Modelling of the lignin peroxidase LIII of Phlebia radiata: use of a sequence template generated from a 3-D structure

A model of the lignin peroxidase LIII of Phlebia radiata wasconstructed on the basis of the structure of cytochrome c peroxidase(CCP). Because of the low percentage of amino acid identitybetween the CCP and the lignin peroxidase LIII of Phlebia radiata,alignment of the sequences was based on the generation of atemplate from a knowledge of the 3-D structure of CCP and consensussequences of lignin peroxidases. This approach gave an alignmentin which all the insertions in the lignin peroxidase were placedat loop regions of CCP, with a 21.1% identity for these twoproteins. The model was constructed using this alignment andthe computer program COMPOSER, which assembles the model asa series of rigid fragments derived from CCP and other proteins.Manual intervention was required for some of the longer loopregions. The -helices forming the structural framework, andespecially the haem environment of CCP, are conserved in theLIII model and the core is close packed without holes. A possiblesite of the substrate oxidation at the haem edge of LIII isdiscussed.     

An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure

A 3-D model of a protein can be constructed from its amino acidsequence and the 3-D structures of one or more homologues byannealing three sets of fragments: the structurally conservedregions, structurally variable regions and the side chains.The method encoded in the computer program COMPOSER was assessedby generating 3-D models of eight proteins whose crystal structuresare already known and for which 3-D structures of homologuesare available. In the structurally conserved regions, differencesbetween modelled and X-ray structures are smaller than the differencesbetween the X-ray structures of the modelled protein and thehomologues used to build the model. When several homologuesare used, the contributions of the known structures are weighted,preferably by the square of sequence similarity; this is especiallyimportant when the similarities of the homologues to the modelledstructure differ greatly. The ‘collar’ extensionapproach, in which a similar region of different length in ahomologue is used to extend the framework, can result in a moreaccurate model. If known homologues comprise more than one relatedgroup of proteins and they are both distantly related to theunknown, then alignment of the sequence to be modelled witheach group of homologues facilitates identification of structurallyconserved regions of the unknown and leads to an improved model.Models have root mean square differences (r.m.s.d.s) with thestructures defined by X-ray analysis of between 0.73 and 1.56Å for all C atoms, for seven of the eight models. Forthe model of mucor pepsin, where the closest homologue has 33%sequence identity and 20% of the residues are in structurallyvariable regions, the r.m.s.d. for the framework region is 1.71Å and the r.m.s.d. for all C atoms is 3.47 Â.     

Influence of FeO/SiO2 and CaO/SiO2 Ratios in Iron‐Saturated ZnO‐Rich Fayalite Slags on the Corrosion of MgO

The corrosion behavior of MgO in iron‐saturated ZnO‐rich fayalite (ZFS) slags having various FeO/SiO₂ ratio and CaO/SiO₂ ratio was investigated using MgO crucible tests for 12 h at 1200°C. The FeO/SiO₂ and CaO/SiO₂ ratios in the ZFS slags were varied from 1.0 to 2.2, and from 0.04 to 0.32, respectively. In all of the tests, it was observed that MgO dissolves into ZFS slags and that (Zn,Fe,Mg)₂SiO₄ olivine and (Zn,Fe,Mg)O solid solution are formed at the crucible/slag interface. The MgO dissolution decreased with the FeO/SiO₂ ratio up to a value of 1.7 and then slightly increased, whereas it continuously increased with the CaO/SiO₂ ratio. There is no obvious relationship between the amount of olivine and the FeO/SiO₂ ratio or CaO/SiO₂ ratio. In comparison, the formation of (Zn,Fe,Mg)O solid solution is enhanced by increasing the FeO/SiO₂ ratio or CaO/SiO₂ ratio in ZFS slags. The results suggest that MgO corrosion is the lowest for FeO/SiO₂ and CaO/SiO₂ ratios around 1.7 and 0, respectively.     

Use of Repetitive Sequences for Molecular and Cytogenetic Characterization of Avena Species from Portugal

Genomic diversity of Portuguese accessions of Avena species—diploid A. strigosa and hexaploids A. sativa and A. sterilis—was evaluated through molecular and cytological analysis of 45S rDNA, and other repetitive sequences previously studied in cereal species—rye subtelomeric sequence (pSc200) and cereal centromeric sequence (CCS1). Additionally, retrotransposons and microsatellites targeting methodologies—IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism)—were performed. A very high homology was detected for ribosomal internal transcribed sequences (ITS1 and ITS2) between the species analyzed, although nucleolar organizing regions (NOR) fluorescent in situ hybridization (FISH) analysis revealed distinct number of Nor loci between diploid and hexaploid species. Moreover, morphological diversity, evidenced by FISH signals with different sizes, was observed between distinct accessions within each species. pSc200 sequences were for the first time isolated from Avena species but proven to be highly similar in all genotypes analyzed. The use of primers designed for CCS1 unraveled a sequence homologous to the Ty3/gypsy retrotransposon Cereba, that was mapped to centromeric regions of diploid and hexaploid species, being however restricted to the more related A and D haplomes. Retrotransposon-based methodologies disclosed species- and accessions-specific bands essential for the accurate discrimination of all genotypes studied. Centromeric, IRAP and REMAP profiles therefore allowed accurate assessment of inter and intraspecific variability, demonstrating the potential of these molecular markers on future oat breeding programs.     

Calculation of separation columns by nonlinear block successive relaxation methods

A novel technique: nonlinear block successive relaxation (NBSR) method, is proposed to solve the steady-state balance equations describing separation columns. The NBSR methods are a generalization of point relaxation methods frequently used towards solution of elliptic partial differential equations. Aspects of partitioning of the original set of equations into blocks as well as ordering of blocks is discussed. Problems arising in construction of a universal program based on the NBSR methods are presented. A new procedure making use of grouping of equations according to the set of trays is proposed. Aspects of calculation of separation equipments by this procedure is discussed. It is shown that overlapping blocks may essentially improve the convergence properties of the algorithm. The procedure is very simple and can be easily used towards calculation of large separation problems on a small computer. The method described is illustrated on calculation of an absorption column. Application of the NBSR methods to solution of a complex plant is suggested.     

The hydrocarbon fraction of virgin olive oil and changes resulting from refining

In numerous Spanish virgin olive oils, 6,10-dimethyl-1-undecene, various sesquiterpenes, the series ofn-alkanes from C14 to C35, n-8-heptadecene and squalene are the only less volatile components detected by gas chromatography in the hydrocarbon fraction. In oils from olives of the Arbequine variety, a series ofn-9-alkenes has also been found. In refined oils, notable features are the absence of the most volatile compounds and the appearance of other hydrocarbons produced during the refining process. Among these,n-alkanes, alkadienes (mainlyn-hexacosadiene), stigmasta-3,5-diene, isomerization products of squalene, isoprenoidal polyolefins coming from hydroxy derivatives of squalene and steroidal hydrocarbons derived from 24-methylene cycloartanol were identified. Physical refining produces larger amounts of degradation products and greater losses ofn-alkanes than chemical processing. Squalene is the major hydrocarbon component in all oils, both virgin and refined. The ranges of concentration for the different hydrocarbons found in Spanish virgin olive oils are presented.     

Pinpointing biomarkers in proteomic LC/MS data by moving-window discriminant analysis

The identification of differential patterns in data originating from combined measurement techniques such as LC/MS is pivotal to proteomics. Although "shotgun proteomics" has been employed successfully to this end, this method also has severe drawbacks, because of its dependence on largely untargeted MS/MS sequencing and databases for statistical analyses. Alternatively, several MS-signal-based (MS/MS-independent) methods have been published that are mainly based on (univariate) Student's t-tests. Here, we present a more robust multivariate alternative employing linear discriminant analysis. Like the t-test-based methods, it is applied directly to LC/MS data, instead of using MS/MS measurements. We demonstrate the method on a number of simulated data sets, as well as on a spike-in LC/MS data set, and show its superior performance over t-tests.     

Light interactions with gold nanorods and cells: implications for photothermal nanotherapeutics

Gold nanorods (AuNR) can be tailored to possess an intense and narrow longitudinal plasmon (LP) absorption peak in the far-red to near-infrared wavelength region, where tissue is relatively transparent to light. This makes AuNRs excellent candidates as contrast agents for photoacoustic imaging, and as photothermal therapeutic agents. The favorable optical properties of AuNR which depend on the physical parameters of shape, size and plasmonic coupling effects, are required to be stable during use. We investigate the changes that are likely to occur in these physical parameters in the setting of photothermal therapeutics, and the influence that these changes have on the optical properties and the capacity to achieve target cell death. To this end we study 3 sets of interactions: pulsed light with AuNR, AuNR with cells, and pulsed light with cells incubated with AuNR. In the first situation we ascertain the threshold value of fluence required for photothermal melting or reshaping of AuNR to shorter AuNR or nanospheres, which results in drastic changes in optical properties. In the second situation when cells are exposed to antibody-conjugated AuNR, we observe using transmission electron microscopy (TEM) that the particles are closely packed and clustered inside vesicles in the cells. Using dark-field microscopy we show that plasmonic interactions between AuNRs in this situation causes blue-shifting of the LP absorption peak. As a consequence, no direct lethal damage to cells can be inflicted by laser irradiation at the LP peak. On the other hand, using irradiation at the transverse peak (TP) wavelength in the green, at comparative fluences, extensive cell death can be achieved. We attribute this behavior on the one hand to the photoreshaping of AuNR into spheres and on the other hand to clustering of AuNR inside cells. Both effects create sufficiently high optical absorption at 532 nm, which otherwise would have been present at the LP peak. We discuss implications of these finding on the application of these particles in biomedicine.     

Content of uranium in urine of uranium miners as a tool for estimation of intakes of long-lived alpha radionuclides

Uranium in the urine of 10 uranium miners (hewers), 27 members of general population and 11 family members of miners was determined by the High-Resolution ICP-MS method. Concentration of uranium in urine of the miners was converted to daily excretion of (238)U under the assumption that the daily excretion of urine is 2 l and compared with the modelled excretion of (238)U. Daily excretion of (238)U was modelled using input data from personal dosemeters from a component for measurement of intake of long-lived alpha radionuclides. A reasonable agreement between evaluated and measured values was found. The uncertainty of inhalation intakes, derived from measurements of filters from personal dosemeters, and uncertainty of concentration of uranium in urine are discussed.     

Disorder effect in the transmission spectra of a noncompact single layer of dielectric spheres derived from microwave spectroscopy

Single layers of dielectric spheres are an interesting system to study from the fundamental and applied points of view. In this paper we present a systematic study of the influence of structural disorder on the transmission spectra of arrangements of spheres of different compactness. Glass sphere (ε=7) planes were built and their transmission spectra in the microwave range measured. Transmission behavior of this system is highly tolerant to disorder. Even in completely disordered arrangements, there is a highly rejected band with the dips of the spectrum observable. These results suggest that the collective modes of the sphere planes are formed by weakly coupled Mie modes of the individual spheres, and this coupling is governed by the average distance among the spheres. Disorder tolerance allows simpler fabrication procedures where the position of the spheres does not need to be precisely controlled.