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  1. Article ; Online: Structured sequences emerge from random pool when replicated by templated ligation.

    Kudella, Patrick W / Tkachenko, Alexei V / Salditt, Annalena / Maslov, Sergei / Braun, Dieter

    Proceedings of the National Academy of Sciences of the United States of America

    2021  Volume 118, Issue 8

    Abstract: The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error ... ...

    Abstract The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error threshold to avoid that replicated specific sequences become random because of the incorporated replication errors [M. Eigen,
    MeSH term(s) DNA-Directed DNA Polymerase/metabolism ; Evolution, Molecular ; Nucleic Acid Conformation ; Oligonucleotides/chemistry ; Origin of Life ; Templates, Genetic
    Chemical Substances Oligonucleotides ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
    Language English
    Publishing date 2021-01-27
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2018830118
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Book ; Online: Ligation of random oligomers leads to emergence of autocatalytic sequence network

    Kudella, Patrick W. / Tkachenko, Alexei V. / Maslov, Sergei / Braun, Dieter

    2020  

    Abstract: The emergence of longer information-carrying and functional nucleotide polymers from random short strands was a major stepping stone at the dawn of life. But the formation of those polymers under temperature oscillation required some form of selection. A ...

    Abstract The emergence of longer information-carrying and functional nucleotide polymers from random short strands was a major stepping stone at the dawn of life. But the formation of those polymers under temperature oscillation required some form of selection. A plausible mechanism is template-based ligation where theoretical work already suggested a reduction in information entropy. Here, we show how nontrivial sequence patterns emerge in a system of random 12mer DNA sequences subject to enzyme-based templated ligation reaction and temperature cycling. The strands acted both as a template and substrates of the reaction and thereby formed longer oligomers. The selection for templating sequences leads to the development of a multiscale ligation landscape. A position-dependent sequence pattern emerged with a segregation into mutually complementary pools of A-rich and T-rich sequences. Even without selection for function, the base pairing of DNA with ligation showed a dynamics resembling Darwinian evolution.

    Comment: 11 pages, 5 figures, SI attached
    Keywords Physics - Biological Physics
    Subject code 612
    Publishing date 2020-08-18
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: Fission of Lipid-Vesicles by Membrane Phase Transitions in Thermal Convection.

    Kudella, Patrick W / Preißinger, Katharina / Morasch, Matthias / Dirscherl, Christina F / Braun, Dieter / Wixforth, Achim / Westerhausen, Christoph

    Scientific reports

    2019  Volume 9, Issue 1, Page(s) 18808

    Abstract: Unilamellar lipid vesicles can serve as model for protocells. We present a vesicle fission mechanism in a thermal gradient under flow in a convection chamber, where vesicles cycle cold and hot regions periodically. Crucial to obtain fission of the ... ...

    Abstract Unilamellar lipid vesicles can serve as model for protocells. We present a vesicle fission mechanism in a thermal gradient under flow in a convection chamber, where vesicles cycle cold and hot regions periodically. Crucial to obtain fission of the vesicles in this scenario is a temperature-induced membrane phase transition that vesicles experience multiple times. We model the temperature gradient of the chamber with a capillary to study single vesicles on their way through the temperature gradient in an external field of shear forces. Starting in the gel-like phase the spherical vesicles are heated above their main melting temperature resulting in a dumbbell-deformation. Further downstream a temperature drop below the transition temperature induces splitting of the vesicles without further physical or chemical intervention. This mechanism also holds for less cooperative systems, as shown here for a lipid alloy with a broad transition temperature width of 8 K. We find a critical tether length that can be understood from the transition width and the locally applied temperature gradient. This combination of a temperature-induced membrane phase transition and realistic flow scenarios as given e.g. in a white smoker enable a fission mechanism that can contribute to the understanding of more advanced protocell cycles.
    Language English
    Publishing date 2019-12-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-019-55110-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Proton gradients and pH oscillations emerge from heat flow at the microscale.

    Keil, Lorenz M R / Möller, Friederike M / Kieß, Michael / Kudella, Patrick W / Mast, Christof B

    Nature communications

    2017  Volume 8, Issue 1, Page(s) 1897

    Abstract: Proton gradients are essential for biological systems. They not only drive the synthesis of ATP, but initiate molecule degradation and recycling inside lysosomes. However, the high mobility and permeability of protons through membranes make pH gradients ... ...

    Abstract Proton gradients are essential for biological systems. They not only drive the synthesis of ATP, but initiate molecule degradation and recycling inside lysosomes. However, the high mobility and permeability of protons through membranes make pH gradients very hard to sustain in vitro. Here we report that heat flow across a water-filled chamber forms and sustains stable pH gradients. Charged molecules accumulate by convection and thermophoresis better than uncharged species. In a dissociation reaction, this imbalances the reaction equilibrium and creates a difference in pH. In solutions of amino acids, phosphate, or nucleotides, we achieve pH differences of up to 2 pH units. The same mechanism cycles biomolecules by convection in the created proton gradient. This implements a feedback between biomolecules and a cyclic variation of the pH. The finding provides a mechanism to create a self-sustained proton gradient to drive biochemical reactions.
    Language English
    Publishing date 2017-12-01
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 2041-1723
    ISSN (online) 2041-1723
    DOI 10.1038/s41467-017-02065-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Exploring the Limits of Cell Adhesion under Shear Stress within Physiological Conditions and beyond on a Chip.

    Stamp, Melanie E M / Jötten, Anna M / Kudella, Patrick W / Breyer, Dominik / Strobl, Florian G / Geislinger, Thomas M / Wixforth, Achim / Westerhausen, Christoph

    Diagnostics (Basel, Switzerland)

    2016  Volume 6, Issue 4

    Abstract: Cell adhesion processes are of ubiquitous importance for biomedical applications such as optimization of implant materials. Here, not only physiological conditions such as temperature or pH, but also topographical structures play crucial roles, as ... ...

    Abstract Cell adhesion processes are of ubiquitous importance for biomedical applications such as optimization of implant materials. Here, not only physiological conditions such as temperature or pH, but also topographical structures play crucial roles, as inflammatory reactions after surgery can diminish osseointegration. In this study, we systematically investigate cell adhesion under static, dynamic and physiologically relevant conditions employing a lab-on-a-chip system. We screen adhesion of the bone osteosarcoma cell line SaOs-2 on a titanium implant material for pH and temperature values in the physiological range and beyond, to explore the limits of cell adhesion, e.g., for feverish and acidic conditions. A detailed study of different surface roughness
    Language English
    Publishing date 2016-10-21
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662336-5
    ISSN 2075-4418
    ISSN 2075-4418
    DOI 10.3390/diagnostics6040038
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