MOVIPAC: Vibrational spectroscopy with a robust meta‐program for massively parallel standard and inverse calculations

We present the software package MO VI PAC for calculations of vibrational spectra, namely infrared, Raman, and Raman Optical Activity (ROA) spectra, in a massively parallelized fashion. MO VI PAC unites the latest versions of the programs SNF and AKIRA alongside with a range of helpful add‐ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization and meta‐program design, MO VI PAC focuses in particular on the calculation of vibrational spectra of very large molecules containing on the order of a hundred atoms. For this purpose, it also offers different subsystem approaches such as Mode‐ and Intensity‐Tracking to selectively calculate specific features of the full spectrum. Furthermore, an approximation to the entire spectrum can be obtained using the Cartesian Tensor Transfer Method. We illustrate these capabilities using the example of a large π‐helix consisting of 20 (S)‐alanine residues. In particular, we investigate the ROA spectrum of this structure and compare it to the spectra of α‐ and 3₁₀‐helical analogs. © 2012 Wiley Periodicals, Inc.     

Genetic Manipulation of the Fusarium fujikuroi Fusarin Gene Cluster Yields Insight into the Complex Regulation and Fusarin Biosynthetic Pathway

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Deoxygenation of Aromatic Ketones Using Transfer Hydrogenolysis with Raney Nickel in 2-Propanol

Aryl ketones are readily deoxygenated to their corresponding aryl alkanes upon treatment with Raney nickel catalyst in boiling 2-propanol.

Contamination of therapeutic human immunoglobulin preparations with apolipoprotein H (β2‐glycoprotein I)

Polyclonal immunoglobulin (Ig) concentrates are important biological medicinal products and the assurance of their quality and safety is crucial. In our present approach we used proteomic methods to check the purity of commercial Ig products of different origin. The experimental setup included nonreducing 2DE or DIGE combined with MALDI‐TOF and the thrombin generation assay, a routine safety test for pharmaceutical Ig preparations, and was complemented by a specific immunoassay. 2DE patterns displayed contaminations with trace amounts of human apolipoprotein H (Apo‐H), transferrin, albumin, and its fragments. In contrast to the latter, Apo‐H is a protein that is active in the coagulation cascade, and thus a potential involvement in thromboembolic events in vivo cannot be excluded. It was found by 2DE and MALDI‐TOF to be a contaminant of several Ig preparations. Spiking experiments of Ig preparations with pure Apo‐H demonstrated an Apo‐H concentration dependent increase in thrombin generation assay values. Traces of Apo‐H are possibly also contributing to unwanted side effects, as already known for factor XIa. The significance of Apo‐H contaminations for these side effects might be verified by detailed analyses of pharmacovigilance data.     

A Chimeric DNA/RNA Antiparallel Quadruplex with Improved Stability

Nucleic acid quadruplexes are proposed to play a role in the regulation of gene expression, are often present in aptamers selected for specific binding functions and have potential applications in medicine and biotechnology. Therefore, understanding their structure and thermodynamic properties and designing highly stable quadruplexes is desirable for a variety of applications. Here, we evaluate DNA→RNA substitutions in the context of a monomolecular, antiparallel quadruplex, the thrombin-binding aptamer (TBA, GGTTGGTGTGGTTGG) in the presence of either K⁺ or Sr²⁺. TBA predominantly folds into a chair-type configuration containing two G-tetrads, with G residues in both syn and anti conformation. All chimeras with DNA→RNA substitutions (G→g) at G residues requiring the syn conformation demonstrated strong destabilization. In contrast, G→g substitutions at Gs with anti conformation increased stability without affecting the monomolecular chair-type topology. None of the DNA→RNA substitutions in loop positions affected the quadruplex topology; however, these substitutions varied widely in their stabilizing or destabilizing effects in an unpredictable manner. This analysis allowed us to design a chimeric DNA/RNA TBA construct that demonstrated substantially improved stability relative to the all-DNA construct. These results have implications for a variety of quadruplex-based applications including for the design of dynamic nanomachines.     

Match statistics for sequence-based alleles in profiles from forensic PCR-mps kits

The first autosomal sequence-based allele (aka SNP-STR haplotype) frequency database for forensic massively parallel sequencing (MPS) has been published, thereby removing one of the remaining barriers to implementing MPS in casework. The database was developed using a specific set of flank trim sites. If different trim sites or different kits with different primers are used for casework, then SNP-STR haplotypes may be detected that do not have frequencies in the database. We describe a procedure to address calculation of match probabilities when casework samples are generated using an MPS kit with different trim sites than those present in the relevant population frequency database. The procedure provides a framework for comparison of any MPS kit or database combination while also accommodating comparison of MPS and CE profiles.     

Total Synthesis of a Partial Structure from Arabinogalactan and Its Application for Allergy Prevention

Arabinogalactan, a microheterogeneous polysaccharide occurring in plants, is known for its allergy-protective activity, which could potentially be used for preventive allergy treatment. New treatment options are highly desirable, especially in a preventive manner, due to the constant rise of atopic diseases worldwide. The structural origin of the allergy-protective activity of arabinogalactan is, however, still unclear and isolation of the polysaccharide is not feasible for pharmaceutical applications due to a variation of the activity of the natural product and contaminations with endotoxins. Therefore, a pentasaccharide partial structure was selected for total synthesis and subsequently coupled to a carrier protein to form a neoglycoconjugate. The allergy-protective activity of arabinogalactan could be reproduced with the partial structure in subsequent in vivo experiments. This is the first example of a successful simplification of arabinogalactan with a single partial structure while retaining its allergy-preventive potential.     

Terminal Ligand and Packing Effects on Slow Relaxation in an Isostructural Set of [Dy(H2dapp)X2]+ Single Molecule Magnets**

We report three structurally related single ion Dy compounds using the pentadentate ligand 2,6-bis((E)-1-(2-(pyridin-2-yl)-hydrazineylidene)ethyl)pyridine (H₂dapp) [Dy(H₂dapp)(NO₃)₂]NO₃ ( 1 ), [Dy(H₂dapp)(OAc)₂]Cl ( 2 ) and [Dy(H₂dapp)(NO₃)₂]Cl_0.92(NO₃)_0.08 ( 3 ). The (H₂dapp) occupies a helical twisted pentagonal equatorial arrangement with two anionic ligands in the axial positions. Further influence on the electronic and magnetic structure is provided by a closely associated counterion interacting with the central N−H group of the (H₂dapp). The slow relaxation of the magnetisation shows that the anionic acetates give the greatest slowing down of the magnetisation reversal. Further influence on the relaxation properties of compounds 1 and 2 is the presence of short nitrate-nitrate intermolecular ligand contact opening further lattice relaxation pathways.     

Light‐induced degradation of PECVD aluminium oxide passivated silicon solar cells

Light‐induced degradation (LID) has been identified to be a critical issue for solar cells processed on boron‐doped silicon substrates. Typically, Czochralski‐grown silicon (Cz‐Si) has been reported to suffer from stronger LID than block‐cast multicrystalline silicon (mc‐Si) due to higher oxygen concentrations. This work investigates LID under conditions practically relevant under module operation on different cell types. It is shown that aluminium oxide (AlOx) passivated mc‐Si solar cells degrade more than a reference aluminium back surface field mc‐Si cell and, remarkably, an AlOx passivated Cz‐Si solar cell. The defect which is activated by illumination is shown to be doubtful a sole bulk effect while the AlOx passivation might play a certain role. This work may contribute to a re‐evaluation of the suitability of boron‐doped Cz‐ and mc‐Si for solar cells with very high efficiencies. (© 2015 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)