Ribo-seQC: comprehensive analysis of cytoplasmic and organellar ribosome profiling data

Summary: Ribosome profiling enables genome-wide analysis of translation with unprecedented resolution. We present Ribo-seQC, a versatile tool for the comprehensive analysis of Ribo-seq data, providing in-depth insights on data quality and translational profiles for cytoplasmic and organelle ribosomes. Ribo-seQC automatically generates platform-independent HTML reports, offering a detailed and easy-to-share basis for collaborative Ribo-seq projects. Availability: Ribo-seQC is available at https://github.com/ohlerlab/RiboseQC and submitted to Bioconductor. Contact: uwe.ohler{at}mdc-berlin.d

Stochastic analysis of surface roughness

For the characterization of surface height profiles we present a new stochastic approach which is based on the theory of Markov processes. With this analysis we achieve a characterization of the complexity of the surface roughness by means of a Fokker-Planck or Langevin equation, providing the complete stochastic information of multiscale joint probabilities. The method was applied to different road surface profiles which were measured with high resolution. Evidence of Markov properties is shown. Estimations for the parameters of the Fokker-Planck equation are based on pure, parameter free data analysis

Long-time behaviour of discretizations of the simple pendulum equation

We compare the performance of several discretizations of the simple pendulum equation in a series of numerical experiments. The stress is put on the long-time behaviour. We choose for the comparison numerical schemes which preserve the qualitative features of solutions (like periodicity). All these schemes are either symplectic maps or integrable (preserving the energy integral) maps, or both. We describe and explain systematic errors (produced by any method) in numerical computations of the period and the amplitude of oscillations. We propose a new numerical scheme which is a modification of the discrete gradient method. This discretization preserves (almost exactly) the period of small oscillations for any time step.Comment: 41 pages, including 18 figures and 4 table

Nucleon-deuteron elastic scattering as a tool to probe properties of three-nucleon forces

Faddeev equations for elastic Nd scattering have been solved using modern NN forces combined with the Tucson-Melbourne two-pion exchange three-nucleon force, with a modification thereof closer to chiral symmetry and the Urbana IX three-nucleon force. Theoretical predictions for the differential cross section and several spin observables using NN forces only and NN forces combined with three-nucleon force models are compared to each other and to the existing data. A wide range of energies from 3 to 200 MeV is covered. Especially at the higher energies striking three-nucleon force effects are found, some of which are supported by the still rare set of data, some are in conflict with data and thus very likely point to defects in those three-nucleon force models.Comment: 30 pages, 14 Postscript figures; now minor changes in figures and reference

Three-Nucleon Force Effects in Nucleon Induced Deuteron Breakup: Predictions of Current Models (I)

An extensive study of three-nucleon force effects in the entire phase space of the nucleon-deuteron breakup process, for energies from above the deuteron breakup threshold up to 200 MeV, has been performed. 3N Faddeev equations have been solved rigorously using the modern high precision nucleon-nucleon potentials AV18, CD Bonn, Nijm I, II and Nijm 93, and also adding 3N forces. We compare predictions for cross sections and various polarization observables when NN forces are used alone or when the two pion-exchange Tucson-Melbourne 3NF was combined with each of them. In addition AV18 was combined with the Urbana IX 3NF and CD Bonn with the TM' 3NF, which is a modified version of the TM 3NF, more consistent with chiral symmetry. Large but generally model dependent 3NF effects have been found in certain breakup configurations, especially at the higher energies, both for cross sections and spin observables. These results demonstrate the usefulness of the kinematically complete breakup reaction in testing the proper structure of 3N forces.Comment: 42 pages, 20 ps figures, 2 gif figure

Signatures of three-nucleon interactions in few-nucleon systems

Recent experimental results in three-body systems have unambiguously shown that calculations based only on nucleon-nucleon forces fail to accurately describe many experimental observables and one needs to include effects which are beyond the realm of the two-body potentials. This conclusion owes its significance to the fact that experiments and calculations can both be performed with a high accuracy. In this review, both theoretical and experimental achievements of the past decade will be underlined. Selected results will be presented. The discussion on the effects of the three-nucleon forces is, however, limited to the hadronic sector. It will be shown that despite the major successes in describing these seemingly simple systems, there are still clear discrepancies between data and the state-of-the-art calculations.Comment: accepted for publication in Rep. Prog. Phy

Ligand Binding Ensembles Determine Graded Agonist Efficacies at a G Protein-Coupled Receptor

G protein-coupled receptors (GPCRs) constitute the largest family of membrane receptors and modulate almost every physiological process in humans. Binding of agonists to GPCRs induces a shift from inactive to active receptor conformations. Biophysical studies of the dynamic equilibrium of receptors suggest that a portion of receptors can remain in inactive states even in the presence of saturating concentrations of agonist and G protein mimetic. However, the molecular details of agonist-bound inactive receptors are poorly understood. Here we use the model of bitopic orthosteric/allosteric (i.e. dualsteric) agonists for muscarinic M2 receptors to demonstrate the existence and function of such inactive agonist-receptor complexes on a molecular level. Employing all-atom molecular dynamics (MD) simulations, dynophores (i.e. a combination of static 3D-pharmacophores and MD-based conformational sampling), ligand design and receptor mutagenesis, we show that inactive agonist-receptor complexes can result from agonist binding to the allosteric vestibule alone, whereas the dualsteric binding mode produces active receptors. Each agonist forms a distinct ligand binding ensemble, and different agonist efficacies depend on the fraction of purely allosteric (i.e. inactive) vs. dualsteric (i.e. active) binding modes. We propose that this concept may explain why agonist-receptor complexes can be inactive and that adopting multiple binding modes may be generalized also to small agonists, where binding modes will be only subtly different and confined to only one binding site

Oxidative Stress and Vascular Function: Implications for Pharmacologic Treatments

Production of considerable amounts of reactive oxygen species (ROS) eventually leads to oxidative stress. A key role of oxidative stress is evident in the pathologic mechanisms of endothelial dysfunction and associated cardiovascular diseases. Vascular enzymes such as NADPH oxidases, xanthine oxidase, and uncoupled endothelial nitric oxide synthase are involved in the production of ROS. The question remains whether pharmacologic approaches can effectively combat the excessive ROS production in the vasculature. Interestingly, existing registered cardiovascular drugs can directly or indirectly act as antioxidants, thereby preventing the damaging effects of ROS. Moreover, new compounds targeting NADPH oxidases have been developed. Finally, food-derived compounds appear to be effective inhibitors of oxidative stress and preserve vascular function

Mitochondrial oxidative stress and nitrate tolerance – comparison of nitroglycerin and pentaerithrityl tetranitrate in Mn-SOD(+/- )mice

BACKGROUND: Chronic therapy with nitroglycerin (GTN) results in a rapid development of nitrate tolerance which is associated with an increased production of reactive oxygen species (ROS). According to recent studies, mitochondrial ROS formation and oxidative inactivation of the organic nitrate bioactivating enzyme mitochondrial aldehyde dehydrogenase (ALDH-2) play an important role for the development of nitrate and cross-tolerance. METHODS: Tolerance was induced by infusion of wild type (WT) and heterozygous manganese superoxide dismutase mice (Mn-SOD(+/-)) with ethanolic solution of GTN (12.5 μg/min/kg for 4 d). For comparison, the tolerance-free pentaerithrityl tetranitrate (PETN, 17.5 μg/min/kg for 4 d) was infused in DMSO. Vascular reactivity was measured by isometric tension studies of isolated aortic rings. ROS formation and aldehyde dehydrogenase (ALDH-2) activity was measured in isolated heart mitochondria. RESULTS: Chronic GTN infusion lead to impaired vascular responses to GTN and acetylcholine (ACh), increased the ROS formation in mitochondria and decreased ALDH-2 activity in Mn-SOD(+/- )mice. In contrast, PETN infusion did not increase mitochondrial ROS formation, did not decrease ALDH-2 activity and accordingly did not lead to tolerance and cross-tolerance in Mn-SOD(+/- )mice. PETN but not GTN increased heme oxygenase-1 mRNA in EA.hy 926 cells and bilirubin efficiently scavenged GTN-derived ROS. CONCLUSION: Chronic GTN infusion stimulates mitochondrial ROS production which is an important mechanism leading to tolerance and cross-tolerance. The tetranitrate PETN is devoid of mitochondrial oxidative stress induction and according to the present animal study as well as numerous previous clinical studies can be used without limitations due to tolerance and cross-tolerance