Towards experiments with highly charged ions at HESR

The atomic physics collaboration SPARC is a part of the APPA pillar at the future Facility for Antiproton and Ion Research. It aims at atomic-physics research across virtually the full range of atomic matter. An emphasis of this contribution are the atomic physics experiments addressing the collision dynamics in strong electro-magnetic fields as well as the fundamental interactions between electrons and heavy nuclei at the HESR. Here we give a short overview about the central instruments for SPARC experiments at this storage ring.     

Effects of NR1 splicing on NR1/NR3B-type excitatory glycine receptors

Background  

N-methyl-D-aspartate receptors (NMDARs) are the most complex of ionotropic glutamate receptors (iGluRs). Subunits of this subfamily assemble into heteromers, which – depending on the subunit combination – may display very different pharmacological and electrophysiological properties. The least studied members of the NMDAR family, the NR3 subunits, have been reported to assemble with NR1 to form excitatory glycine receptors in heterologous expression systems. The heterogeneity of NMDARs in vivo is in part conferred to the receptors by splicing of the NR1 subunit, especially with regard to proton sensitivity.     

Photoactivated Psoralens Elicit Defense Genes and Phytoalexin Production in the Pea Plant

In the pea plant ( Pisum sativum ), compounds that intercalate into DNA induce the production of ∼20 major proteins similar to the pattern induced during nonhost disease resistance to the bean fungal pathogen, Fusarium solani f.sp. phaseoli . The pea phytoalexin, pisatin, as well as RNA homologous to several disease-resistance response (DRR) genes accumulate following treatment with these compounds. Psoralen was chosen to characterize this interaction further because it intercalates into DNA and, following irradiation with 365 nm UV light (UV₃₆₅), forms covalent bonds with pyrimidines on either or both strands of DNA. This produces monoadducts or cross-links, respectively. Dose experiments showed that 60 μg/mL 4'-aminomethyl-4,5',8-trimethylpsoralen followed by 18 J/cm² UV₃₆₅ was sufficient to produce an accumulation of pisatin similar to that produced in response to the fungus. Under these inducing conditions, there was an average of 0.19 adducts per kb of pea genomic DNA. The accumulation of pisatin and the RNA of several DRR genes by psoralen required photoactivation, which suggests that covalent binding to DNA was necessary for induction. As the promoters of several putative fungal-induced pea genes contain long stretches of d(AT)_n, which is the preferred psoralen photobinding site, restriction fragments spanning DRR genes were examined after in vivo psoralen treatment. The rate of crosslinking was compared between fungal-induced and noninduced genes using a modified Southern blot analysis. Implications of the induction of the DRR due to psoralen binding are discussed.     

Synthesis and structure of iron(iii) diamine-bis(phenolate) complexes

The structures and properties of six new iron(iii) diamine-bis(phenolate) complexes are reported. Reaction of anhydrous FeX(3) salts (where X = Cl or Br) with the diprotonated tripodal tetradentate ligands 2-pyridylamino-N,N-bis(2-methylene-4-methyl-6-tert-butylphenol), H(2)[L(1)], and N,N-dimethyl-N',N'-bis(2-methylene-4-methyl-6-tert-butylphenol)ethylenediamine, H(2)[L(2)], produces the trigonal bipyramidal iron(iii) complexes, [L(1)]FeCl , [L(1)]FeBr , [L(2)]FeCl and [L(2)]FeBr . Reaction of FeX(3) with the related linear tetradentate ligand N,N'-bis(4,6-tert-butyl-2-methylphenol)-N,N'-bismethyl-1,2-diaminoethane, H(2)[L(3)], generates square pyramidal iron(iii) complexes, [L(3)]FeCl and [L(3)]FeBr . Complexes have been characterized using electronic absorption spectroscopy and magnetometry. Single crystal X-ray molecular structures have been determined for complexes 1, 3, 5 and 6.     

Efficient removal of DNA from proteomic samples prior to two-dimensional map analysis

Several methods have been described in the literature for removal of DNA from protein samples prior to proteome analysis. They in general involve protein precipitation techniques. In other protocols, DNAse treatment is suggested prior to precipitation of proteins in excess acetone. All these methods have been evaluated and found to perform poorly in DNA removal, as illustrated by two-dimensional (2D) maps where horizontal and vertical sample streaking are still substantial. Such removal is in general necessary in tissue lysates and especially when analysing sub-cellular organelles, such as nuclei, where the high DNA levels strongly interfere with proteome analysis. Another method is proposed here for efficient DNA removal: two-phase extraction of DNA in chloroform/phenol/isoamyl alcohol, a procedure commonly used to rid DNA samples of protein contaminants, but rarely applied to protein preparation. This extraction is not very efficient if performed at slightly acidic to neutral pH values, but it performs extremely well at pH values of 9.5 or higher. The 2D maps thus obtained of Escherichia coli lysates as well as extracts from purified nuclei of eukaryotic cells are not only devoid of any vertical or horizontal streaking, but exhibit many more spots, especially in the alkaline region of the 2D gels, suggesting that these basic proteins were in general lost to proteome analysis due to co-precipitation in tenacious protein–DNA complexes. It is hypothesized that the alkaline pH values adopted in the two-phase extraction help to fully disrupt any residual DNA–protein complexes, due to strong Coulombic repulsion.     

Corrosion studies and interfacial bonding of urea/poly(dimethylsiloxane) sol/gel hydrophobic coatings on AA 2024 aluminum alloy

Bis[(ureapropyl)triethoxysilane] bis(propyl)-terminated-polydimethylsiloxane 1000 (PDMSU), an organic-inorganic hybrid, diluted in either EtOH or a mixture of EtOH-PrOH, was used in thin film form (<200 nm) to inhibit the corrosion of AA 2024 alloy. Potentiodynamic, time-dependent cyclovoltammetric measurements and salt spray tests showed that the corrosion inhibition of the latter was 10 times higher than that of the former films. This was correlated with the higher degree of hydrolysis and the formation of more open polyhedral silsesquioxane species (T2) in the bulk heat-treated PDMSU/EtOH-PrOH xerogels (29Si NMR spectra). The structure of the coatings deposited on AA 2024 Al alloy was deduced from the infrared reflection-absorption (IR RA) spectra, which revealed more extensive urea-urea interactions and more efficient silane-Al interface bonding for the PDMSU/EtOH-PrOH coatings with higher corrosion inhibition. Ex situ IR RA potentiodynamic spectroelectrochemical measurements of PDMSU coatings revealed that their degradation did not proceed via the formation of silanol groups and consequent hydration of the coatings but that they decomposed above E(corr) by forming fragments composed of -CH2- segments in an all-trans conformation.     

A highly crystalline microporous hybrid organic-inorganic aluminosilicate resembling the AFI-type zeolite

ECS-14, a crystalline microporous hybrid organic-inorganic aluminosilicate, has been synthesized by using 1,4-bis-(triethoxysilyl)-benzene (BTEB) as a source of silica. Its structure contains a system of linear channels with 12-membered ring openings, running along the [001] direction, resembling the pore architecture of the AFI framework type.     

Purification and Characterisation of a Thermostable β-Xylosidase from <Emphasis Type="Italic">Aspergillus niger</Emphasis> van Tieghem of Potential Application in Lignocellulosic Bioethanol Production

A locally isolated strain of Aspergillus niger van Tieghem was found to produce thermostable β-xylosidase activity. The enzyme was purified by cation and anion exchange and hydrophobic interaction chromatography. Maximum activity was observed at 70–75 °C and pH 4.5. The enzyme was found to be thermostable retaining 91 and 87% of its original activity after incubation for 72 h at 60 and 65 °C, respectively, with 52% residual activity detected after 18 h at 70 °C. Available data indicates that the purified β-xylosidase is more thermostable over industrially relevant prolonged periods at high temperature than those reported from other A. niger strains. Maximum activity was observed on p-nitrophenyl-β-d-xylopyranoside and the enzyme also hydrolysed p-nitrophenyl β-d-glucopyranoside and p-nitrophenyl α-l-arabinofuranoside. The purified enzyme acted synergistically with A. niger endo-1,4-β-xylanase in the hydrolysis of beechwood xylan at 65 °C. During hydrolysis of pretreated straw lignocellulose at 70 °C using a commercial lignocellulosic enzyme cocktail, inclusion of the purified enzyme resulted in a 19-fold increase in the amount of xylose produced after 6 h. The results observed indicate potential suitability for industrial application in the production of lignocellulosic bioethanol where thermostable β-xylosidase activity is of growing interest to maximise the enzymatic hydrolysis of lignocellulose.     

Interaction of a peptide from the pre-transmembrane domain of the severe acute respiratory syndrome coronavirus spike protein with phospholipid membranes

The severe acute respiratory syndrome coronavirus (SARS-CoV) envelope spike (S) glycoprotein, a Class I viral fusion protein, is responsible for the fusion between the membranes of the virus and the target cell. In order to gain new insight into the protein membrane alteration leading to the viral fusion mechanism, a peptide pertaining to the putative pre-transmembrane domain (PTM) of the S glycoprotein has been studied by infrared and fluorescence spectroscopies regarding its structure, its ability to induce membrane leakage, aggregation, and fusion, as well as its affinity toward specific phospholipids. We demonstrate that the SARS-CoV PTM peptide binds to and interacts with phospholipid model membranes, and, at the same time, it adopts different conformations when bound to membranes of different compositions. As it has been already suggested for other viral fusion proteins such as HIV gp41, the region of the SARS-CoV protein where the PTM peptide resides could be involved in the merging of the viral and target cell membranes working synergistically with other membrane-active regions of the SARS-CoV S glycoprotein to heighten the fusion process and therefore might be essential for the assistance and enhancement of the viral and cell fusion process.