PLAN DU SITE PHILOSOPHIE HISTORY OF BIOLOGY PHILOSOPHY SITE MAP



1967-1971 IBPC-1981 REG-1986 REG-1991 REG-1996 GGB-2001 GGB-2006 AMA-2011 AMA-2016
1972-1974 IBPC-1982 REG-1987 REG-1992 REG-1997 GGB-2002 GGB-2007 AMA-2012 ICAN-2017 
1975-1978 BRC-1983 REG-1988 REG-1993 REG-1998 GGB-2003 GGB-2008 AMA-2013 ICAN-2018
IBPC-1979 BRC-1984 REG-1989 REG-1994 REG-1999 GGB-2004 AMA-2009 AMA-2014 Cochin-2019
IBPC-1980 BRC-1985 REG-1990 REG-1995 GGB-2000 GGB-2005 AMA-2010 AMA-2015  

Publications in the domain of Philosophy, History of Sciences and Ethics

Symplectic Biology

Lectures and seminars

Publications listed at PubMed

Publications listed at Google Scholar

 


 


PM Binder, A Danchin
Life's demons: information and order in biology. What subcellular machines gather and process the information necessary to sustain life?
EMBO Reports (2011) 12: 495-499 PubMed

In his seventeenth-century classic, Novum Organum, Francis Bacon wrote, “we cannot command nature except by obeying her” (Bacon, 2010). Although our knowledge of living systems is much improved since Bacon’s time, we are still far from understanding—or commanding—all the complex mechanisms of life. To take full advantage of living organisms for the benefit of mankind, we will need to understand those mechanisms to the furthest possible extent. To do so will require that the concept of information and the theories of information science take a more-prominent role in the understanding of living systems...

A Danchin
Les gènes du démon de Maxwell : est-il possible de construire une usine cellulaire ?
Maxwell’s demon’s genes: Can we build a cell factory?
Comptes Rendus de l'Académie des Sciences, Chimie (2011) 14: 413-419 microme


A Danchin, PM Binder, S Noria
Antifragility and tinkering in biology (and in business): Flexibility provides an efficient epigenetic way to manage risk
Genes (2011), 2: 998-1016; doi:10.3390/genes2040998 microme

F Piette, S D'Amico, G Mazzucchelli, A Danchin, P Leprince, G Feller
Life in the cold: a proteomic study of cold-repressed proteins in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125.
Applied and Environmental Microbiology (2011) 77: 3881-3883   PubMed

M Porcar, A Danchin, V de Lorenzo, VA dos Santos, N Krasnogor, S Rasmussen, A Moya
The ten grand challenges of synthetic life
Systems and Synthetic Biology (2011) 5: 1-9 PubMed microme

H Rohde, J Qin, Y Cui, D Li, NJ Loman, M Hentschke, W Chen, Fei Pu, Y Peng, J Li, F Xi, S Li, Y Li, Z Zhang, X Yang, M Zhao, Peng Wang, Y Guan, Z Cen, X Zhao, M Christner, R Kobbe, S Loos, J Oh, L Yang, A Danchin, GF Gao, Y Song, Y Li, H Yang, J Wang, J Xu, the E. coli O104:H4 Genome Analysis Crowd-sourcing consortium, MJ Pallen, J Wang, M Aepfelbacher, R Yang
Open-source genomics of an isolate from a german family outbreak of Shiga-toxin-producing Escherichia coli O104:H4
New England Journal of Medicine (2011) 365: 718-724 PubMed microme

Y Wang, J Yang, OO Lee, S Dash, SC Lau, A Al-Suwailem, TY Wong, A Danchin, PY Qian
Hydrothermally generated aromatic compounds are consumed by bacteria colonizing in Atlantis II Deep of the Red Sea.
ISME J (2011) 5: 1652-1659 PubMed


Y Wang, JK Yang, OO Lee, TG Li, A Al-Suwailem, A Danchin, P-Y Qian
Bacterial niche-specific genome expansion Is coupled with highly frequent gene disruptions in deep-sea sediments
PLoS ONE (2011) 6: e29149 PubMed

B Wilmes, H Kock, S Glagla, D Albrecht, B Voigt, S Markert, A Gardebrecht, R Bode, A Danchin, G Feller, M Hecker, M Schweder
Cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125.
Applied and Environmental Microbiology (2011) 77: 1276-1283 pubmed   

Admiration ou plagiat ?
Alfred Döblin et la science
Scénarios romanesques: virus contre bactéries multirésistantes
Esprit de géométrie, esprit de finesse
En marge de l'histoire de la Serbie, les déshérités Grecs cf Histoire de Petros Kokkalis
Épidémie de conspirations
Avons-nous déshumanisé la filiation ?
Le dangereux virus de la rumeur
Ni Adam, ni Ève


 


RM Couture, A Sekowska, G Fang, A Danchin
Linking selenium biogeochemistry to the sulfur-dependent biological detoxification of arsenic
Environ Microbiol (2012) 14: 1612-1623. doi: 10.1111/j.1462-2920.2012.02758.x. PubMed microme pdf

A Danchin
Scaling up synthetic biology: Do not forget the chassis
FEBS Letters (2012)586: 2129-2137. PubMed microme

A Danchin
Synthetic biology's flywheel
EMBO Reports (2012) 13: 92 PubMed

A Danchin
I geni del diavoletto di Maxwell
Prometeo 117: 120-125


S Engelen, D Vallenet, C Médigue, A Danchin
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC
BMC Genomics (2012) 13: 69. PubMed microme

Karsch-Mizrachi I, Nakamura Y, Cochrane G; International Nucleotide Sequence Database Collaboration
Miyano S, Nakamura H, Sugano S, Danchin A, Savakis B, Weissenbach J, Weng Z, Salzberg S

The International Nucleotide Sequence Database Collaboration
Nucleic Acids Research (2012) 40: D33-D37 pubmed

MF Liu, S Cescau, U Mechold, J Wang, D Cohen, A Danchin, HJ Boulouis, F Biville
Identification of a new nanoRNase in Bartonella
Microbiology (2012)158: 886-895 pubmedtarpol

G Postic, A Danchin, U Mechold
Characterization of NrnA homologs from Mycobacterium tuberculosis and Mycoplasma pneumoniae
RNA (2012) 18: 155-165 PubMed microme

M Schmidt, M Porcar, V Schächter, A Danchin, I Mahmutoglu
Biofuels, pp
L Pei, M Morange, R Armstrong, A Danchin, M Porcar
Biomaterials, pp
In: Synthetic Biology. Industrial and Environmental Applications (Editor M Schmidt), Wiley VCH, Weinheim (2012) tarpol
sb

E Toledano, V Ogryzko, A Danchin, D Ladant, U Mechold
3’‐5’phosphoadenosine phosphate is an inhibitor of Poly(ADP-ribose) Polymerase 1 and a potential mediator of the lithium-dependent inhibition of PARP‐1 in vivo
Biochemical Journal (2012) 443: 485-490. PubMed

The biology of luxury (October 16th 2012)

luxury2   luxury
jordan_times

The anti-fragile life of the economy   abc_science    chloregycn_comments

The anti-fragile life of the economy may be its saving grace taipei_times
A vida anti-frágil da economia      publico
Antifragilität. Was die Wirtschaft von der Evolution lernen kann welt
La vie antifragile de l'économie

 

Chercheurs de catastrophes : la morale grippée
Aurons-nous assez de coqs pour vaincre la grippe ?
La loterie gagnante de l'accident
L'américanisation soviétique du genre

 



CG Acevedo-Rocha, G Fang, M Schmidt, DW Ussery, A Danchin
From essential to persistent genes: a functional approach to constructing synthetic life
Trends Genet. (2013) 29: 273-279. doi: 10.1016/j.tig.2012.11.001 pubmed

E Belda, A Sekowska, F Le Fèvre, A Morgat, D Mornico, C Ouzounis, D Vallenet, C Médigue, A Danchin
An updated metabolic view of the Bacillus subtilis 168 genome
Microbiology (2013) 159: 757-770. doi: 10.1099/mic.0.064691-0 pubmed

A Danchin
To understand and solve, share, foresee
Ludus Vitalis (2013) XXI: 263-265 pdf


A Danchin, A Sekowska
Constraints in the design of the synthetic bacterial chassis
Methods in Microbiology (2013) 40: 39-68

A pour Andromède : la biologie et ses lois

 



CM Chan, A Danchin, P Marlière, A Sekowska
Paralogous metabolism: S-alkyl-cysteine degradation in Bacillus subtilis
Environ Microbiol (2014) 16: 101-117 pubmed

A Danchin, A Sekowska
The logic of metabolism and its fuzzy consequences
Environ Microbiol (2014) 16: 19-28 pubmed

A Danchin
Comment effacer la mémoire de sa mère, ou pourquoi les bébés naissent-ils très jeunes ?
L'Archicube (2014) 16: 55-61

A Danchin
The emergence of the first cells
Encyclopedia of Molecular Cell Biology and Molecular Medicine (2014) doi: 10.1002/3527600906.mcb.20130025
Abstract The scenario proposed here builds on the critical need for compartmentalisation at the origin of life. In a first step, the surface of minerals compartmentalised and selected the reactive compounds that formed primitive metabolism. Subsequently, RNA molecules replaced mineral surfaces after the discovery of nitrogen fixation and the emergence of ribonucleotides, in parallel with a machinery for synthesis of peptides, coenzymes and lipids. Then, the RNA-metabolism world developed into an RNA-genome world based on RNA as informational templates rather than substrates. Bordered by lipids, the first cells were phagocytes, Protokarya, which put together two compartments stemming from the RNA-metabolism world (the cytoplasm) and the RNA-genome world (the nucleus). Emergence of stable deoxyribonucleotides allowed the clustering together of genes into chromosomes. Phagocytosis created the opportunity for an escape based on an alternative metabolism of membrane lipids and conquest of extreme environments, with the Archaea, and on the emergence of a robust and phagocyte-resistant envelope, with the Bacteria. Reductive evolution allowed bacteria with a modified enveloped to be phagocyted again as symbionts of Protokarya, leading to the final generation of the Eukarya. Continuation of horizontal transfer of the genetic material initially resulting from phagocytosis was carried on with the emergence of gene transfer via specialised conjugation machineries and viruses.


Kyrpides, NC, Hugenholtz, P, Eisen, JA, Woyke, T, Goker, M, Parker, CT, Amann, R, Beck, BJ, Chain, PSG, Chun, J, Colwell, RR, Danchin, A, Dawyndt, P, Dedeurwaerdere, T, DeLong, EF; Detter, JC, De Vos, P, Donohue, TJ, Dong, X-Z, Ehrlich, DS, Fraser, C, Gibbs, R, Gilbert, J, Gilna, P, Glockner, FO, Jansson, JK, Keasling, JD, Knight, R, Labeda, D, Lapidus, Al, Lee, J-S, Li, W-J, Ma, J, Markowitz, V, Moore, ERB, Morrison, M, Meyer, F, Nelson, KE, Ohkuma, M, Ouzounis, CA, Pace, N, Parkhill, J, Qin, N, Rossello-Mora, R, Sikorski, J, Smith, D, Sogin, M, Stevens, R, Stingl, U, Suzuki, K-I, Taylor, D, Tiedje, JM, Tindall, B, Wagner, M, Weinstock, G, Weissenbach, J, White, O, Wang, J, Zhang, L, Zhou, Y-G, Field, D, Whitman, WB, Garrity, GM, Klenk, H-P
Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strain
PLoS Biology (2014) 12: e1001920

Icarie, l'Ile radieuse



Risk Engineering
A Danchin
The cellular chassis as the basis for new functionalities: Shortcomings and requirements
In: Synthetic Biology. Character and Impact (Editors B.M. Giese, C. Pade, H. Wigger, A. von Gleich), Springer, Berlin (2015)
  sb

M Porcar, A Danchin, V de Lorenzo
Confidence, tolerance, and allowance in biological engineering: The nuts and bolts of living things
BioEssays (2015) 37: 95-102
Abstract The emphasis of systems and synthetic biology on quantitative understanding of biological objects and their eventual re-design has raised the question of whether description and construction standards that are commonplace in electric and mechanical engineering are applicable to live systems. The tuning of genetic devices to deliver a given activity is generally context-dependent, thereby undermining the re-usability of parts, and predictability of function, necessary for manufacturing new biological objects. Tolerance (acceptable limits within the unavoidable divergence of a nominal value) and allowance (deviation introduced on purpose for the sake of flexibility and hence modularity, i.e. fitting together with a variety of other components) are key aspects of standardization that need to be brought to biological design. These should endow functional building blocks with a pre-specified level of confidence for bespoke biosystems engineering. However, in the absence of more fundamental knowledge, fine-tuning necessarily relies on evolutionary/combinatorial gravitation toward a fixed objective

V de Lorenzo, A Sekowska, A Danchin,
Chemical reactivity drives spatiotemporal organisation of bacterial metabolism
FEMS Microbiology Reviews (2015) 39: 96-119
Abstract We examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects

A Danchin, A Sekowska

The logic of metabolism
Perspectives in Science (2015) 6: 15-26



M Blaxter, A Danchin, B Savakis, K Fukami-Kobayashi, K Kurokawa, S Sugano, RJ Roberts, SL Salzberg, CI Wu
Reminder to deposit DNA sequences
Science (2016) 352: 780 doi: 10.1126/science.aaf7672

E Belda, RG van Heck, MJ Lopez-Sanchez, S Cruveiller, V Barbe, C Fraser, HP Klenk, J Petersen, A Morgat, PI Nikel, D Vallenet, Z Rouy, A Sekowska, VA Martins Dos Santos, V de Lorenzo, A Danchin, C Médigue
The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis
Environ Microbiol (2016) 18: 3403-3424. doi: 10.1111/1462-2920.13230

A Danchin
From function to structure take the archaeal TRAM
Environ Microbiol (2016) 18: 2776-2778 doi: 10.1111/1462-2920.13300

A Danchin
Nature or manufacture: What should we fear most?
C R Biol (2016) 339: 329-335. doi: 10.1016/j.crvi.2016.05.001

A Danchin, G Fang
Unknown unknowns: essential genes in quest for function
Microb Biotechnol. (2016) 9: 530-540 doi: 10.1111/1751-7915.12384

PI Nikel, M Chavarría, A Danchin, V de Lorenzo
From dirt to industrial applications: Pseudomonas putida as a Synthetic Biology chassis for hosting harsh biochemical reactions
Curr Opin Chem Biol (2016) 34: 20-29 doi: 10.1016/j.cbpa.2016.05.011

A Sekowska, S Wendel, EC Fischer, MH Nørholm, A Danchin
Generation of mutation hotspots in ageing bacterial colonies
Sci Rep (2016) 6: 2. doi: 10.1038/s41598-016-0005-4

K Timmis, JL Ramos, W de Vos, S Vlaeminck, A Prieto, A Danchin, W Verstraete, V de Lorenzo
Microbial Biotechnology-2020
Microb Biotechnol. (2016) 9: 529 doi: 10.1111/1751-7915.12403

Y Wang, JM Huang, SL Wang, ZM Gao, AQ Zhang, A Danchin, LS He
Genomic characterization of symbiotic mycoplasmas from the stomach of deep-sea isopod Bathynomus sp.
Environ Microbiol (2016) 18: 2646-2659 doi: 10.1111/1462-2920.13411



A Danchin
Coping with inevitable accidents of metabolism
Microb Biotechnol. (2017) 10: 57-72 doi: 10.1111/1751-7915.12461

K Bastard, A Perret, A Mariage, T Bessonnet, A Pinet-Turpault, J-L Petit, E Darii, P Bazire, C Vergne-Vaxelaire, C Brewee, A Debard, V Pellouin, M Besnard-Gonnet, F Artiguenave, C Médigue, D Vallenet, A Danchin, A Zaparucha, J Weissenbach, M Salanoubat, V de Berardinis
Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis
Nat Chem Biol. (2017)13: 858-866 doi:10.1038/nchembio.2397

A Danchin
From chemical metabolism to life: the origin of the genetic coding process
Beilstein J Org Chem. (2017) 13: 1119-1135 doi:10.3762/bjoc.13.111

A Danchin, S Braham
Coenzyme B12 synthesis as a baseline to study metabolite contribution of animal microbiota
Microb Biotechnol. (2017) 10: 688-701 doi:10.1111/1751-7915.12722

Timmis K, de Vos WM, Ramos JL, Vlaeminck SE, Prieto A, Danchin A, Verstraete W, de Lorenzo V, Lee SY, Brüssow H, Timmis JK, Singh BK
The contribution of microbial biotechnology to sustainable development goals
Microb Biotechnol. (2017) 10: 984-987 doi: 10.1111/1751-7915.12818

Timmis K, de Lorenzo V, Verstraete W, Ramos JL, Danchin A, Brüssow H, Singh BK, Timmis JK
The contribution of microbial biotechnology to economic growth and employment creation
Microb Biotechnol. (2017) 10: 1137-1144 doi: 10.1111/1751-7915.12845

He LS, Zhang PW, Huang JM, Zhu FC, Danchin A, Wang Y
The enigmatic genome of an obligate ancient Spiroplasma symbiont in a hadal holothurian.
Appl Environ Microbiol. (2017) 84:  e01965-17 doi: 10.1128/AEM.01965-17

A Danchin
CRISPR-Cas, accélérateur de la recherche génétique du XXIe siècle
L'Humanité Dimanche 2 novembre 2017

A. Danchin
Produit de l'écriture, la science fait l'humanité de l'homme
Qu'est-ce que la science pour vous ? (2017) pp. 71-75    Éditions matériologiques, Paris
science

A Danchin
The holy grail of genetic engineering
Project Syndicate 14 december 2017

Korea
gulf
hongkong
zhhongkong
russia
liban
wef
china
russian2
lebanon
ruised
independent




R Borriss, A Danchin, CR Harwood, C Médigue, EPC Rocha, A Sekowska, D Vallenet
Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement
Microb Biotechnol. (2018) 11: 3-17 doi: 10.1111/1751-7915.12461

Y Wang, FC Zhu, LS He, A Danchin
Unique tRNA gene profile suggests paucity of nucleotide modifications in anticodons of a deep-sea symbiotic Spiroplasma
Nucleic Acids Res. (2018) 46: 2197-2203 doi:10.1111/1751-7915.12461

A Danchin
Bacteria in the ageing gut: Did the taming of fire promote a long human lifespan?
Environ Microbiol. (2018) 20: 1066-1087 doi:10.1111/1462-2920.14255

A Danchin, C Ouzounis, T Tokuyasu, JD Zucker
No wisdom in the crowd: genome annotation in the era of big data - current status and future prospects
Microb Biotechnol. (2018) 11: 588-605 doi:10.1111/1751-7915.13284

A Danchin
Retour sur les origines de la vie: De l'atome aux molécules, reproduction, réplication
Med Sci (Paris) (2018) 34: 857-864 doi:10.1051/medsci/2018212

A Danchin
Retour sur les origines de la vie: Des métabolites aux cellules
Med Sci (Paris) (2018) 34: 984-899 doi:10.1051/medsci/2018234

A Danchin, A Sekowska, S Noria

Chapter 5. Functional requirements in the program and the cell chassis for next-generation synthetic biology pp. 81-108
In: Synthetic Biology: Parts, Devices and Applications (2018) Christina Smolke (Editor)
Sang Yup Lee (Series Editor), Jens Nielsen (Series Editor), Gregory Stephanopoulos (Series Editor), Wiley
doi:10.1002/9783527688104.ch5          

ISBN: 978-3-527-68808-1


sb

A Danchin
Multiple clocks in the evolution of living organisms pp. 101-118
In: Molecular Mechanisms of Microbial Evolution (2018)
edited by Pabulo H. Rampelotto, Springer
ISBN: 978-3-319-69078-0
evolution