In: eLife, 2020, vol. 9, p. e57915
Conjugative transfer of the integrative and conjugative element ICEclc in Pseudomonas requires development of a transfer competence state in stationary phase, which arises only in 3–5% of individual cells. The mechanisms controlling this bistable switch between non-active and transfer competent cells have long remained enigmatic. Using a variety of genetic tools and epistasis experiments in...
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In: SIAM Journal on Applied Mathematics, 2019, vol. 79, no. 4, p. 1173–1196
We investigate a broad family of stochastically modeled reaction networks by looking at their stationary distributions. Most known results on stationary distributions assume weak reversibility and zero deficiency. We first explicitly give product-form stationary distributions for a class of mostly non-weakly-reversible autocatalytic reaction networks of arbitrary deficiency. We provide...
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In: Bulletin of Mathematical Biology, 2019, vol. 81, no. 5, p. 1461–1478
Here, we present a theoretical investigation with potential insights on developmental mechanisms. Three biological factors, consisting of two diffusing factors and a cell- autonomous immobile transcription factor are combined with different feedback mechanisms. This results in four different situations or fur patterns. Two of them reproduce classical Turing patterns: (1) regularly spaced...
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In: Scientific Reports, 2018, vol. 8, no. 1, p. 11272
Organisms use environmental cues for directed navigation. Understanding the basic logic behind navigational decisions critically depends on the complexity of the nervous system. Due to the comparably simple organization of the nervous system of the fruit fly larva, it stands as a powerful model to study decision-making processes that underlie directed navigation. We have quantitatively...
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In: PLOS Computational Biology, 2018, vol. 14, no. 2, p. e1005988
The consensus that complexity begets stability in ecosystems was challenged in the seventies, a result recently extended to ecologically-inspired networks. The approaches assume the existence of a feasible equilibrium, i.e. with positive abundances. However, this key assumption has not been tested. We provide analytical results complemented by simulations which show that equilibrium...
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In: Environmental Microbiology, 2018, vol. 20, no. 1, p. 241–258
Whole-cell bacterial bioreporters are proposed as alternatives to chemical analysis of, for example, pollutants in environmental compartments. Commonly based on reporter gene induction, bioreporters produce a detectable signal within 30 min to a few hours after exposure to the chemical target, which is impractical for applications aiming at a fast response. In an attempt to attain faster...
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In: PLOS Computational Biology, 2016, vol. 12, no. 12, p. e1005295
The calcium ion (Ca²⁺), a universal signaling molecule, is widely recognized to play a fundamental role in the regulation of various biological processes. Agonist–evoked Ca²⁺ signals often manifest as rhythmic changes in the cytosolic free Ca²⁺ concentration (ccyt) called Ca²⁺ oscillations. Stimuli intensity was found to be proportional to the oscillation frequency...
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In: Proc. R. Soc. B, 2016, vol. 283, no. 1824, p. 20152702
Networks play a prominent role in the study of complex systems of interacting entities in biology, sociology, and economics. Despite this diversity, we demonstrate here that a statistical model decomposing networks into matching and centrality components provides a comprehensive and unifying quantification of their architecture. The matching term quantifies the assortative structure in which node...
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In: PLoS ONE, 2015, vol. 10, no. 3, p. e0118238
The plant hormone auxin plays a central role in growth and morphogenesis. In shoot apical meristems, auxin flux is polarized through its interplay with PIN proteins. Concentration-based mathematical models of the flux can explain some aspects of phyllotaxis for the L1 surface layer, where auxin accumulation points act as sinks and develop into primordia. The picture differs in the interior of the...
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In: Behavioural Brain Research, 2011, vol. 219, no. 1, p. 132-141
We aimed to determine whether human subjects’ reliance on different sources of spatial information encoded in different frames of reference (i.e., egocentric versus allocentric) affects their performance, decision time and memory capacity in a short-term spatial memory task performed in the real world. Subjects were asked to play the Memory game (a.k.a. the Concentration game) without an...
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