Calpains and cytokines in fibrillating human atria

Atrial fibrillation (AF) is accompanied by intracellular calcium overload. The purpose of this study was to assess the role of calcium-dependent calpains and cytokines during AF. Atrial tissue samples from 32 patients [16 with chronic AF and 16 in sinus rhythm (SR)] undergoing open heart surgery were studied. Atrial expression of calpain I and II, calpastatin, troponin T (TnT), troponin C (TnC), and cytokines [interleukin (IL)-1 beta, IL-2, IL-6, IL-8, IL-10, transforming growth factor (TGF)-beta 1, and tumor necrosis factor-alpha] were determined. Expression of calpain I was increased during AF (461 +/- 201% vs. 100 +/- 34%, P < 0.05). Amounts of calpain II and calpastatin were unchanged. Total calpain enzymatic activity was more than doubled during AF (35.2 +/- 17.7 vs. 12.4 +/- 9.2 units, P < 0.05). In contrast to TnC, TnT levels were reduced in fibrillating atria by 26% (P < 0.05), corresponding to the myofilament disintegration seen by electron microscopy. Small amounts of only IL-2 and TGF-beta 1 mRNA and protein were detected regardless of the underlying cardiac rhythm. In conclusion, atria of patients with permanent AF show evidence of calpain I activation that might contribute to structural remodeling and contractile dysfunction, whereas there is no evidence of activation of tissue cytokines.     

Functional architecture of RNA polymerase I

Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 A cryo-electron microscopic structure for the complete 14-subunit yeast Pol I, a homology model for the core enzyme, and the crystal structure of the subcomplex A14/43. In the resulting hybrid structure of Pol I, A14/43, the clamp, and the dock domain contribute to a unique surface interacting with promoter-specific initiation factors. The Pol I-specific subunits A49 and A34.5 form a heterodimer near the enzyme funnel that acts as a built-in elongation factor and is related to the Pol II-associated factor TFIIF. In contrast to Pol II, Pol I has a strong intrinsic 3'-RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3'-end trimming.     

The pygmy mole cricket Xya variegata as an indicator for dynamic river systems

There is an urgent need to conserve and restore dynamic floodplains as one of the last wildernesses in Europe and to maintain their unique plant and animal communities. Disturbance-dependent ecosystems such as natural floodplains harbour many highly specialised and endangered insect species. One of these species is the pygmy mole cricket Xya variegata Latreille, 1809 (Orthoptera: Tridactylidae), a floodplain specialist of the Ponto-Mediterranean region. However, as with many endangered insect species detailed knowledge on the requirements of X. variegata is largely unknown, even though such knowledge is of particular importance for successful nature conservation. The aim of this study was to analyze the ecological requirements of X. variegata and to verify the species’ suitability as an indicator for dynamic river systems of the Ponto-Mediterranean region. Therefore, microhabitat analyses were conducted in August 2010 on 42 plots in a nearly natural floodplain of the western Spanish Pyrenees. The results show that patch occupancy in X. variegata was determined by a high amount of fine sediment particles and low vegetation coverage. Moreover, population sizes were positively correlated with low vegetation and gravel/stone coverage. The plots with the highest population sizes (29 and 36 individuals/0.5 m²) had no vegetation at all. Habitats of X. variegata were usually located distant to the main channel; that is areas where fine sediment particles are deposited after a flood event. Disturbance is thus mandatory for the persistence of the species and makes X. variegata a suitable indicator for dynamic river systems.     

Characterization of single nucleotide polymorphism markers for eelgrass (Zostera marina)

We characterized 37 single nucleotide polymorphism (SNP) makers for eelgrass Zostera marina. SNP markers were developed using existing EST (expressed sequence tag)-libraries to locate polymorphic loci and develop primers from the functional expressed genes that are deposited in The ZOSTERA database (V1.2.1). SNP loci were genotyped using a single-base-extension approach which facilitated high-throughput genotyping with minimal optimization time. These markers show a wide range of variability among 25 eelgrass populations and will be useful for population genetic studies including evaluation of population structure, historical demography, and phylogeography. Potential applications include haplotype inference of physically linked SNPs and identification of genes under selection for temperature and desiccation stress.     

Rhodopsin photoproducts in 2D crystals

The published electron microscope and X-ray structures of rhodopsin have made available a detailed picture of the inactive dark state of rhodopsin. Yet, the photointermediates of rhodopsin that ultimately lead to the activated receptor species still await a similar analysis. Such an analysis first requires the generation and characterization of the photoproducts that can be obtained in crystals of rhodopsin. We therefore studied with Fourier-transform infrared (FTIR) difference spectroscopy the photoproducts in 2D crystals of bovine rhodopsin in a p22(1)2(1) crystal form. The spectra obtained by cryotrapping revealed that in this crystal form the still inactive early intermediates batho, lumi, and meta I are similar to those obtained from rhodopsin in native disk membranes, although the transition from lumi to meta I is shifted to a higher temperature. However, at room temperature, the formation of the active state, meta II, is blocked in the crystalline environment. Instead, an intermediate state is formed that bears some features of meta II but lacks the specific conformational changes required for activity. Despite being unable to activate its cognate G protein, transducin, to a significant extent, this intermediate state is capable of interacting with functional transducin-derived peptides to a limited extent. Therefore, while unable to support formation of rhodopsin's active state meta II, 2D p22(1)2(1) crystals proved to be very suitable for determining 3D structures of its still inactive precursors, batho, lumi, and meta I. In future studies, FTIR spectroscopy may serve as a sensitive assay to screen crystals grown under altered conditions for potential formation of the active state, meta II.     

The PDZ protein MPP2 interacts with c-Src in epithelial cells

c-Src is a non-receptor tyrosine kinase involved in regulating cell proliferation, cell migration and cell invasion and is tightly controlled by reversible phosphorylation on regulatory sites and through protein-protein interactions. The interaction of c-Src with PDZ proteins was recently identified as novel mechanism to restrict c-Src function. The objective of this study was to identify and characterise PDZ proteins that interact with c-Src to control its activity. By PDZ domain array screen, we identified the interaction of c-Src with the PDZ protein Membrane Protein Palmitoylated 2 (MPP2), a member of the Membrane-Associated Guanylate Kinase (MAGUK) family, to which also the Discs large (Dlg) tumour suppressor protein belongs. The function of MPP2 has not been established and the functional significance of the MPP2 c-Src interaction is not known. We found that in non-transformed breast epithelial MCF-10A cells, endogenous MPP2 associated with the cytoskeleton in filamentous structures, which partially co-localised with microtubules and c-Src. MPP2 and c-Src interacted in cells, where c-Src kinase activity promoted increased interaction of c-Src with MPP2. We furthermore found that MPP2 was able to negatively regulate c-Src kinase activity in cells, suggesting that the functional significance of the MPP2-c-Src interaction is to restrict Src activity. Consequently, the c-Src-dependent disorganisation of the cortical actin cytoskeleton of epithelial cells expressing c-Src was suppressed by MPP2. In conclusion we demonstrate here that MPP2 interacts with c-Src in cells to control c-Src activity and morphological function.     

Automated force field optimisation of small molecules using a gradient-based workflow package

In this study, the recently developed gradient-based optimisation workflow for the automated development of molecular models is for the first time applied to the parameterisation of force fields for molecular dynamics simulations. As a proof-of-concept, two small molecules (benzene and phosgene) are considered. In order to optimise the underlying intermolecular force field (described by the (12,6)-Lennard-Jones and the Coulomb potential), the energetic and diameter parameters ε and σ are fitted to experimental physical properties by gradient-based numerical optimisation techniques. Thereby, a quadratic loss function between experimental and simulated target properties is minimised with respect to the force field parameters. In this proof-of-concept, the considered physical target properties are chosen to be diverse: density, enthalpy of vapourisation and self-diffusion coefficient are optimised simultaneously at different temperatures. We found that in both cases, the optimisation could be successfully concluded by fulfillment of a pre-defined stopping criterion. Since a fairly small number of iterations were needed to do so, this study will serve as a good starting point for more complex systems and further improvements of the parametrisation task.