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  1. Article ; Online: Science, method and critical thinking.

    Danchin, Antoine

    Microbial biotechnology

    2023  Volume 16, Issue 10, Page(s) 1888–1894

    Abstract: Science is founded on a method based on critical thinking. A prerequisite for this is not only a sufficient command of language but also the comprehension of the basic concepts underlying our understanding of reality. This constraint implies an awareness ...

    Abstract Science is founded on a method based on critical thinking. A prerequisite for this is not only a sufficient command of language but also the comprehension of the basic concepts underlying our understanding of reality. This constraint implies an awareness of the fact that the truth of the World is not directly accessible to us, but can only be glimpsed through the construction of models designed to anticipate its behaviour. Because the relationship between models and reality rests on the interpretation of founding postulates and instantiations of their predictions (and is therefore deeply rooted in language and culture), there can be no demarcation between science and non-science. However, critical thinking is essential to ensure that the link between models and reality is gradually made more adequate to reality, based on what has already been established, thus guaranteeing that science progresses on this basis and excluding any form of relativism.
    MeSH term(s) Thinking ; Science
    Language English
    Publishing date 2023-07-18
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2406063-X
    ISSN 1751-7915 ; 1751-7915
    ISSN (online) 1751-7915
    ISSN 1751-7915
    DOI 10.1111/1751-7915.14315
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Pasteur and "motivated" research.

    Danchin, Antoine

    Comptes rendus biologies

    2022  Volume 345, Issue 3, Page(s) 109–119

    Abstract: Pasteur's originality in the way he developed pure research is to have understood the importance, for society, of the underlying motivation. Curiosity, of course, is a strong motivation, which explains why we seek to understand the origin of life. But, ... ...

    Abstract Pasteur's originality in the way he developed pure research is to have understood the importance, for society, of the underlying motivation. Curiosity, of course, is a strong motivation, which explains why we seek to understand the origin of life. But, in front of the immensity of the possible choices, why not, also, choose to start from questions of economic interest (diseases of beer and wine, diseases affecting the silk industry ...) Finally, of course, health is a constant preoccupation, but the diseases, which have no borders, often come from tropical countries and Asia especially. It is therefore necessary to settle there, but not to come and impose one's point of view, but on the contrary to use the knowledge coming from the local culture in order to open new ways of understanding the reality of the world.
    MeSH term(s) Microbiology/history ; Research
    Language English
    Publishing date 2022-11-10
    Publishing country France
    Document type Journal Article
    ZDB-ID 2072863-3
    ISSN 1768-3238 ; 1631-0691
    ISSN (online) 1768-3238
    ISSN 1631-0691
    DOI 10.5802/crbiol.89
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Biological innovation in the functional landscape of a model regulator, or the lactose operon repressor.

    Danchin, Antoine

    Comptes rendus biologies

    2021  Volume 344, Issue 2, Page(s) 111–126

    Abstract: The operon model was proposed six decades ago. And yet, despite all this time, the lactose operon repressor, LacI, remains a subject of major interest. While it is well established that LacI can exist in two functional forms, one that renders the operon ... ...

    Abstract The operon model was proposed six decades ago. And yet, despite all this time, the lactose operon repressor, LacI, remains a subject of major interest. While it is well established that LacI can exist in two functional forms, one that renders the operon inactive via binding of LacI to DNA and another, bound to an inducer that does not allow repression, how it switches from one to the other is still not well understood. The construction of a library of several tens of thousands of LacI mutants has revealed some unexpected features. In particular, the transition implemented in some of them reveals a new type of transcription regulation: band-pass (OFF/ON/OFF) and band-stop (ON/OFF/ON) filters. This makes it natural to think that it is the network of hydrogen bonds associated with the water bound to the molecule that allows the remote interconnection between the binding site to an inducer molecule and the one that binds it to the DNA.
    MeSH term(s) Binding Sites ; DNA ; Escherichia coli Proteins/genetics ; Lac Operon ; Lac Repressors/genetics ; Lac Repressors/metabolism
    Chemical Substances Escherichia coli Proteins ; Lac Repressors ; DNA (9007-49-2)
    Language English
    Publishing date 2021-07-02
    Publishing country France
    Document type News
    ZDB-ID 2072863-3
    ISSN 1768-3238 ; 1631-0691
    ISSN (online) 1768-3238
    ISSN 1631-0691
    DOI 10.5802/crbiol.52
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.B 1008: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular
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  4. Article ; Online: In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology.

    Danchin, Antoine

    Microbial biotechnology

    2021  Volume 15, Issue 1, Page(s) 42–64

    Abstract: Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that ... ...

    Abstract Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.
    MeSH term(s) Computational Biology ; Synthetic Biology
    Language English
    Publishing date 2021-09-27
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2406063-X
    ISSN 1751-7915 ; 1751-7915
    ISSN (online) 1751-7915
    ISSN 1751-7915
    DOI 10.1111/1751-7915.13937
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Three overlooked key functional classes for building up minimal synthetic cells.

    Danchin, Antoine

    Synthetic biology (Oxford, England)

    2021  Volume 6, Issue 1, Page(s) ysab010

    Abstract: Assembly of minimal genomes revealed many genes encoding unknown functions. Three overlooked functional categories account for some of them. Cells are prone to make errors and age. As a first key function, discrimination between proper and changed ... ...

    Abstract Assembly of minimal genomes revealed many genes encoding unknown functions. Three overlooked functional categories account for some of them. Cells are prone to make errors and age. As a first key function, discrimination between proper and changed entities is indispensable. Discrimination requires management of information, an authentic, yet abstract, currency of reality. For example proteins age, sometimes very fast. The cell must identify, then get rid of old proteins without destroying young ones. Implementing discrimination in cells leads to the second set of functions, usually ignored. Being abstract, information must nevertheless be embodied into material entities, with unavoidable idiosyncratic properties. This brings about novel unmet needs. Hence, the buildup of cells elicits specific but awkward material implementations, 'kludges' that become essential under particular settings, while difficult to identify. Finally, a third functional category characterizes the need for growth, with metabolic implementations allowing the cell to put together the growth of its cytoplasm, membranes, and genome, spanning different spatial dimensions. Solving this metabolic quandary, critical for engineering novel synthetic biology chassis, uncovered an unexpected role for CTP synthetase as the coordinator of nonhomothetic growth. Because a significant number of SynBio constructs aim at creating cell factories we expect that they will be attacked by viruses (it is not by chance that the function of the CRISPR system was identified in industrial settings). Substantiating the role of CTP, natural selection has dealt with this hurdle
    Language English
    Publishing date 2021-04-20
    Publishing country England
    Document type Journal Article
    ISSN 2397-7000
    ISSN (online) 2397-7000
    DOI 10.1093/synbio/ysab010
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Pasteur and “motivated” research

    Danchin, Antoine

    Comptes Rendus Biologies, Vol 345, Iss 3, Pp 109-

    2022  Volume 119

    Abstract: Pasteur’s originality in the way he developed pure research is to have understood the importance, for society, of the underlying motivation. Curiosity, of course, is a strong motivation, which explains why we seek to understand the origin of life. But, ... ...

    Abstract Pasteur’s originality in the way he developed pure research is to have understood the importance, for society, of the underlying motivation. Curiosity, of course, is a strong motivation, which explains why we seek to understand the origin of life. But, in front of the immensity of the possible choices, why not, also, choose to start from questions of economic interest (diseases of beer and wine, diseases affecting the silk industry .) Finally, of course, health is a constant preoccupation, but the diseases, which have no borders, often come from tropical countries and Asia especially. It is therefore necessary to settle there, but not to come and impose one’s point of view, but on the contrary to use the knowledge coming from the local culture in order to open new ways of understanding the reality of the world.
    Keywords Pasteur’s quadrant ; Speculative research ; Research policy ; Research applications ; HKU Pasteur Research Centre Ltd ; Abduction ; Pastorian spirit ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-10-01T00:00:00Z
    Publisher Académie des sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: Zinc, an unexpected integrator of metabolism?

    Danchin, Antoine

    Microbial biotechnology

    2020  Volume 13, Issue 4, Page(s) 895–898

    Abstract: Even when they no longer require the presence of iron, cells use zinc as a divalent cation, involved in a large variety of catalytic and regulatory functions. This metal is so important that it appears that ribosomes are instrumental in its ultimate ... ...

    Abstract Even when they no longer require the presence of iron, cells use zinc as a divalent cation, involved in a large variety of catalytic and regulatory functions. This metal is so important that it appears that ribosomes are instrumental in its ultimate storage. Here, we summarize a detailed analysis which investigates the way the global cell metabolism is integrated by zinc. This integration results from the zinc-dependent way in which the one-carbon metabolism is always coupled to the translation process, not only via methionine and S-adenosylmethionine, but via the complex set-up of the modification of the position 34 of the anticodon of tRNAs.
    MeSH term(s) Anticodon ; RNA, Transfer/genetics ; Ribosomes ; Zinc
    Chemical Substances Anticodon ; RNA, Transfer (9014-25-9) ; Zinc (J41CSQ7QDS)
    Language English
    Publishing date 2020-03-09
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2406063-X
    ISSN 1751-7915 ; 1751-7915
    ISSN (online) 1751-7915
    ISSN 1751-7915
    DOI 10.1111/1751-7915.13549
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Isobiology: A Variational Principle for Exploring Synthetic Life.

    Danchin, Antoine

    Chembiochem : a European journal of chemical biology

    2020  Volume 21, Issue 13, Page(s) 1781–1792

    Abstract: Most developments in synthetic biology try to depart from life as we know it, attempting to create orthogonal constructions. Here, following a variational principle, I try to explore how slight changes in the buildup of cells reveal critical features of ... ...

    Abstract Most developments in synthetic biology try to depart from life as we know it, attempting to create orthogonal constructions. Here, following a variational principle, I try to explore how slight changes in the buildup of cells reveal critical features of life's physics. In a first section, I suggest that we use stable isotopes of the atoms of life to see how living cells fare, beginning with life in heavy water. Subsequently, isotopes of the other main biogenic atoms are suggested as an extension of the variational principle, despite their likely very small influence on the course of biological activity. Finally, two atoms of the second row of Mendeleev's table, boron and fluorine are explored as a further extension of the principle. The use of the former is still in its infancy, whereas the latter, based on existing fluorinases, could open the door to a more general use of halogens in synthetic biology.
    MeSH term(s) Boron/chemistry ; Boron/metabolism ; Carbon Isotopes/chemistry ; Carbon Isotopes/metabolism ; Deuterium Oxide/chemistry ; Fluorine/chemistry ; Fluorine/metabolism ; Nitrogen Isotopes/chemistry ; Nitrogen Isotopes/metabolism ; Oxygen Isotopes/chemistry ; Oxygen Isotopes/metabolism ; Synthetic Biology ; Water/chemistry
    Chemical Substances Carbon Isotopes ; Nitrogen Isotopes ; Oxygen Isotopes ; Water (059QF0KO0R) ; Fluorine (284SYP0193) ; Deuterium Oxide (J65BV539M3) ; Boron (N9E3X5056Q)
    Language English
    Publishing date 2020-04-02
    Publishing country Germany
    Document type Journal Article ; Review
    ZDB-ID 2020469-3
    ISSN 1439-7633 ; 1439-4227
    ISSN (online) 1439-7633
    ISSN 1439-4227
    DOI 10.1002/cbic.202000060
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: SynBio 2.0, a new era for synthetic life: Neglected essential functions for resilience.

    Danchin, Antoine / Huang, Jian Dong

    Environmental microbiology

    2022  Volume 25, Issue 1, Page(s) 64–78

    MeSH term(s) Synthetic Biology
    Language English
    Publishing date 2022-08-31
    Publishing country England
    Document type Editorial
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.16140
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Biological innovation in the functional landscape of a model regulator, or the lactose operon repressor

    Danchin, Antoine

    Comptes Rendus Biologies, Vol 344, Iss 2, Pp 111-

    2021  Volume 126

    Abstract: The operon model was proposed six decades ago. And yet, despite all this time, the lactose operon repressor, LacI, remains a subject of major interest. While it is well established that LacI can exist in two functional forms, one that renders the operon ... ...

    Abstract The operon model was proposed six decades ago. And yet, despite all this time, the lactose operon repressor, LacI, remains a subject of major interest. While it is well established that LacI can exist in two functional forms, one that renders the operon inactive via binding of LacI to DNA and another, bound to an inducer that does not allow repression, how it switches from one to the other is still not well understood. The construction of a library of several tens of thousands of LacI mutants has revealed some unexpected features. In particular, the transition implemented in some of them reveals a new type of transcription regulation: band-pass (OFF/ON/OFF) and band-stop (ON/OFF/ON) filters. This makes it natural to think that it is the network of hydrogen bonds associated with the water bound to the molecule that allows the remote interconnection between the binding site to an inducer molecule and the one that binds it to the DNA.
    Keywords Allostery ; Synthetic biology ; Logic gate ; Band-pass filter ; Band-stop filter ; Memory of water ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher Académie des sciences
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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