Conserved substitution patterns around nucleosome footprints in eukaryotes and Archaea derive from frequent nucleosome repositioning through evolution.

Nucleosomes, the basic repeat units of eukaryotic chromatin, have been suggested to influence the evolution of eukaryotic genomes, both by altering the propensity of DNA to mutate and by selection acting to maintain or exclude nucleosomes in particular locations. Contrary to the popular idea that nucleosomes are unique to eukaryotes, histone proteins have also been discovered in some archaeal genomes. Archaeal nucleosomes, however, are quite unlike their eukaryotic counterparts in many respects, including their assembly into tetramers (rather than octamers) from histone proteins that lack N- and C-terminal tails. Here, we show that despite these fundamental differences the association between nucleosome footprints and sequence evolution is strikingly conserved between humans and the model archaeon Haloferax volcanii. In light of this finding we examine whether selection or mutation can explain concordant substitution patterns in the two kingdoms. Unexpectedly, we find that neither the mutation nor the selection model are sufficient to explain the observed association between nucleosomes and sequence divergence. Instead, we demonstrate that nucleosome-associated substitution patterns are more consistent with a third model where sequence divergence results in frequent repositioning of nucleosomes during evolution. Indeed, we show that nucleosome repositioning is both necessary and largely sufficient to explain the association between current nucleosome positions and biased substitution patterns. This finding highlights the importance of considering the direction of causality between genetic and epigenetic change

Chromatin*is*an*ancient*innovation*conserved*between*Archaea*and*Eukarya* *

It has been known since the 1990s that the DNA of archaea is wrapped around histones to form 10 complexes that closely resemble the nucleosomes found in eukaryotes, albeit with four rather 11 than eight histone subunits. Nucleosomes are the fundamental units of chromatin, the highly-12 ordered and compact structure that all the DNA in a cell is packed into. Now we know exactl

Computationally efficient implementation of hybrid functionals in SIESTA

In this work we have implemented hybrid functionals into the SIESTA code, with the main goal to implement a fast general solver within the SIESTA framework that performs efficiently and scales linearly with increasing system size. We describe the implementation of the solver and apply it to study the properties of five insulating materials; NaCl, CaF2, CeO2, TiO2 and HfO2. We show that a systematic improvement in the basic description of the properties of these materials over standard Density Functional approaches can be obtained at a reasonable additional computational cost

Advances in Polyhydroxyalkanoate (PHA) Production, Volume 2

Nowadays, we are witnessing highly dynamic research activities related to the intriguing field of biodegradable materials with plastic-like properties. These activities are stimulated by the strengthened public awareness of prevailing ecological issues connected to growing piles of plastic waste and increasing greenhouse gas emissions; this goes hand-in-hand with the ongoing depletion of fossil feedstocks, which are traditionally used to produce full carbon backbone polymers. Polyhydroxyalkanoate (PHA) biopolyesters, a family of plastic-like materials with versatile material properties, are increasing considered to be a future-oriented solution for diminishing these concerns. PHA production is based on renewable resources and occurs in a bio-mediated fashion through the action of living organisms. If accomplished in an optimized way, PHA production and the entire PHA lifecycle are embedded into nature´s closed cycles of carbon. Sustainable and efficient PHA production requires understanding and improvement of all the individual process steps. Holistic improvement of PHA production, applicable on an industrially relevant scale, calls for, inter alia, consolidated knowledge about the enzymatic and genetic particularities of PHA-accumulating organisms, an in-depth understanding of the kinetics of the bioprocess, the selection of appropriate inexpensive fermentation feedstocks, tailoring of PHA composition at the level of its monomeric constituents, optimized biotechnological engineering, and novel strategies for PHA recovery from biomass characterized by low energy and chemical requirements. This Special Issue represents a comprehensive compilation of articles in which these individual aspects have been addressed by globally recognized experts