In silico sequence evolution with site-specific interactions along phylogenetic trees

Motivation: A biological sequence usually has many sites whose evolution depends on other positions of the sequence, but this is not accounted for by commonly used models of sequence evolution. Here we introduce a Markov model of nucleotide sequence evolution in which the instantaneous substitution rate at a site depends on the states of other sites. Based on the concept of neighbourhood systems, our model represents a universal description of arbitrarily complex dependencies among sites. Results: We show how to define complex models for some illustrative examples and demonstrate that our method provides a versatile resource for simulations of sequence evolution with site-specific interactions along a tree. For example, we are able to simulate the evolution of RNA taking into account both secondary structure as well as pseudoknots and other tertiary interactions. To this end, we have developed a program Simulating Site-Specific Interactions (SISSI) that simulates evolution of a nucleotide sequence along a phylogenetic tree incorporating user defined site-specific interactions. Furthermore, our method allows to simulate more complex interactions among nucleotide and other character based sequences. 2006 Oxford University Press

Conformations of high-generation dendritic polyelectrolytes

We perform monomer-resolved computer simulations of high-generation dendritic molecules, varying the amount of charge and the spacer length between subsequent generations. Charged entities (monomers and counterions) are simulated with the explicit Coulomb interaction, employing the Ewald summation technique. We discover considerable stretching of the molecules with increasing generation number and spacer length, whereas the effects of charging are less pronounced on the overall size of the molecule than those of the former two parameters. For large generations and spacer lengths, charging of the molecules leads to both the opening of large voids within the dendrimer and to charge distributions that are nearly uniform along the molecule's extent. These findings suggest both the possible usage of charge dendrimers as efficient encapsulating agents and their character as realizations of model charged colloids with a uniform charge distribution in their interior

Heinrich Heine's Pictures of travel /

Translation of: Reisebilder.Mode of access: Internet

Physiology, phylogeny, and LUCA

Genomes record their own history. But if we want to look all the way back to life’s beginnings some 4 billion years ago, the record of microbial evolution that is preserved in prokaryotic genomes is not easy to read. Microbiology has a lot in common with geology in that regard. Geologists know that plate tectonics and erosion have erased much of the geological record, with ancient rocks being truly rare. The same is true of microbes. Lateral gene transfer (LGT) and sequence divergence have erased much of the evolutionary record that was once written in genomes, and it is not obvious which genes among sequenced genomes are genuinely ancient. Which genes trace to the last universal ancestor, LUCA? The classical approach has been to look for genes that are universally distributed. Another approach is to make all trees for all genes, and sift out the trees where signals have been overwritten by LGT. What is left ought to be ancient. If we do that, what do we find

Replication Files for: The Long-Term Costs of Government Surveillance – Insights from Stasi Spying in East Germany

Journal of the European Economic Association, forthcomin

Nano-coating protects biofunctional materials

The demand to develop convergent technology platforms, such as bio-functionalized medical devices, is rapidly increasing. However, the loss of biological function of the effector molecules during sterilization represents a significant and general problem. Therefore, we have developed and characterized a nano-coating (NC) formulation capable of maintaining the functionality of proteins on biological-device combination products. As a proof of concept, the NC preserved the structural and functional integrity of an otherwise highly fragile antibody immobilized on polyurethane during deleterious sterilizing irradiation (≥ 25 kGy). The NC procedure enables straight-forward terminal sterilization of bio-functionalized materials while preserving optimal conditioning of the bioactive surface.© Elsevier Ltd 201

Varieties of Governance. Dynamics, Strategies, Capacities

This edited collection examines various facets of governance - the organization and steering of political processes within society - for a better understanding of the complexities of contemporary policy making