-28068-4_1
The Mechanistic Benefits of Microbial Symbionts 2019-07-02
2015 John A. Baross, William F. Martin
The Ribofilm as a Concept for Life’s Origins
published pages: 13-15, ISSN: 0092-8674, DOI: 10.1016/j.cell.2015.06.038
Cell 162/1 2019-07-02
2017 William F. Martin
Unmiraculous facultative anaerobes (comment on DOI 10.1002/bies.201600174)
published pages: 1700041, ISSN: 0265-9247, DOI: 10.1002/bies.201700041
BioEssays 39/6 2019-07-02
2016 Nick Lane, William F. Martin
Mitochondria, complexity, and evolutionary deficit spending
published pages: E666-E666, ISSN: 0027-8424, DOI: 10.1073/pnas.1522213113
Proceedings of the National Academy of Sciences 113/6 2019-07-02
2016 Sven B. Gould, Sriram G. Garg, William F. Martin
Bacterial Vesicle Secretion and the Evolutionary Origin of the Eukaryotic Endomembrane System
published pages: 525-534, ISSN: 0966-842X, DOI: 10.1016/j.tim.2016.03.005
Trends in Microbiology 24/7 2019-07-02
2015 Vincenzo Carbone, Linley R. Schofield, Yanli Zhang, Carrie Sang, Debjit Dey, Ingegerd M. Hannus, William F. Martin, Andrew J. Sutherland-Smith, Ron S. Ronimus
Structure and Evolution of the Archaeal Lipid Synthesis Enzyme sn -Glycerol-1-phosphate Dehydrogenase
published pages: 21690-21704, ISSN: 0021-9258, DOI: 10.1074/jbc.M115.647461
Journal of Biological Chemistry 290/35 2019-07-02
2015 Chuan Ku, Shijulal Nelson-Sathi, Mayo Roettger, Filipa L. Sousa, Peter J. Lockhart, David Bryant, Einat Hazkani-Covo, James O. McInerney, Giddy Landan, William F. Martin
Endosymbiotic origin and differential loss of eukaryotic genes
published pages: 427-432, ISSN: 0028-0836, DOI: 10.1038/nature14963
Nature 524/7566 2019-07-02
2016 Filipa L. Sousa, Sinje Neukirchen, John F. Allen, Nick Lane, William F. Martin
Lokiarchaeon is hydrogen dependent
published pages: 16034, ISSN: 2058-5276, DOI: 10.1038/nmicrobiol.2016.34
Nature Microbiology 1/5 2019-07-02
2016 Sriram G. Garg, William F. Martin
Mitochondria, the Cell Cycle, and the Origin of Sex via a Syncytial Eukaryote Common Ancestor
published pages: 1950-1970, ISSN: 1759-6653, DOI: 10.1093/gbe/evw136
Genome Biology and Evolution 8/6 2019-07-02
2016 William Martin, Madeline Weiss, Sinje Neukirchen, Shijulal Nelson-Sathi, Filipa Sousa
Physiology, phylogeny, and LUCA
published pages: 582-587, ISSN: 2311-2638, DOI: 10.15698/mic2016.12.545
Microbial Cell 3/12 2019-07-02
2015 Shijulal Nelson-Sathi, Filipa L. Sousa, Mayo Roettger, Nabor Lozada-Chávez, Thorsten Thiergart, Arnold Janssen, David Bryant, Giddy Landan, Peter Schönheit, Bettina Siebers, James O. McInerney, William F. Martin
Origins of major archaeal clades correspond to gene acquisitions from bacteria
published pages: 77-80, ISSN: 0028-0836, DOI: 10.1038/nature13805
Nature 517/7532 2019-07-02
2016 Chuan Ku, William F. Martin
A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule
published pages: , ISSN: 1741-7007, DOI: 10.1186/s12915-016-0315-9
BMC Biology 14/1 2019-07-02
2017 William F. Martin
Physiology, phylogeny, and the energetic roots of life
published pages: , ISSN: 0031-5362, DOI: 10.18054/pb.v118i4.4737
Periodicum Biologorum 118/4 2019-07-02
2017 William F. Martin
Physiology, anaerobes, and the origin of mitosing cells 50 years on
published pages: 2–10, ISSN: 0022-5193, DOI: 10.1016/j.jtbi.2017.01.004
Journal of Theoretical Biology 434 2019-07-02
2016 William F. Martin, Filipa L. Sousa
Early Microbial Evolution: The Age of Anaerobes
published pages: a018127, ISSN: 1943-0264, DOI: 10.1101/cshperspect.a018127
Cold Spring Harbor Perspectives in Biology 8/2 2019-07-02
2016 William F. Martin, Sinje Neukirchen, Verena Zimorski, Sven B. Gould, Filipa L. Sousa
Energy for two: New archaeal lineages and the origin of mitochondria
published pages: 850-856, ISSN: 0265-9247, DOI: 10.1002/bies.201600089
BioEssays 38/9 2019-07-02
2017 William Martin
Symbiogenesis, gradualism, and mitochondrial energy in eukaryote origin
published pages: 141-158, ISSN: 0031-5362, DOI: 10.18054/pb.v119i3.5694
Periodicum Biologorum 119/3 2019-07-02
2017 William F. Martin, Rüdiger Cerff
Physiology, phylogeny, early evolution, and GAPDH
published pages: 1823–1834, ISSN: 0033-183X, DOI: 10.1007/s00709-017-1095-y
Protoplasma 254 2019-07-02
2016 Madeline C. Weiss, Filipa L. Sousa, Natalia Mrnjavac, Sinje Neukirchen, Mayo Roettger, Shijulal Nelson-Sathi, William F. Martin
The physiology and habitat of the last universal common ancestor
published pages: 16116, ISSN: 2058-5276, DOI: 10.1038/nmicrobiol.2016.116
Nature Microbiology 1/9 2019-07-02
2017 William F. Martin, Aloysius G. M. Tielens, Marek Mentel, Sriram G. Garg, Sven B. Gould
The Physiology of Phagocytosis in the Context of Mitochondrial Origin
published pages: e00008-17, ISSN: 1092-2172, DOI: 10.1128/MMBR.00008-17
Microbiology and Molecular Biology Reviews 81/3 2019-07-02
2016 Filipa L. Sousa, Shijulal Nelson-Sathi, William F. Martin
One step beyond a ribosome: The ancient anaerobic core
published pages: 1027-1038, ISSN: 0005-2728, DOI: 10.1016/j.bbabio.2016.04.284
Biochimica et Biophysica Acta (BBA) - Bioenergetics 1857/8 2019-07-02
2018 William F. Martin, John F. Allen
An Algal Greening of Land
published pages: 256-258, ISSN: 0092-8674, DOI: 10.1016/j.cell.2018.06.034
Cell 174/2 2019-04-18
2018 Marie Gerlitz, Michael Knopp, Nils Kapust, Joana C. Xavier, William F. Martin
Elusive data underlying debate at the prokaryote-eukaryote divide
published pages: , ISSN: 1745-6150, DOI: 10.1186/s13062-018-0221-x
Biology Direct 13/1 2019-04-18
2018 Madeline C. Weiss, Martina Preiner, Joana C. Xavier, Verena Zimorski, William F. Martin
The last universal common ancestor between ancient Earth chemistry and the onset of genetics
published pages: e1007518, ISSN: 1553-7404, DOI: 10.1371/journal.pgen.1007518
PLOS Genetics 14/8 2019-04-18
2018 Michiel L. Bexkens, Verena Zimorski, Maarten J. Sarink, Hans Wienk, Jos F. Brouwers, Johan F. De Jonckheere, William F. Martin, Fred R. Opperdoes, Jaap J. van Hellemond, Aloysius G.M. Tielens
Lipids Are the Preferred Substrate of the Protist Naegleria gruberi, Relative of a Human Brain Pathogen
published pages: 537-543.e3, ISSN: 2211-1247, DOI: 10.1016/j.celrep.2018.09.055
Cell Reports 25/3 2019-04-18
2017 William F. Martin, Mayo Roettger, Chuan Ku, Sriram G. Garg, Shijulal Nelson-Sathi, Giddy Landan
Late Mitochondrial Origin Is an Artifact
published pages: 373-379, ISSN: 1759-6653, DOI: 10.1093/gbe/evx027
Genome Biology and Evolution 9/2 2019-07-02
2018 Joana C. Xavier, Martina Preiner, William F. Martin
Something special about CO-dependent CO 2 fixation
published pages: 4181-4195, ISSN: 1742-464X, DOI: 10.1111/febs.14664
The FEBS Journal 285/22 2019-05-27
2018 Martina Preiner, Joana Xavier, Filipa Sousa, Verena Zimorski, Anna Neubeck, Susan Lang, H. Greenwell, Karl Kleinermanns, Harun Tüysüz, Tom McCollom, Nils Holm, William Martin
Serpentinization: Connecting Geochemistry, Ancient Metabolism and Industrial Hydrogenation
published pages: 41, ISSN: 2075-1729, DOI: 10.3390/life8040041
Life 8/4 2019-05-27

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