Quantitative Proteomics and Differential Protein Abundance Analysis after Depletion of Putative mRNA Receptors in the ER Membrane of Human Cells Identifies Novel Aspects of mRNA Targeting to the ER

In human cells, one-third of all polypeptides enter the secretory pathway at the endoplasmic reticulum (ER). The specificity and efficiency of this process are guaranteed by targeting of mRNAs and/or polypeptides to the ER membrane. Cytosolic SRP and its receptor in the ER membrane facilitate the cotranslational targeting of most ribosome-nascent precursor polypeptide chain (RNC) complexes together with the respective mRNAs to the Sec61 complex in the ER membrane. Alternatively, fully synthesized precursor polypeptides are targeted to the ER membrane post-translationally by either the TRC, SND, or PEX19/3 pathway. Furthermore, there is targeting of mRNAs to the ER membrane, which does not involve SRP but involves mRNA- or RNC-binding proteins on the ER surface, such as RRBP1 or KTN1. Traditionally, the targeting reactions were studied in cell-free or cellular assays, which focus on a single precursor polypeptide and allow the conclusion of whether a certain precursor can use a certain pathway. Recently, cellular approaches such as proximity-based ribosome profiling or quantitative proteomics were employed to address the question of which precursors use certain pathways under physiological conditions. Here, we combined siRNA-mediated depletion of putative mRNA receptors in HeLa cells with label-free quantitative proteomics and differential protein abundance analysis to characterize RRBP1- or KTN1-involving precursors and to identify possible genetic interactions between the various targeting pathways. Furthermore, we discuss the possible implications on the so-called TIGER domains and critically discuss the pros and cons of this experimental approach.     

Simulation of thick adhesive layers at finite strains utilizing an associated flow rule in a thermodynamically consistent framework

The application of elastoplastic material models is commonly used for the modelling of adhesive layers with high strength adhesives as realized with polyurethane or epoxy resin. To fulfill thermodynamic consistency often restrictions on the choice of material parameters are requested. One of them is the introduction of a non-associated flow rule, which always ensures positive dissipation. Nevertheless, this assumption is a non-essential criterion, which will be addressed in this work. Continuing along this argumentation, the constitutive relations for the material is modified based on an associated flow rule. The applied model for the simulation of the adhesives is based on a small strain theory. A yield surface including two stress invariants, the hydrostatic pressure as well as the deviator stress state, set the elastic limit of the material response. Linear as well as exponential hardening is incorporated and material softening that arises subsequently is also included by substituting effective invariants in the yield function. This material model as proposed from literature was extended to finite strain application with the concept of generalized stress-strain-measure, which was realized in a previous work. (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Advanced FEM for free surface flow with application to landslides

An advanced space-time finite element method is presented to investigate movements of landslides and their interaction with flexible structures. The mechanics of liquefied soil is described by Navier-Stokes-equations for visco-plastic non-newtonian fluid. Likewise the fluid the kinematics of the structure is described by velocities, taking large rotations into account. This leads to a monolithic fluid-structure interaction approach considering the multi-field problem as a whole. The discretized model equations are assembled in a single set of algebraic equations, which are solved by applying Newton-Raphson scheme. Free surface motion of landslide is described by the level-set method. To reduce computational effort the fragmented finite element method is used, where only active finite elements are evaluated. A pde-based extrapolation of the velocity-field is applied to ensure an accurate transport of distance function, which defines the profile in space and time of the free surfaces. (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim)     

Extractive Fermentation of Xylanase from Aspergillus tamarii URM 4634 in a Bioreactor

Of the many reported applications for xylanase, its use as a food supplement has played an important role for monogastric animals, because it can improve the utilisation of nutrients. The aim of this work was to produce xylanase by extractive fermentation in an aqueous two-phase system using Aspergillus tamarii URM 4634, increasing the scale of production in a bioreactor, partially characterising the xylanase and evaluating its influence on monogastric digestion in vitro. Through extractive fermentation in a bioreactor, xylanase was obtained with an activity of 331.4 U mL^?1 and 72 % yield. The xylanase was stable under variable pH and temperature conditions, and it was optimally active at pH 3.6 and 90 °C. Xylanase activity potentiated the simulation of complete monogastric digestion by 6 %, and only Mg²⁺ inhibited its activity. This process provides a system for efficient xylanase production by A. tamarii URM 4634 that has great potential for industrial use.     

First total synthesis of piperodione and analogs

Piperodione (3), a secondary metabolite previously isolated from the Javanese pepper plant Piper retrofractum in 0.0002% isolated yield was synthesized in a convergent strategy utilizing a Mannich and a Stetter reaction. An over-all yield of 76% could be achieved. Several analogs were prepared by this synthetic sequence. None of the compounds showed a significant cytotoxicity for human tumor cells (photometric sulforhodamine B assay).     

A Practical and Inexpensive One‐Pot Synthesis of Bis(indenyl)­dimethyltitanium with Aqueous Workup Procedure

A simple, reliable, and reproducible procedure for the multi‐gram synthesis of highly pure bis(indenyl)dimethyltitanium is presented. The procedure relies on a one‐pot conversion of inexpensive indene, methyllithium, and titanium tetrachloride to [Ind₂TiMe₂] and a convenient and quick aqueous workup protocol. Overall, quantities of several grams of [Ind₂TiMe₂] can be synthesized within a few hours. The procedure can also be used for the synthesis of [Cp₂TiMe₂] from cyclopentadiene, methyllithium, and titanium tetrachloride.     

A Novel Chemoselective Cleavage of (tert‐Butyl)(dimethyl)silyl (TBS) Ethers Catalyzed by Ce(SO4)2⋅4 H2O

(tert‐Butyl)(dimethyl)silyl (^tBuMe₂Si; TBS) phenyl/alkyl ethers were efficiently cleaved to the corresponding parent hydroxy compounds in good yields using catalytic amounts of Ce(SO₄)₂?4 H₂O by microwave‐assisted or conventional heating in MeOH. Intramolecular and competitive experiments demonstrated the chemoselective deprotection of TBS ethers in the presence of triisopropylsilyl (ⁱPr₃Si; TIPS) and (tert‐butyl)(diphenyl)silyl (^tBuPh₂Si; TBDPS) ethers.     

Sol–gel processing and electrochemical characterization of monoclinic Li3FeF6

To find new cathode materials for future applications in lithium-ion batteries, lithium transition metal fluorides represent an interesting class of materials. In principle the Li intercalation voltage can be increased by replacing oxygen in the cathode host structure with the more electronegative fluorine. A facile pyrolytic sol–gel process with trifluoroacetic acid as fluorine source was established to synthesize monoclinic Li₃FeF₆ using nontoxic chemicals. The acicular Li₃FeF₆ powder was characterized with X-ray diffraction and a detailed structure model was calculated by Rietveld analysis. For the preparation of cathode films to cycle versus lithium monoclinic Li₃FeF₆ was ball milled with carbon and binder down to nanoscale. After 100 cycles galvanostatic cycling (C/20) 47 % fully reversible capacity of the initial capacity (129 mAh/g) could be retained. To the best of our knowledge the results presented in this work include the first rate performance test for monoclinic Li₃FeF₆ up to 1 C maintaining a capacity of 71 mAh/g. The redox reaction involving Fe³⁺/Fe²⁺ during Li insertion/extraction was confirmed by post-mortem XPS and cyclic voltammetry.     

Nanobiomolecular Multiprotein Clusters on Electrodes for the Formation of a Switchable Cascadic Reaction Scheme

A supramolecular multicomponent protein architecture on electrodes is developed that allows the establishment of bidirectional electron transfer cascades based on interprotein electron exchange. The architecture is formed by embedding two different enzymes (laccase and cellobiose dehydrogenase) and a redox protein (cytochrome c) by means of carboxy‐modified silica nanoparticles in a multiple layer format. The construct is designed as a switchable dual analyte detection device allowing the measurement of lactose and oxygen, respectively. As the switching force we apply the electrode potential, which ensures control of the redox state of cytochrome c. The two signal chains are operating in a non‐separated matrix and are not disturbed by the other biocatalyst.