Strontium Diffusion in Magnetron Sputtered Gadolinia‐Doped Ceria Thin Film Barrier Coatings for Solid Oxide Fuel Cells

Strontium (Sr) diffusion in magnetron sputtered gadolinia‐doped ceria (CGO) thin films is investigated. For this purpose, a model system consisting of a screen printed (La,Sr)(Co,Fe)O_3?δ (LSCF) layer, and thin films of CGO and yttria‐stabilized zirconia (YSZ) is prepared to simulate a solid oxide fuel cell. This setup allows observation of Sr diffusion by observing SrZrO₃ formation using X‐ray diffraction while annealing. Subsequent electron microscopy confirms the results. This approach presents a simple method for assessing the quality of CGO barriers without the need for a complete fuel cell test setup. CGO films with thicknesses ranging from 250 nm to 1.2 μm are tested at temperatures from 850 °C to 1000 °C which yields an in‐depth understanding of Sr diffusion through CGO thin films that may be of high scientific and technical interest for implementation of novel fuel cell materials. Sr is found to diffuse along column/grain boundaries in the CGO films but by modifying the film thickness and microstructure the breaking temperature of the barrier can be increased.     

DNA polymerase Family X: Function,structure, and cellular roles

The X family of DNA polymerases in eukaryotic cells consists of terminal transferase and DNA polymerases β, λ, and μ. These enzymes have similar structural portraits, yet different biochemical properties, especially in their interactions with DNA. None of these enzymes possesses a proofreading subdomain, and their intrinsic fidelity of DNA synthesis is much lower than that of a polymerase that functions in cellular DNA replication. In this review, we discuss the similarities and differences of three members of Family X: polymerases β, λ, and μ. We focus on biochemical mechanisms, structural variation, fidelity and lesion bypass mechanisms, and cellular roles. Remarkably, although these enzymes have similar three-dimensional structures, their biochemical properties and cellular functions differ in important ways that impact cellular function.     

Dynamics of the Morphological Degradation of Si‐Based Anodes for Li‐Ion Batteries Characterized by In Situ Synchrotron X‐Ray Tomography

The alloying reaction of silicon with lithium in negative electrodes for lithium‐ion batteries causes brutal morphological changes that severely degrade their cyclability. In this study, the dynamics of their expansion and contraction, of their cracking in the bulk and of their debonding at the interface with the current collector are visualized by in situ synchrotron X‐ray computed tomography and quantified from appropriate 3D imaging analyses. Two electrodes made with same silicon material having reasonable particle size distribution from an applied point of view are compared: one fabricated according to a standard process and the other one prepared with a maturation step, which consists in storing the electrode in a humid atmosphere for a few days before drying and cell assembly. All morphological degradations are significantly restrained for the matured electrode, confirming the great efficiency of this maturation step to produce a more ductile and resilient electrode architecture, which is at the origin of the major improvement in their cyclability.     

Emerging High-Level Tigecycline Resistance: Novel Tetracycline Destructases Spread via the Mobile Tet(X)

Antibiotic resistance in bacteria has become a great threat to global public health. Tigecycline is a next-generation tetracycline that is the final line of defense against severe infections by pan-drug-resistant bacterial pathogens. Unfortunately, this last-resort antibiotic has been challenged by the recent emergence of the mobile Tet(X) orthologs that can confer high-level tigecycline resistance. As it is reviewed here, these novel tetracycline destructases represent a growing threat to the next-generation tetracyclines, and a basic framework for understanding the molecular epidemiology and resistance mechanisms of them is presented. However, further large-scale epidemiological and functional studies are urgently needed to better understand the prevalence and dissemination of these newly discovered Tet(X) orthologs among Gram-negative bacteria in both human and veterinary medicine.     

Small‐angle X‐ray scattering reveals architecture and A2B2 stoichiometry of the UvrA–UvrB DNA damage sensor

The UvrA–UvrB (AB) protein complex operates in the bacterial nucleotide excision repair pathway as the main sensor of DNA damage. Crystallographic analysis of the AB complex revealed a linear UvrB–UvrA–UvrA–UvrB arrangement of subunits with an internal two‐fold axis that became incorporated into the crystal. Here, we have used small‐angle X‐ray scattering (SAXS) to show close correspondence between the crystal structure and the entity in solution. This result confirms the number and disposition of subunits in the crystallographic model and rules out other possible arrangements suggested by packing in the crystal. The current SAXS analysis failed to detect significant changes to the structure as a function of nucleotide. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

Lipase Catalyzed Resolution of (±)-2-Substituted 1-Propanol Derivatives Possessing an Aromatic Ring

For the purpose of the chiral synthesis of natural products, lipase-catalyzed kinetic resolutions of three types of 2-substituted 1-propanol derivatives (each having an aromatic ring) was investigated. In every case, chiral recognition of the primary alcohol unit took place to provide the corresponding alcohols and the acetates in high optical purity. The (2S,3S)-5-aryl-2-methyl-3-hydroxy-4E-pentenol 5 was formally converted into the antibiotic, (-)-oudemansin X.     

Ataxia telangiectasia resists gene cloning: An account of parameters determining gene transfer into human recipient cells

Summary A subclone of an SV40-transformed fibroblast cell line from a patient with Ataxia telangiectasia (AT) with a relatively high rate of DNA uptake was isolated. However, more than 65000 independent genomic transfectants (using wild-type human DNA) did not contain the functional AT gene. This number represents the statistical distribution of an amount of DNA equivalent to more than three times the haploid human genome. The transfectants were screened by an X ray selection protocol that could rescue a single wild-type cell out of a population of 10⁶ AT cells. This suggests a reversion frequency for AT of below 10^-8. The DNA uptake into human cells is compared with that into NIH3T3 cells and future possibilities for the isolation of human repair genes are discussed.     

Scientific workflow optimization for improved peptide and protein identification

Background

Peptide-spectrum matching is a common step in most data processing workflows for mass spectrometry-based proteomics. Many algorithms and software packages, both free and commercial, have been developed to address this task. However, these algorithms typically require the user to select instrument- and sample-dependent parameters, such as mass measurement error tolerances and number of missed enzymatic cleavages. In order to select the best algorithm and parameter set for a particular dataset, in-depth knowledge about the data as well as the algorithms themselves is needed. Most researchers therefore tend to use default parameters, which are not necessarily optimal.

Results

We have applied a new optimization framework for the Taverna scientific workflow management system (http://ms-utils.org/Taverna_Optimization.pdf) to find the best combination of parameters for a given scientific workflow to perform peptide-spectrum matching. The optimizations themselves are non-trivial, as demonstrated by several phenomena that can be observed when allowing for larger mass measurement errors in sequence database searches. On-the-fly parameter optimization embedded in scientific workflow management systems enables experts and non-experts alike to extract the maximum amount of information from the data. The same workflows could be used for exploring the parameter space and compare algorithms, not only for peptide-spectrum matching, but also for other tasks, such as retention time prediction.

Conclusion

Using the optimization framework, we were able to learn about how the data was acquired as well as the explored algorithms. We observed a phenomenon identifying many ammonia-loss b-ion spectra as peptides with N-terminal pyroglutamate and a large precursor mass measurement error. These insights could only be gained with the extension of the common range for the mass measurement error tolerance parameters explored by the optimization framework.