@article{KielarXinXuetal.2019,
  author    = {Kielar, Charlotte and Xin, Yang and Xu, Xiaodan and Zhu, Siqi and Gorin, Nelli and Grundmeier, Guido and M{\"o}ser, Christin and Smith, David M. and Keller, Adrian},
  title     = {Effect of staple age on DNA origami nanostructure assembly and stability},
  series = {Molecules},
  volume    = {24},
  journal   = {Molecules},
  number    = {14},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {1420-3049},
  doi       = {10.3390/molecules24142577},
  pages     = {12},
  year      = {2019},
  abstract  = {DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at -20 degrees C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.},
  language  = {en}
}
@article{RaatzvanVelzenGaedke2019,
  author    = {Raatz, Michael and van Velzen, Ellen and Gaedke, Ursula},
  title     = {Co-adaptation impacts the robustness of predator-prey dynamics against perturbations},
  series = {Ecology and Evolution},
  volume    = {9},
  journal   = {Ecology and Evolution},
  number    = {7},
  publisher = {John Wiley \& Sons},
  address   = {Hoboken, NJ},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.5006},
  pages     = {3823 -- 3836},
  year      = {2019},
  abstract  = {Global change threatens the maintenance of ecosystem functions that are shaped by the persistence and dynamics of populations. It has been shown that the persistence of species increases if they possess larger trait adaptability. Here, we investigate whether trait adaptability also affects the robustness of population dynamics of interacting species and thereby shapes the reliability of ecosystem functions that are driven by these dynamics. We model co-adaptation in a predator-prey system as changes to predator offense and prey defense due to evolution or phenotypic plasticity. We investigate how trait adaptation affects the robustness of population dynamics against press perturbations to environmental parameters and against pulse perturbations targeting species abundances and their trait values. Robustness of population dynamics is characterized by resilience, elasticity, and resistance. In addition to employing established measures for resilience and elasticity against pulse perturbations (extinction probability and return time), we propose the warping distance as a new measure for resistance against press perturbations, which compares the shapes and amplitudes of pre- and post-perturbation population dynamics. As expected, we find that the robustness of population dynamics depends on the speed of adaptation, but in nontrivial ways. Elasticity increases with speed of adaptation as the system returns more rapidly to the pre-perturbation state. Resilience, in turn, is enhanced by intermediate speeds of adaptation, as here trait adaptation dampens biomass oscillations. The resistance of population dynamics strongly depends on the target of the press perturbation, preventing a simple relationship with the adaptation speed. In general, we find that low robustness often coincides with high amplitudes of population dynamics. Hence, amplitudes may indicate the robustness against perturbations also in other natural systems with similar dynamics. Our findings show that besides counteracting extinctions, trait adaptation indeed strongly affects the robustness of population dynamics against press and pulse perturbations.},
  language  = {en}
}