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  • 1
    Publication Date: 2014-12-17
    Description: Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses—the so-called transfer function—and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the involved biological parts. This is achieved by adopting an enzymology-like framework, where transfer functions are described in terms of their input affinity constant and maximal response. As a proof of concept, we characterize a set of Lux homoserine-lactone-inducible genetic devices with different levels of Lux receptor and signal molecule. Our model fits the experimental results and predicts the impact of the receptor's ribosome-binding site strength, as a tunable parameter that affects gene expression. The evolutionary implications are outlined.
    Keywords: Synthetic Biology and Assembly Cloning, Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2015-07-11
    Description: Subduction zones exhibit variable degrees of interseismic coupling as resolved by inversions of geodetic data and analyses of seismic energy release. The degree to which a plate boundary fault is coupled can have profound effects on its seismogenic behaviour. Here we use GPS measurements to estimate co- and post-seismic deformation from the 2012 August 27, M w 7.3 megathrust earthquake offshore El Salvador, which was a tsunami earthquake. Inversions of estimated coseismic displacements are in agreement with published seismically derived source models, which indicate shallow (〈20 km depth) rupture of the plate interface. Measured post-seismic deformation in the first year following the earthquake exceeds the coseismic deformation. Our analysis indicates that the post-seismic deformation is dominated by afterslip, as opposed to viscous relaxation, and we estimate a post-seismic moment release one to eight times greater than the coseismic moment during the first 500 d, depending on the relative location of coseismic versus post-seismic slip on the plate interface. We suggest that the excessive post-seismic motion is characteristic for the El Salvador–Nicaragua segment of the Central American margin and may be a characteristic of margins hosting tsunami earthquakes.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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