Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites

A new soil-borne species belonging to the Penicillium section Canescentia is described, Penicillium arizonense sp. nov. (type strain CBS 141311(T) = IBT 12289(T)). The genome was sequenced and assembled into 33.7 Mb containing 12,502 predicted genes. A phylogenetic assessment based on marker genes confirmed the grouping of P. arizonense within section Canescentia. Compared to related species, P. arizonense proved to encode a high number of proteins involved in carbohydrate metabolism, in particular hemicellulases. Mining the genome for genes involved in secondary metabolite biosynthesis resulted in the identification of 62 putative biosynthetic gene clusters. Extracts of P. arizonense were analysed for secondary metabolites and austalides, pyripyropenes, tryptoquivalines, fumagillin, pseurotin A, curvulinic acid and xanthoepocin were detected. A comparative analysis against known pathways enabled the proposal of biosynthetic gene clusters in P. arizonense responsible for the synthesis of all detected compounds except curvulinic acid. The capacity to produce biomass degrading enzymes and the identification of a high chemical diversity in secreted bioactive secondary metabolites, offers a broad range of potential industrial applications for the new species P. arizonense. The description and availability of the genome sequence of P. arizonense, further provides the basis for biotechnological exploitation of this species

Reconstruction of the yeast protein-protein interaction network involved in nutrient sensing and global metabolic regulation

<p>Abstract</p> <p>Background</p> <p>Several protein-protein interaction studies have been performed for the yeast <it>Saccharomyces cerevisiae </it>using different high-throughput experimental techniques. All these results are collected in the BioGRID database and the SGD database provide detailed annotation of the different proteins. Despite the value of BioGRID for studying protein-protein interactions, there is a need for manual curation of these interactions in order to remove false positives.</p> <p>Results</p> <p>Here we describe an annotated reconstruction of the protein-protein interactions around four key nutrient-sensing and metabolic regulatory signal transduction pathways (STP) operating in <it>Saccharomyces cerevisiae</it>. The reconstructed STP network includes a full protein-protein interaction network including the key nodes Snf1, Tor1, Hog1 and Pka1. The network includes a total of 623 structural open reading frames (ORFs) and 779 protein-protein interactions. A number of proteins were identified having interactions with more than one of the protein kinases. The fully reconstructed interaction network includes all the information available in separate databases for all the proteins included in the network (nodes) and for all the interactions between them (edges). The annotated information is readily available utilizing the functionalities of network modelling tools such as Cytoscape and CellDesigner.</p> <p>Conclusions</p> <p>The reported fully annotated interaction model serves as a platform for integrated systems biology studies of nutrient sensing and regulation in <it>S. cerevisiae</it>. Furthermore, we propose this annotated reconstruction as a first step towards generation of an extensive annotated protein-protein interaction network of signal transduction and metabolic regulation in this yeast.</p

Equilibrium and non-equilibrium dynamics of a hole in a bilayer antiferromagnet

The dynamics of charge carriers in lattices of quantum spins is a long standing and fundamental problem. Recently, a new generation of quantum simulation experiments based on atoms in optical lattices has emerged that gives unprecedented insights into the detailed spatial and temporal dynamics of this problem, which compliments earlier results from condensed matter experiments. Focusing on observables accessible in these new experiments, we explore here the equilibrium as well as non-equilibrium dynamics of a mobile hole in two coupled antiferromagnetic spin lattices. Using a self-consistent Born approximation, we calculate the spectral properties of the hole in the bilayer and extract the energy bands of the quasiparticles, corresponding to magnetic polarons that are either symmetric or anti-symmetric under layer exchange. These two kinds of polarons are degenerate at certain momenta due to the antiferromagnetic symmetry, and we, furthermore, examine how the momentum of the ground state polaron depends on the interlayer coupling strength. The long time dynamics of a hole initially created in one layer is shown to be characterised by oscillations between the two layers with a frequency given by the energy difference between the symmetric and the anti-symmetric polaron. We finally demonstrate that the expansion velocity of a hole initially created at a given lattice site is governed by the ballistic motion of polarons. It moreover depends non-monotonically on the interlayer coupling, eventually increasing as a quantum phase transition to a disordered state is approached

Orientation-dependent ionization yields from strong-field ionization of fixed-in-space linear and asymmetric top molecules

The yield of strong-field ionization, by a linearly polarized probe pulse, is studied experimentally and theoretically, as a function of the relative orientation between the laser field and the molecule. Experimentally, carbonyl sulfide, benzonitrile and naphthalene molecules are aligned in one or three dimensions before being singly ionized by a 30 fs laser pulse centered at 800 nm. Theoretically, we address the behaviour of these three molecules. We consider the degree of alignment and orientation and model the angular dependence of the total ionization yield by molecular tunneling theory accounting for the Stark shift of the energy level of the ionizing orbital. For naphthalene and benzonitrile the orientational dependence of the ionization yield agrees well with the calculated results, in particular the observation that ionization is maximized when the probe laser is polarized along the most polarizable axis. For OCS the observation of maximum ionization yield when the probe is perpendicular to the internuclear axis contrasts the theoretical results.Comment: 14 pages, 4 figure

OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis

Background: The quantitative analysis of metabolic fluxes, i. e., in vivo activities of intracellular enzymes and pathways, provides key information on biological systems in systems biology and metabolic engineering. It is based on a comprehensive approach combining (i) tracer cultivation on C-13 substrates, (ii) C-13 labelling analysis by mass spectrometry and (iii) mathematical modelling for experimental design, data processing, flux calculation and statistics. Whereas the cultivation and the analytical part is fairly advanced, a lack of appropriate modelling software solutions for all modelling aspects in flux studies is limiting the application of metabolic flux analysis