Pineapple Lectin AcmJRL Binds SARS-CoV-2 Spike Protein in a Carbohydrate-Dependent Fashion

The highly glycosylated spike protein of SARS-CoV-2 is essential for infection and constitutes a prime target for antiviral agents and vaccines. The pineapple-derived jacalin-related lectin AcmJRL is present in the medication bromelain in significant quantities and has previously been described to bind mannosides. Here, we performed a large ligand screening of AcmJRL by glycan array analysis, quantified the interaction with carbohydrates and validated high-mannose glycans as preferred ligands. Because the SARS-CoV-2 spike protein was previously reported to carry a high proportion of high-mannose N-glycans, we tested the binding of AcmJRL to the recombinantly produced extraviral domain of spike protein. We could demonstrate that AcmJRL binds the spike protein with a low-micromolar KD in a carbohydrate-dependent fashion

Oscillations and temporal signalling in cells

ArXiv pre-print: http://arxiv.org/abs/q-bio/0703047.-- Final full-text version of the paper available at: http://dx.doi.org/10.1088/1478-3975/4/2/R01.PMID: 17664651The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce oscillations in gene expression or protein concentration using a framework of simple mathematical models. We focus on three eukaryotic genetic regulatory networks which show ultradian oscillations, with a time period of the order of hours, and involve, respectively, proteins important for development (Hes1), apoptosis (p53) and immune response (NF-κB). We argue that underlying all three is a common design consisting of a negative feedback loop with time delay which is responsible for the oscillatory behaviour.SK, MHJ and KS acknowledge support from the Danish National Research Foundation and Villum Kann Rasmussen Foundation. GT acknowledges support from the FIRB 2003 program of the Italian Ministry for University and Scientific Research

Dimethyl ether in its ground state, v=0, and lowest two torsionally excited states, v11=1 and v15=1, in the high-mass star-forming region G327.3-0.6

The goal of this paper is to determine the respective importance of solid state vs. gas phase reactions for the formation of dimethyl ether. This is done by a detailed analysis of the excitation properties of the ground state and the torsionally excited states, v11=1 and v15=1, toward the high-mass star-forming region G327.3-0.6. With the Atacama Pathfinder EXperiment 12 m submillimeter telescope, we performed a spectral line survey. The observed spectrum is modeled assuming local thermal equilibrium. CH3OCH3 has been detected in the ground state, and in the torsionally excited states v11=1 and v15=1, for which lines have been detected here for the first time. The emission is modeled with an isothermal source structure as well as with a non-uniform spherical structure. For non-uniform source models one abundance jump for dimethyl ether is sufficient to fit the emission, but two components are needed for the isothermal models. This suggests that dimethyl ether is present in an extended region of the envelope and traces a non-uniform density and temperature structure. Both types of models furthermore suggest that most dimethyl ether is present in gas that is warmer than 100 K, but a smaller fraction of 5%-28% is present at temperatures between 70 and 100 K. The dimethyl ether present in this cooler gas is likely formed in the solid state, while gas phase formation probably is dominant above 100 K. Finally, the v11=1 and v15=1 torsionally excited states are easily excited under the density and temperature conditions in G327.3-0.6 and will thus very likely be detectable in other hot cores as well.Comment: 12 pages (excluding appendices), 8 figures, A&A in pres

GeneTrail—advanced gene set enrichment analysis

We present a comprehensive and efficient gene set analysis tool, called ‘GeneTrail’ that offers a rich functionality and is easy to use. Our web-based application facilitates the statistical evaluation of high-throughput genomic or proteomic data sets with respect to enrichment of functional categories. GeneTrail covers a wide variety of biological categories and pathways, among others KEGG, TRANSPATH, TRANSFAC, and GO. Our web server provides two common statistical approaches, ‘Over-Representation Analysis’ (ORA) comparing a reference set of genes to a test set, and ‘Gene Set Enrichment Analysis’ (GSEA) scoring sorted lists of genes. Besides other newly developed features, GeneTrail's statistics module includes a novel dynamic-programming algorithm that improves the P-value computation of GSEA methods considerably. GeneTrail is freely accessible at http://genetrail.bioinf.uni-sb.d

Design of Polymer-Embedded Heterogeneous Fenton Catalysts for the Conversion of Organic Trace Compounds

Advanced oxidation processes are the main way to remove persistent organic trace compounds from water. For these processes, heterogeneous Fenton catalysts with low iron leaching and high catalytic activity are required. Here, the preparation of such catalysts consisting of silica-supported iron oxide (Fe2O3/SiOx) embedded in thermoplastic polymers is presented. The iron oxide catalysts are prepared by a facile sol–gel procedure followed by thermal annealing (calcination). These materials are mixed in a melt compounding process with modified polypropylenes to stabilize the Fe2O3 catalytic centers and to further reduce the iron leaching. The catalytic activity of the composites is analyzed by means of the Reactive Black 5 (RB5) assay, as well as by the conversion of phenol which is used as an example of an organic trace compound. It is demonstrated that embedding of silica-supported iron oxide in modified polypropylene turns the reaction order from pseudo-first order (found for Fe2O3/SiOx catalysts), which represents a mainly homogeneous Fenton reaction, to pseudo-zeroth order in the polymer composites, indicating a mainly heterogeneous, surface-diffusion-controlled process