Ultrafast Photoconversion Dynamics of the Knotless Phytochrome SynCph2

The family of phytochrome photoreceptors contains proteins with different domain architectures and spectral properties. Knotless phytochromes are one of the three main subgroups classified by their distinct lack of the PAS domain in their photosensory core module, which is in contrast to the canonical PAS-GAF-PHY array. Despite intensive research on the ultrafast photodynamics of phytochromes, little is known about the primary kinetics in knotless phytochromes. Here, we present the ultrafast P_r ⇆ P_fr photodynamics of SynCph2, the best-known knotless phytochrome. Our results show that the excited state lifetime of P_r* (~200 ps) is similar to bacteriophytochromes, but much longer than in most canonical phytochromes. We assign the slow P_r* kinetics to relaxation processes of the chromophore-binding pocket that controls the bilin chromophore’s isomerization step. The P_fr photoconversion dynamics starts with a faster excited state relaxation than in canonical phytochromes, but, despite the differences in the respective domain architectures, proceeds via similar ground state intermediate steps up to Meta-F. Based on our observations, we propose that the kinetic features and overall dynamics of the ultrafast photoreaction are determined to a great extent by the geometrical context (i.e., available space and flexibility) within the binding pocket, while the general reaction steps following the photoexcitation are most likely conserved among the red/far-red phytochromes.     

Mechanical properties and biodegradability of LDPE blends with fatty‐acid esters of amylose and starch

In the present article a series of low‐density polyethylene (LDPE) blends with different amounts of fatty esters of amylose and starch, were prepared in a Haake‐Buchler Reomixer. The tensile as well as the dynamic thermomechanical (DMTA) properties of the blends were measured. It was found that as the amount of the esters increases in the blends, the tensile strength and especially the elongation at break decrease nonlinearly. Scanning electron microscopy (SEM) was used to assess the interfacial adhesion between LDPE and the corresponding esters. The incompatibility of the blends was also verified with DMTA and differential scanning calorimetry (DSC). From the biodegradation studies of the blends during exposure in activated sludge, it was found that all esters are biodegradable, although to a much lesser degree compared to pure strach. The biodegradation rate of the composites is relatively small due to the low biodegradation rate of the pure esters. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 71: 1089–1100, 1999     

Metabolic labeling of Escherichia coli genomic DNA with erythrosine‐11‐dUTP for functional imaging via correlative microscopy

The fluorescent metabolic labeling of microorganisms genome is an advanced imaging technique to observe and study the native shapes, structural changes, functions, and tracking of nucleic acids in single cells or tissues. We have attempted to visualize the newly synthesized DNA within the intact nucleoid of ice‐embedded proliferating cells of Escherichia coli K‐12 (thymidine‐requiring mutant, strain N4316) via correlative light‐electron microscopy. For that purpose, erythrosine‐11‐dUTP was synthesized and used as a modified analog of the exogenous thymidine substrate for metabolic incorporation into the bacterial chromosome. The formed fluorescent genomic DNA during in cellulo polymerase reaction caused a minimal cellular arrest and cytotoxicity of E. coli at certain controlled conditions. The stained cells were visualized in typical red emission color via an epifluorescence microscope. They were further ice‐embedded and examined with a Hilbert differential contrast transmission electron microscopy. At high‐resolution, the ultrastructure of tagged nucleoid appeared with significantly higher electron dense in comparison to the unlabeled one. The enhanced contrast areas in the chromosome were ascribed to the presence of iodine contents from erythrosine dye. The presented labeling approach might be a powerful strategy to reveal the structural and dynamic changes in natural DNA replication including the relationship between newly synthesized in vivo nucleic acid and the physiological state of the cell.     

Sensitization and Intergranular Corrosion Behavior of High Nitrogen Type 304LN Stainless Steels for Reprocessing and Waste Management Applications

High nitrogen 304LN stainless steels (SS) intended for chloride and nitric acid environments in spent nuclear fuel reprocessing and waste management applications were evaluated for their sensitization and intergranular corrosion (IGC) resistance. For this purpose, high nitrogen (0.132 pct, 0.193 pct and 0.406 pct) containing, impurity-controlled, vanadium-added 304LN SS alloys were developed. For comparison, 304L SS, which is currently used in reprocessing plants, was also studied. These stainless steels were subjected to heat treatment at 948 K (675 °C) for various durations ranging from 1 to 1000 hours and tested for susceptibility to IGC as per ASTM A262 Practice A and E tests. The degree of sensitization was estimated with the double loop electrochemical potentiokinetic reactivation technique. The increase in nitrogen content resulted in higher hardness and finer grain size. Based on the detailed microstructural and corrosion studies, it was determined that an addition of 0.132 pct and 0.193 pct nitrogen showed better IGC resistance and an additional increase in nitrogen resulted in deterioration resulting from chromium nitride precipitation, which was confirmed by electrochemical phase separation and X-ray diffraction studies. The onset of desensitization was faster for the alloy with 0.132 pct nitrogen as well as 0.406 pct nitrogen because of the lower nitrogen content in the former case and the finer grain size in the latter case. The higher hardness and superior IGC resistance of 0.132 pct and 0.193 pct nitrogen containing Type 304LN SS suggests the suitability of this alloy for nitric acid- and chloride-containing environments of reprocessing and waste management plants.     

X-ray diffraction topography investigation of the core in Bi12SiO20 crystals

The core in a large Bi₁₂SiO₂₀ crystal as well as the regions free of optical inhomogenities was examined by X-ray double-crystal diffraction topography. It was established that the observed defects in the central core are two-dimensional. The absorption of some impurities as well as the composition changes observed in this area by other authors, should be considered as a consequence of the formation of these defects.     

Efficient keyword search over virtual XML views

Emerging applications such as personalized portals, enterprise search, and web integration systems often require keyword search over semi-structured views. However, traditional information retrieval techniques are likely to be expensive in this context because they rely on the assumption that the set of documents being searched is materialized. In this paper, we present a system architecture and algorithm that can efficiently evaluate keyword search queries over virtual (unmaterialized) XML views. An interesting aspect of our approach is that it exploits indices present on the base data and thereby avoids materializing large parts of the view that are not relevant to the query results. Another feature of the algorithm is that by solely using indices, we can still score the results of queries over the virtual view, and the resulting scores are the same as if the view was materialized. Our performance evaluation using the INEX data set in the Quark (Bhaskar et al. in Quark: an efficient XQuery full-text implementation. In: SIGMOD, 2006) open-source XML database system indicates that the proposed approach is scalable and efficient.     

Immobilization and stretching of 5′‐pyrene‐terminated DNA on carbon film deposited on electron microscope grid

The immobilization and stretching of randomly coiled DNA molecules on hydrophobic carbon film is a challenging microscopic technique, which possess various applications, especially for genome sequencing. In this report the pyrenyl nucleus is used as an anchor moiety to acquire higher affinity of double stranded DNA to the graphite surface. DNA and pyrene are joined through a linker composed of four aliphatic methylene groups. For the preparation of pyrene‐terminated DNA a multifunctional phosphoramidite monomer compound was designed. It contains pyrenylbutoxy group as an anchor moiety for π‐stacking attachment to the carbon film, 2‐cyanoethyloxy, and diisopropylamino as coupling groups for conjugation to activated oligonucleotide chain or DNA molecule. This monomer derivative was suitable for incorporation into automated solid‐phase DNA synthesis and was attached to the 5′ terminus of the DNA chain through a phosphodiester linkage. The successful immobilization and stretching of pyrene‐terminated DNA was demonstrated by conventional 100 kV transmission electron microscope. The microscopic analysis confirmed the stretched shape of the negatively charged nucleic acid pieces on the hydrophobic carbon film. Microsc. Res. Tech. 78:994–1000, 2015. © 2015 Wiley Periodicals, Inc.     

Oxidative stability of oil-in-water emulsions containing iron chelates: Transfer of iron from chelates to milk proteins at interface

Iron supplementation can promote oxidation of food matrices as well as cell lipids. The oxidative stability of oil/water emulsions stabilised by β-lactoglobulin (BLG) or sodium caseinate (SC) was studied in the presence of Fe-bisglycinate, NaFe-EDTA or FeSO₄. Lipid oxidation was evaluated by following the peroxide value (PV) and the thiobarbituric acid reactive substances (TBARS) over 7 days. At pH 6.5, for Fe-bisglycinate iron complement, the oxidation kinetics was more reduced with BLG than with SC. Contrarily to BLG, SC possesses phosphate groups that have more affinity for iron ions than carboxylate residues. Both BLG and SC stabilised emulsions were more oxidised with Fe-bisglycinate or FeSO₄ than with NaFe-EDTA. At pH 3.5, lipid oxidation was higher compared to pH 6.5. These results indicate that the competition for iron complexation between functional groups of protein and salt counter-ions (glycinate, sulphate or EDTA) appear as a key factor in oxidation.     

Mechanical properties and viscoelastic behavior of basalt fiber‐reinforced polypropylene

In the present article, a series of commercial‐grade polypropylenes (PP) filled with different contents of short basalt fibers were studied. This composite material presented deterioration of both mechanical characteristics, for example, stress and strain at yield with increasing of the fiber content. On the other hand, the impact strength was fourfold higher than that of unfilled PP. A poor adhesion between the PP matrix and the basalt fibers was detected. This is why interfacial interactions were promoted by the adding of poly(propylene‐g‐maleic anhydride) (PP‐g‐MA). It was observed that the tensile properties of the obtained materials and their impact strengths increased significantly with increasing of the amount of PP‐g‐MA in the blend. The adhesion improvement was confirmed by scanning electron microscopy as well. Fourier transform infrared spectroscopy was applied to assess if any chemical interactions in the system PP/PP‐g‐MA/basalt fibers exist. Dynamic mechanical thermal analysis data showed an increase of the storage modulus with increasing fiber content. The conclusion was made that the modification of the PP matrix led to a higher stiffness but its value remained constant, irrespective of the PP‐g‐MA content. With increasing fiber content, damping in the β‐region decreased, but increase of the coupling agent content restored its value back to that of PP. The loss modulus spectra presented a strong influence of fiber content on the α‐relaxation process of PP. The position of the peaks of the above‐mentioned relaxation processes are discussed as well. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 74: 523–531, 1999     

Electron microscopic visualization of complementary labeled DNA with platinum‐containing guanine derivative

The object of the present report is to provide a method for a visualization of DNA in TEM by complementary labeling of cytosine with guanine derivative, which contains platinum as contrast‐enhanced heavy element. The stretched single‐chain DNA was obtained by modifying double‐stranded DNA. The labeling method comprises the following steps: (i) stretching and adsorption of DNA on the support film of an electron microscope grid (the hydrophobic carbon film holding negative charged DNA); (ii) complementary labeling of the cytosine bases from the stretched single‐stranded DNA pieces on the support film with platinum containing guanine derivative to form base‐specific hydrogen bond; and (iii) producing a magnified image of the base‐specific labeled DNA. Stretched single‐stranded DNA on a support film is obtained by a rapid elongation of DNA pieces on the surface between air and aqueous buffer solution. The attached platinum‐containing guanine derivative serves as a high‐dense marker and it can be discriminated from the surrounding background of support carbon film and visualized by use of conventional TEM observation at 100 kV accelerated voltage. This method allows examination of specific nucleic macromolecules through atom‐by‐atom analysis and it is promising way toward future DNA‐sequencing or molecular diagnostics of nucleic acids by electron microscopic observation. Microsc. Res. Tech. 79:280–284, 2016. © 2016 Wiley Periodicals, Inc.