Research on oxidation by air and tempering of Raney nickel electrocatalysts for the H2 anodes of alkali combustion materials cells

The controlled oxidation in air of Raney nickel electrocatalysts was studied, with special attention paid to the quantitative analysis of nickel hydroxide. The content of the latter was determined through X-ray studies, thermogravimetric measurements, and spectral photometric examinations. The dependence of the content on the drying of activated catalyst is determined. The influence of nickel hydroxide on the electrochemical parameters of the catalyst, such as diffusion polarization, is studied, including a measurement of the exchange current density using the potential drop method. Conservation by oxidation in air with ancillary stabilization of the oxide in an H2 flow at 300 C is explored, including reduction by H2, the influence of tempering time, and structural studies on conserved and stabilized catalyst, long term research on the catalyst, including the influence of aging on the reduced catalyst, and the results of impedance measurements are presented

Systematic errors in peptide and protein identification and quantification by modified peptides

The principle of shotgun proteomics is to use peptide mass spectra in order to identify corresponding sequences in a protein database. The quality of peptide and protein identification and quantification critically depends on the sensitivity and specificity of this assignment process. Many peptides in proteomic samples carry biochemical modifications, and a large fraction of unassigned spectra arise from modified peptides. Spectra derived from modified peptides can erroneously be assigned to wrong amino acid sequences. However, the impact of this problem on proteomic data has not yet been investigated systematically. Here we use combinations of different database searches to show that modified peptides can be responsible for 20-50 % of false positive identifications in deep proteomic datasets. These false positive hits are particularly problematic as they have significantly higher scores and higher intensities than other false positive matches. Furthermore, these wrong peptide assignments lead to hundreds of false protein identifications and systematic biases in protein quantification. We devise a "cleaned search" strategy to address this problem and show that this considerably improves the sensitivity and specificity of proteomic data. In summary, we show that modified peptides cause systematic errors in peptide and protein identification and quantification and should therefore be considered to further improve the quality of proteomic data annotation

Yos9p assists in the degradation of certain non-glycosylated proteins from the endoplasmic reticulum

The HRD ubiquitin ligase recognizes and ubiquitylates proteins of the endoplasmic reticulum that display structural defects. Here, we apply quantitative proteomics to characterize the substrate spectrum of the HRD complex. Among the identified substrates is Erg3p, a glycoprotein involved in sterol-synthesis. We characterize Erg3p and demonstrate that the elimination of Erg3p requires Htm1p and Yos9p, two proteins that partake in the glycan-dependent turnover of aberrant proteins. We further show that the HRD ligase also mediates the breakdown of Erg3p and CPY* engineered to lack N-glycans. The degradation of these non-glycosylated substrates is enhanced by a mutant variant of Yos9p that has lost its affinity for oligosaccharides, indicating that Yos9p has a previously unrecognized role in the quality control of non-glycosylated proteins

Unconventional order-disorder phase transition in improper ferroelectric hexagonal manganites

The improper ferroelectricity in YMnO$_3$ and other related multiferroic hexagonal manganites are known to cause topologically protected ferroelectric domains that give rise to rich and diverse physical phenomena. The local structure and structural coherence across the ferroelectric transition, however, were previously not well understood. Here we reveal the evolution of the local structure with temperature in YMnO$_3$ using neutron total scattering techniques, and interpret them with the help of first-principles calculations. The results show that, at room temperature, the local and average structures are consistent with the established ferroelectric $P6_3cm$ symmetry. On heating, both local and average structural analyses show striking anomalies from $\sim 800$ K up to the Curie temperature consistent with increasing fluctuations of the order parameter angle. These fluctuations result in an unusual local symmetry lowering into a \textit{continuum of structures} on heating. This local symmetry breaking persists into the high-symmetry non-polar phase, constituting an unconventional type of order-disorder transition.Comment: 10 pages, 5 figure

Keeping the proportions of protein complex components in check

How do cells maintain relative proportions of protein complex components? Advances in quantitative, genome-wide measurements have begun to shed light onto the roles of protein synthesis and degradation in establishing the precise proportions in living cells: on the one hand, ribosome profiling studies indicate that proteins are already produced in the correct relative proportions. On the other hand, proteomic studies found that many complexes contain subunits that are made in excess and subsequently degraded. Here, we discuss these seemingly contradictory findings, emerging principles, and remaining open questions. We conclude that establishing precise protein levels involves both coordinated synthesis and post-translational fine-tuning via protein degradation

Quantitative GTPase affinity purification identifies Rho family protein interaction partners

Although Rho GTPases are essential molecular switches involved in many cellular processes, an unbiased experimental comparison of their interaction partners was not yet performed. Here, we develop quantitative GTPase affinity purification (qGAP) to systematically identify interaction partners of six Rho GTPases (Cdc42, Rac1, RhoA, RhoB, RhoC, RhoD) depending on their nucleotide loading state. The method works with cell line or tissue-derived protein lysates in combination with SILAC-based or label free quantification, respectively. We demonstrate that qGAP identifies known and novel binding partners that can be validated in an independent assay. Our interaction network for six Rho GTPases contains many novel binding partners, reveals highly promiscuous interaction of several effectors and mirrors evolutionary relationships among Rho GTPases

Extensive allele-specific translational regulation in hybrid mice

Translational regulation is mediated through the interaction between diffusible trans-factors and cis-elements residing within mRNA transcripts. In contrast to extensively studied transcriptional regulation, cis-regulation on translation remains underexplored. Using deep sequencing-based transcriptome and polysome profiling, we globally profiled allele-specific translational efficiency for the first time in an F1 hybrid mouse. Out of 7,156 genes with reliable quantification of both alleles, we found 1,008 (14.1%) exhibiting significant allelic divergence in translational efficiency. Systematic analysis of sequence features of the genes with biased allelic translation revealed that local RNA secondary structure surrounding the start codon and proximal out-of-frame upstream AUGs could affect translational efficiency. Finally, we observed that the cis-effect was quantitatively comparable between transcriptional and translational regulation. Such effects in the two regulatory processes were more frequently compensatory, suggesting that the regulation at the two levels could be coordinated in maintaining robustness of protein expression

Charged domain walls in improper ferroelectric hexagonal manganites and gallates

Ferroelectric domain walls are attracting broad attention as atomic-scale switches, diodes and mobile wires for next-generation nanoelectronics. Charged domain walls in improper ferroelectrics are particularly interesting as they offer multifunctional properties and an inherent stability not found in proper ferroelectrics. Here we study the energetics and structure of charged walls in improper ferroelectric YMnO$_3$, InMnO$_3$ and YGaO$_3$ by first principles calculations and phenomenological modeling. Positively and negatively charged walls are asymmetric in terms of local structure and width, reflecting that polarization is not the driving force for domain formation. The wall width scales with the amplitude of the primary structural order parameter and the coupling strength to the polarization. We introduce general rules for how to engineer $n$- and $p$-type domain wall conductivity based on the domain size, polarization and electronic band gap. This opens the possibility of fine-tuning the local transport properties and design $p$-$n$-junctions for domain wall-based nano-circuitry.Comment: 10 pages, 6 figures, Supp. Info. available on reques