Unloosing the Gordian knot of peroxisome formation

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordPeroxisome biogenesis is governed by molecular machineries, which are either unique to peroxisomes or are partially shared with mitochondria. As peroxisomes have important protective functions in the cell, modulation of their number is important for human health and disease. Significant progress has been made towards our understanding of the mechanisms of peroxisome formation, revealing a remarkable plasticity of the peroxisome biogenesis pathway. Here we discuss most recent findings with particular focus on peroxisome formation in mammalian cells.This work was supported by the Biotechnology and Biological Sciences Research Council (BB/K006231/1, BB/N01541X/1 to M.S.)

Peroxisomal ACBD4 interacts with VAPB and promotes ER-peroxisome associations

This is the author accepted manuscript. The final version is available from Taylor & Francis via the DOI in this record.Cooperation between cellular organelles such as mitochondria, peroxisomes and the ER is essential for a variety of important and diverse metabolic processes. Effective communication and metabolite exchange requires physical linkages between the organelles, predominantly in the form of organelle contact sites. At such contact sites organelle membranes are brought into close proximity by the action of molecular tethers, which often consist of specific protein pairs anchored in the membrane of the opposing organelles. Currently numerous tethering components have been identified which link the ER with multiple other organelles but knowledge of the factors linking the ER with peroxisomes is limited. Peroxisome-ER interplay is important because it is required for the biosynthesis of unsaturated fatty acids, ether-phospholipids and sterols with defects in these functions leading to severe diseases. Here we characterise acyl-CoA binding domain protein 4 (ACBD4) as a tail-anchored peroxisomal membrane protein which interacts with the ER protein, vesicle-associated membrane protein-associated protein–B (VAPB) to promote peroxisome-ER associations.We thank all colleagues who provided plasmids and antibodies, and T Levine for sharing data. This work was supported by BBSRC (BB/K006231/1, BB/N01541X/1). MS is supported by the Marie Curie Initial Training Network action PerFuMe (316723). The authors declare no competing financial interests

An algorithm for the minimum weight design of the general truss

Algorithm for minimum weight design of three dimensional, linear trus

Development of Collembolans after coversion towards organic farming

In Northern Germany, a diverse and complex experimental farm of the Federal Agricultural Research Centre (FAL) was set-up in 2001 covering all main aspects of organic farming. Previously, the 600 ha farm had been managed conventionally. Adjacent conventional farms were used as reference. The aim of this project was to study collembolans, microbial biomass and soil organic carbon in six organically farmed fields managed as a crop rotation of six different crops compared with an adjacent conventionally managed field. We hypothesised that the specific management in organic farming promotes soil biota. Soil samples were taken during the growing season in 2004. Collembolan abundances and microbial biomass were lower under organic management, but, generally, collembolan diversity was higher in organically farmed fields combined with a shifting in the dominance structure of the species. This result reveals that, even after three years, the soil biota is still changing with management conversion

Peroxisome Motility Measurement and Quantification Assay

This is the final version of the article. Available from Bio-protocol via the DOI in this record.Organelle movement, distribution and interaction contribute to the organisation of the eukaryotic cell. Peroxisomes are multifunctional organelles which contribute to cellular lipid metabolism and ROS homeostasis. They distribute uniformly in mammalian cells and move along microtubules via kinesin and dynein motors. Their metabolic cooperation with mitochondria and the endoplasmic reticulum (ER) is essential for the β-oxidation of fatty acids and the synthesis of myelin lipids and polyunsaturated fatty acids. A key assay to assess peroxisome motility in mammalian cells is the expression of a fluorescent fusion protein with a peroxisomal targeting signal (e.g., GFP-PTS1), which targets the peroxisomal matrix and allows live-cell imaging of peroxisomes. Here, we first present a protocol for the transfection of cultured mammalian cells with the peroxisomal marker EGFP-SKL to observe peroxisomes in living cells. This approach has revealed different motile behaviour of peroxisomes and novel insight into peroxisomal membrane dynamics (Rapp et al., 1996; Wiemer et al., 1997; Schrader et al., 2000). We then present a protocol which combines the live-cell approach with peroxisome motility measurements and quantification of peroxisome dynamics in mammalian cells. More recently, we used this approach to demonstrate that peroxisome motility and displacement is increased when a molecular tether, which associates peroxisomes with the ER, is lost (Costello et al., 2017b). Silencing of the peroxisomal acyl-CoA binding domain protein ACBD5, which interacts with ER-localised VAPB, increased peroxisome movement in skin fibroblasts, indicating that membrane contact sites can modulate organelle distribution and motility. The protocols described can be adapted to other cell types and organelles to measure and quantify organelle movement under different experimental conditions.This work was supported by grants from the Biotechnology and Biological Sciences Research Council (BB/K006231/1 and BB/N01541X/1 to M. Schrader). J. Metz and M. Schrader are supported by a Wellcome Trust Institutional Strategic Support Award (WT097835MF and WT105618MA). M. Schrader is supported by Marie Curie Initial Training Network action PerFuMe (316723)

Computing the local pressure in molecular dynamics simulations

Computer simulations of inhomogeneous soft matter systems often require accurate methods for computing the local pressure. We present a simple derivation, based on the virial relation, of two equivalent expressions for the local (atomistic) pressure in a molecular dynamics simulation. One of these expressions, previously derived by other authors via a different route, involves summation over interactions between particles within the region of interest; the other involves summation over interactions across the boundary of the region of interest. We illustrate our derivation using simulations of a simple osmotic system; both expressions produce accurate results even when the region of interest over which the pressure is measured is very small.Comment: 11 pages, 4 figure

Large dimension Configuration Interaction calculations of positron binding to the group II atoms

The Configuration Interaction (CI) method is applied to the calculation of the structures of a number of positron binding systems, including e+Be, e+Mg, e+Ca and e+Sr. These calculations were carried out in orbital spaces containing about 200 electron and 200 positron orbitals up to l = 12. Despite the very large dimensions, the binding energy and annihilation rate converge slowly with l, and the final values do contain an appreciable correction obtained by extrapolating the calculation to the l to infinity limit. The binding energies were 0.00317 hartree for e+Be, 0.0170 hartree for e+Mg, 0.0189 hartree for e+Ca, and 0.0131 hartree for e+Sr.Comment: 13 pages, no figs, revtex format, Submitted to PhysRev

APPLYING TERRAIN AND HYDROLOGICAL EDITING TO TANDEM-X DATA TO CREATE A CONSUMER-READY WORLDDEM PRODUCT

The Geo-intelligence division of Airbus Defence and Space and the German Aerospace Center (DLR) have partnered to produce the first fully global, high-accuracy Digital Surface Model (DSM) using SAR data from the twin satellite constellation: TerraSAR-X and TanDEM-X. The DLR is responsible for the processing and distribution of the TanDEM-X elevation model for the world's scientific community, while Airbus DS is responsible for the commercial production and distribution of the data, under the brand name WorldDEM™. For the provision of a consumer-ready product, Airbus DS undertakes several steps to reduce the effect of radar-specific artifacts in the WorldDEM data. These artifacts can be divided into two categories: terrain and hydrological. Airbus DS has developed proprietary software and processes to detect and correct these artifacts in the most efficient manner. Some processes are fullyautomatic, while others require manual or semi-automatic control by operators

Histochemistry and Cell Biology: 61 years and not tired at all.

This is the author accepted manuscript. The final version is available from Springer via the DOI in this record.Isaac Newton is credited with quipping, “If I have seen further it is by standing on the shoulders of Giants”. This remark, made more than 300 years ago is still relevant for today’s scientists. Certainly, in our field of Histochemistry and Cell Biology, many of the insights we enjoy and techniques we apply in our research are the result of contributions to the literature provided by our scientific forebearers. As Editors of Histochemistry and Cell Biology, we are entrusted with maintaining the high quality and continued success of the journal instituted by its founders M. Chèvremont, Liège; H.W. Deane, New York; P.B. Diezel, F. Duspiva and H. Reznik, Heidelberg; O. Eränkö, Helsinki; P. Gedigk and N. Schümmelfelder, Bonn; W. Gössner, Tübingen; W. Graumann, Göttingen; A. G. E. Pearse, London; W. Sandritter, Frankfurt/Main; T.H. Schiebler, Kiel; G. Siebert, Mainz; and M. Wolman, Tel-Hashomer. The list of the international editors represented a virtual list of “Who’s Who” in histochemistry at that time.Biotechnology & Biological Sciences Research Council (BBSRC