Characterization of alluvial formation by stochastic modelling of paleo-fluvial processes: The concept and method

Modelling fluvial processes is an effective way to reproduce basin evolution and to recreate riverbed morphology. However, due to the complexity of alluvial environments, deterministic modelling of fluvial processes is often impossible. To address the related uncertainties, we derive a stochastic fluvial process model on the basis of the convective Exner equation that uses the statistics (mean and variance) of river velocity as input parameters. These statistics allow for quantifying the uncertainty in riverbed topography, river discharge and position of the river channel. In order to couple the velocity statistics and the fluvial process model, the perturbation method is employed with a non-stationary spectral approach to develop the Exner equation as two separate equations: the first one is the mean equation, which yields the mean sediment thickness, and the second one is the perturbation equation, which yields the variance of sediment thickness. The resulting solutions offer an effective tool to characterize alluvial aquifers resulting from fluvial processes, which allows incorporating the stochasticity of the paleoflow velocity.

Development and characterization of microsatellite markers in the sea squirt, Halocynthia roretzi

We characterized nine new microsatellite markers isolated from (GT) n and (CT) n microsatellite- enriched genomic libraries of the sea squirt ( Halocynthia roretzi ). All markers were polymorphic in 92 individuals from a single natural population with 2–21 (mean 9.22) alleles per locus. The observed and expected heterozy-gosity of these markers were 0.086–0.886 and 0.102–0.870, respectively.One marker (Hr2004) significantly deviated from Hardy–Weinberg equilibrium. These new microsat-ellite markers should be useful for assessing the genetic diversity and population structure in H. roretzi.

Characterization of novel microsatellite markers derived from Korean rose bitterling (Rhodeus uyekii) genomic library

Korean rose bitterling (Rhodeus uyekii) is a freshwater fish endemic to Korea. Natural populations of this species have experienced severe declines as a result of habitat fragmentation and water pollution. To conserve and restore R. uyekii, the genetic diversity of this species needs to be assessed at the population level. Eighteen novel polymorphic microsatellite loci for R. uyekii were developed using an enriched partial genomic library. Polymorphisms at these loci were studied in 150 individuals collected from three populations. The number of alleles at each locus ranged from 3 to 47 (mean = 17.1). Within the populations, the observed heterozygosity ranged from 0.032 to 1.000, expected heterozygosity from 0.082 to 0.967, and polymorphism information content from 0.078 to 0.950. Six loci showed significant deviation from Hardy-Weinberg equilibrium after Bonferroni’s correction, and no significant linkage disequilibrium was detected between most locus pairs, except in three cases. These highly informative microsatellite markers should be useful for genetic population structure analyses of R. uyekii.

Characterization of epitopes for virus-neutralizing monoclonal antibodies to Ross River virus E2 using phage-displayed random peptide libraries

Ross River virus (RRV) is the predominant cause of epidemic polyarthritis in Australia, yet the antigenic determinants are not well defined. We aimed to characterize epitope(s) on RRV-E2 for a panel of monoclonal antibodies (MAbs) that recognize overlapping conformational epitopes on the E2 envelope protein of RRV and that neutralize virus infection of cells in vitro. Phage-displayed random peptide libraries were probed with the MAbs T1E7, NB3C4, and T10C9 using solution-phase and solid-phase biopanning methods. The peptides VSIFPPA and KTAISPT were selected 15 and 6 times, respectively, by all three of the MAbs using solution-phase biopanning. The peptide LRLPPAP was selected 8 times by NB3C4 using solid-phase biopanning; this peptide shares a trio of amino acids with the peptide VSIFPPA. Phage that expressed the peptides VSIFPPA and LRLPPAP were reactive with T1E7 and/or NB3C4, and phage that expressed the peptides VSIFPPA, LRLPPAP, and KTAISPT partially inhibited the reactivity of T1E7 with RRV. The selected peptides resemble regions of RRV-E2 adjacent to sites mutated in neutralization escape variants of RRV derived by culture in the presence of these MAbs (E2 210-219 and 238-245) and an additional region of E2 172-182. Together these sites represent a conformational epitope of E2 that is informative of cellular contact sites on RRV.

Characterization of VOCs from LPG and unleaded petroleum fuelled passenger cars

The study monitored the emissions of volatile organic compounds (VOCs) from the exhaust of cars fuelled by liquefied petroleum gas (LPG) and unleaded petrol (ULP). Six cars, four fuelled by LPG and two by ULP, were tested on a chassis dynamometer at two different cruising modes of operation (60 km h−1 and 80 km h−1) and idle. A total of 33 VOCs were identified in the exhaust of both types of fuels by the use of GC/MS. Due to the complexity of the dataset, Multi Criteria Decision Making (MCDM) software PROMETHEE and GAIA was used to rank the least polluting mode and fuel. The 60 km h−1 driving speed was identified as the cleaner mode of driving as was LPG fuel. The Ozone Formation Potential (OFP) of the VOCs was also calculated by using the incremental reactivity scale. Priority VOCs leading to ozone formation were identified according to the three incremental reactivity scales: MIR, MOIR and EBIR. PROMETHEE was applied to assess the most preferred scale of reactivity for predicting ozone formation potential under different scenarios. The results enhance the understanding of the environmental value of using LPG to power passenger cars.

Experimental and theoretical characterization of 5,10- diminoporphodimethenes: Dearomatized porphyrinoids from palladium-catalyzed hydrazinations of 5,10-diarylporphyrins

A new dearomatized porphyrinoid, 5,10-diiminoporphodimethene (5,10-DIPD), has been prepared by palladium-catalyzed hydrazination of 5,10-dibromo-15,20-bis(3,5-di-tert-butylphenyl)porphyrin and its nickel(II) complex, by using ethyl and 4-methoxybenzyl carbazates. The oxidative dearomatization of the porphyrin ring occurs in high yield. Further oxidation with 2,3-dichloro-5,6-dicyanobenzoquinone forms the corresponding 5,10-bis(azocarboxylates), thereby restoring the porphyrin aromaticity. The UV/visible spectra of the NiII DIPDs exhibit remarkable redshifts of the lowest-energy bands to 780 nm, and differential pulse voltammetry reveals a contracted electrochemical HOMO–LUMO gap of 1.44 V. Density functional theory (DFT) was used to calculate the optimized geometries and frontier molecular orbitals of model 5,10-DIPD Ni7c and 5,10-bis(azocarboxylate) Ni8c. The conformations of the carbamate groups and the configurations of the CNZ unit were considered in conjunction with the NOESY spectra, to generate the global minimum geometry and two other structures with slightly higher energies. In the absence of solution data regarding conformations, ten possible local minimum conformations were considered for Ni8c. Partition of the porphyrin macrocycle into tri- and monopyrrole fragments in Ni7c and the inclusion of terminal conjugating functional groups generate unique frontier molecular orbital distributions and a HOMO–LUMO transition with a strong element of charge transfer from the monopyrrole ring. Time-dependent DFT calculations were performed for the three lowest-energy structures of Ni7c and Ni8c, and weighting according to their energies allowed the prediction of the electronic spectra. The calculations reproduce the lower-energy regions of the spectra and the overall forms of the spectra with high accuracy, but agreement is not as good in the Soret region below 450 nm.

Genetic associations and functional characterization of M1 aminopeptidases and immune-mediated diseases

Endosplasmic reticulum aminopeptidase 1 (ERAP1), endoplasmic reticulum aminopeptidase 2 (ERAP2) and puromycin-sensitive aminopeptidase (NPEPPS) are key zinc metallopeptidases that belong to the oxytocinase subfamily of M1 aminopeptidase family. NPEPPS catalyzes the processing of proteosome-derived peptide repertoire followed by trimming of antigenic peptides by ERAP1 and ERAP2 for presentation on major histocompatibility complex (MHC) Class I molecules. A series of genome-wide association studies have demonstrated associations of these aminopeptidases with a range of immune-mediated diseases such as ankylosing spondylitis, psoriasis, Behçet's disease, inflammatory bowel disease and type I diabetes, and significantly, genetic interaction between some aminopeptidases and HLA Class I loci with which these diseases are strongly associated. In this review, we highlight the current state of understanding of the genetic associations of this class of genes, their functional role in disease, and potential as therapeutic targets.

Microstructural characterization of ultrafine-grain interstitial-free steel by X-ray diffraction line profile analysis

This paper highlights the microstructural features of commercially available interstitial free (IF) steel specimens deformed by equal channel angular pressing (ECAP) up to four passes following the route A. The microstructure of the samples was studied by different techniques of X-ray diffraction peak profile analysis as a function of strain (epsilon). It was found that the crystallite size is reduced substantially already at epsilon=2.3 and it does not change significantly during further deformation. At the same time, the dislocation density increases gradually up to epsilon=4.6. The dislocation densities estimated from X-ray diffraction study are found to correlate very well with the experimentally obtained yield strength of the samples.

Expression, Purification and Characterization of Peanut (Arachis hypogaea) Agglutinin (PNA) from Baculovirus Infected Insect Cells

Peanut (Arachis hypogaea) seed lectin, PNA is widely used to identify tumor specific antigen (T-antigen), Gal beta 1-3GalNAc on the eukaryotic cell surface. The functional amino acid coding region of a cDNA clone, pBSH-PN was PCR amplified and cloned downstream of the polyhedrin promoter in the Autographa californica nucleopolyhedrovirus (AcNPV) based transfer vector pVL1393. Co-transfection of Spodoptera frugiperda cells (Sf9) with the transfer vector, pAcPNA and AcRP6 (a recombinant AcNPV having B-gal downstream of the polyhedrin promoter) DNAs produced a recombinant virus, AcPNA which expresses PNA. Infection of suspension culture of Sf9 cells with plaque purified AcPNA produced as much as 9.8 mg PNA per liter (2.0 x 10(6) cells/ml) of serum-free medium. Intracellularly expressed protein (re-PNA) was purified to apparent homogeneity by affinity chromatography using ECD-Sepharose. Polyclonal antibodies against natural PNA (n-PNA) crossreacted with re-PNA. The subunit molecular weight (30 kDa), hemagglutination activity, and carbohydrate specificity of re-PNA were found to be identical to that of n-PNA, thus confirming the abundant production of a functionally active protein in the baculovirus expression system.

Thermodynamic characterization of the conformational stability of the homodimeric protein, pea lectin

The conformational stability of the homodimeric pea lectin was determined by both isothermal urea-induced and thermal denaturation in the absence and presence of urea. The denaturation profiles were analyzed to obtain the thermodynamic parameters associated with the unfolding of the protein. The data not only conform to the simple A(2) double left right arrow 2U model of unfolding but also are well described by the linear extrapolation model for the nature of denaturant-protein interactions. In addition, both the conformational stability (Delta G(s)) and the Delta C-p for the protein unfolding is quite high, at about 18.79 kcal/ mol and 5.32 kcal/(mol K), respectively, which may be a reflection of the relatively larger size of the dimeric molecule (M-r 49 000) and, perhaps, a consequent larger buried hydrophobic core in the folded protein. The simple two-state (A(2) double left right arrow 2U) nature of the unfolding process, with the absence of any monomeric intermediate, suggests that the quaternary interactions alone may contribute significantly to the conformational stability of the oligomer-a point that may be general to many oligomeric proteins.

Characterization of novel immunodominant antigens of Mycobacterium tuberculosis

Seven novel antigens of Mycobacterium tuberculosis, which had previously been identified based on reactivity to sera from patients with tuberculosis, were characterized. Nucleotide sequence analysis of the genes encoding these seven antigens identified one of them as the FtsH and a second as the aminoimidazole ribotide synthase of M. tuberculosis. Antisera raised to the recombinant forms of each of these seven antigens were used to study the distribution of these proteins within mycobacterial species as well as to determine their subcellular localization and hydrophobicity. Four of the seven antigens were conserved only among pathogenic strains of mycobacteria. Of the seven proteins studied, FtsH and a second protein of unknown identity were localized in membranes. Two were cytosolic, while two others, which had a high proline content, were tightly associated with the cell wall. One protein was secreted. This secreted protein could be identified by serum from a majority of tuberculosis patients but not BCG-vaccinated individuals, suggesting its potential use in the immunodiagnosis of tuberculosis.

Characterization of an Evolutionarily Conserved Metallophosphoesterase That Is Expressed in the Fetal Brain and Associated with the WAGR Syndrome

Among the human diseases that result from chromosomal aberrations, a de novo deletion in chromosome 11p13 is clinically associated with a syndrome characterized by Wilms' tumor, aniridia, genitourinary anomalies, and mental retardation (WAGR). Not all genes in the deleted region have been characterized biochemically or functionally. We have recently identified the first Class III cyclic nucleotide phosphodiesterase, Rv0805, from Mycobacterium tuberculosis, which biochemically and structurally belongs to the superfamily of metallophosphoesterases. We performed a large scale bioinformatic analysis to identify orthologs of the Rv0805 protein and identified many eukaryotic genes that included the human 239FB gene present in the region deleted in the WAGR syndrome. We report here the first detailed biochemical characterization of the rat 239FB protein and show that it possesses metallophosphodiesterase activity. Extensive mutational analysis identified residues that are involved in metal interaction at the binuclear metal center. Generation of a rat 239FB protein with a mutation corresponding to a single nucleotide polymorphism seen in human 239FB led to complete inactivation of the protein. A close ortholog of 239FB is found in adult tissues, and biochemical characterization of the 239AB protein demonstrated significant hydrolytic activity against 2',3'-cAMP, thus representing the first evidence for a Class III cyclic nucleotide phosphodiesterase in mammals. Highly conserved orthologs of the 239FB protein are found in Caenorhabditis elegans and Drosophila and, coupled with available evidence suggesting that 239FB is a tumor suppressor, indicate the important role this protein must play in diverse cellular events.

Synthesis, characterization, and electronic structure studies of cubic Bi1.5ZnTa1.5O7 for photocatalytic applications

Bi1.5ZnTa1.5O7 (BZT) has been synthesized using an alkoxide based sol-gel reaction route. The evolution of the phases produced from the alkoxide precursors and their properties have been characterized as function of temperature using a combination of thermogravimetric analysis (TGA) coupled with mass spectrometry (MS), infrared emission spectrometry (IES), X-ray diffraction (XRD), ultraviolet and visible (UV-Vis) spectroscopy, Raman spectroscopy, and N2 adsorption/desorption isotherms. The lowest sintering temperature (600∘C) to obtain phase pure BZT powders with high surface area (14.5m2/g) has been determined from the thermal decomposition and phase analyses.The photocatalytic activity of the BZT powders has been tested for the decolorization of organic azo-dye and found to be photoactive under UV irradiation.The electronic band structure of the BZT has been investigated using density functional theory (DFT) calculations to determine the band gap energy (3.12 eV) and to compare it with experimental band gap (3.02 eV at 800∘C) from optical absorptionmeasurements. An excellent match is obtained for an assumption of Zn cation substitutions at specifically ordered sites in the BZT structure.

Growth and characterization of pure and doped single crystals of $CuGeO_{3}$

Good quality single crystals of copper metagermanite, CuGeO3, are grown by flux technique. Growth is carried out at relatively low temperatures by using Bi2O3 along with CuO in an optimal flux ratio. Besides rendering the procedure simple, lower growth temperature reduces growth defect concentration. Single crystals of Cu1 - xCoxGeO3 and CuGe1 - yGayO3 are grown by the same method for different values of x and y to investigate the influence of in-chain and off-chain doping on spin-Peierls (SP) transition. Change in color, morphology and surface features as a result of doping are briefly discussed. Spin-Peierls transition of these crystals is studied by susceptibility measurements on a commercial SQUID magnetometer. Cationic substitution resulted in reduction of spin-Peierls transition temperature (T-SP) of CuGeO3. Substitution of magnetic impurity cobalt in-chain site caused more pronounced effects such as suppression of SP phase.

Growth and characterization of $SrBi_{2}Nb_{2}O_{9}$ thin films by pulsed-laser ablation

Polycrystalline films of SrBi2Nb2O9 were grown using pulsed-laser ablation. The ferroelectric properties were achieved by low-temperature deposition followed by a subsequent annealing process. The lower switching voltage was obtained by lowering the thickness, which did not affect the insulating nature of the films. The hysteresis results showed an excellent square-shaped loop with results (P-r=6 mu C/cm(2), E-c=100 kV/cm) in good agreement with earlier reports. The films also exhibited a dielectric constant of 250 and a dissipation factor of 0.02. The transport studies indicated an ohmic behavior, while higher voltages induced a bulk space charge.