Comparison for DNA primary sequence

In this article, two schemes are suggested based on three exons of beta-globin gene belonging to 10 species for comparison of DNA primary sequences. At first, the positions of four nucleic acid bases were extracted, and then based on the information, as the numerical characterization of DNA sequences, the sequence invariants were derived. Sequences comparisons of 10 species selected in this work by using these invariants were performed. The results, especially with scheme 2, are quite satisfactory.

Extraction kinetics of cerium(IV) from sulfuric acid medium by the primary amine N1923 using a constant interfacial area cell with laminar flow

BACKGROUND: Thermodynamic studies on Ce(IV) extraction with primary amine N1923 demonstrate that primary amine N1923 is an excellent extractant for separation of Ce(IV) from Re(III). In order to clarify the mechanism of extraction and to optimize the parameters in practical extraction systems used in the rare earth industry, the extraction kinetics was investigated using a constant interfacial area cell with laminar flow in the present work.RESULTS: The data indicate that the rate constant (k(ao).) becomes constant when stirring speed exceeds 250 rpm. The apparent forward extraction rate is calculated to be 10(-1.70). The activation energy (E.) was calculated to be 20.5 kJ/mol from the slope of log kao against 1000/T. The minimum bulk concentration of the extractant necessary to saturate the interface (C-min) is lower than 10(-5) mol L-1.CONCLUSION: Studies of interfacial tension and the effects of stirring rate and specific interfacial area on the extraction rate show that the extraction rate is kinetically controlled, and a mass transfer model has been proposed. The rate equation has been obtained as: -d[Ce(IV)]/dt = 10(-1.70)[Ce(IV)] [(RNH3)(2)SO4](1.376). The rate-controlling step has been evaluated from analysis of the experimental results.

An investigation on the dispersion of montmorillonite (MMT) primary particles in PP matrix

A novel path of preparing PP/o-MMT nanocomposites, which pay attention to the breaking up of MMT original agglomerates and dispersing of its primary particles, rather than the intercalation or exfoliation degree of o-MMT, was reported. The method of predispersing the o-MMT particles into a polar poly(vinyl alcohol) (PVA) matrix and then melt blending the pre-treated PVA/o-MMT hybrids with PP was studied. 3-isopropenyl-alpha,alpha-dimethylbenzene-isocyanate (TMI) was used as a modifier of PVA to improve the compatibility between PVA and PP matrix. Pre-disperse o-MMT with TMI modified PVA was proved to be an effective way to get a composite with fine o-MMT particles dispersion. But the method, which is pre-dispersing o-MMT with non modified PVA and then using TMI to modify such PVA/o-MMT hybrid, would largely reduce the reaction degree between TMI and PVA because of the relatively lower reaction temperature. Although the latter method also can obtain finer dispersion composites than that with using PP-g-MAH as compatibilizer, the relatively higher degradation degree of PP matrix in this method will limit the use of this nanocomposite.

Interfacial behavior of primary amine N1923 and the kinetics of thorium(IV) extraction in sulfate media

The influences of additive, diluents, temperature, acidity of the aqueous phase on the interfacial behavior of primary amine N1923 in sulfate media have been investigated using the Du Nouy ring method. In addition, the effect of concentration of thorium(IV) loaded in the organic phase on the interfacial tension has also been studied. The interfacial tension isotherms are processed by matching different adsorption equations such as the Gibbs and the Szyszkowski. The surface excess at the saturated interface (Gamma (max)) and the minimum bulk concentration of the extractant necessary to saturate the interface (C-min) under different conditions are calculated according to two adsorption equations to be presented in comprehensive tables and figures. It appears that primary amine N1923 has strong interfacial activity and behaves very differently in various diluents systems. The surface excess at saturated interface increase with the type of diluerits in the following order: chloroform < aromatic hydrocarbons < aliphatic hydrocarbons. The relationship between the interfacial activity and kinetics of thorium extraction by primary amine N1923 has been discussed by considering different factors. However, the interfacial activity of primary amine N1923 is only a qualitative parameter suggesting the interfacial mechanism for thorium extraction, it cannot give strong evidence quantitatively supporting this mechanism.

Primary and secondary crystallization kinetic analysis of nylon 1212

The isothermal and non-isothermal melt-crystallization kinetics of nylon 1212 were investigated by differential scanning calorimetry. Primary and secondary crystallization behaviors were analysed based on different approaches. The results obtained suggested that primary crystallization under isothermal conditions involves three-dimensional spherulite growth initiated by athermal nucleation, while under non-isothermal conditions, the mechanism of primary crystallization is more complex. Secondary crystallization displays a lower-dimensional crystal growth, both in the isothermal and non-isothermal processes. The crystallite morphology of nylon 1212, isothermally crystallized at various temperatures, was observed by polarized optical microscopy. The activation energies of crystallization under isothermal and non-isothermal conditions were also calculated based on different approaches.

Facile syntheses and characterization of hyperbranched poly(ester-amide)s from commercially available aliphatic carboxylic anhydride and multihydroxyl primary amine

A new method for synthesis of novel hyperbranched poly(ester-amide)s from commercially available AA' and CBx type monomers has been developed on the basis of a series of model reactions. The hyperbranched poly(ester-amide)s with multihydroxyl end groups are prepared by thermal polycondensation of carboxyl anhydrides (AA') and multihydroxyl primary amine (CBx) without any catalyst and solvent. The reaction mechanism in the initial stage of polymerization was investigated with in situ H-1 NMR. In the initial stage of the reaction, primary amino groups of 2-amino-2-ethyl-1,3-propanediol (AEPO) or tris(hydroxymethyl)aminomethane (THAM) react rapidly with anhydride, forming an intermediate which can be considered as a new AB(x) type monomer. Further self-polycondensation reactions of the AB. molecules produce hyperbranched polymers. Analysis using H-1 and C-13 NMR spectroscopy revealed the degree of branching of the resulting polymers ranging from 0.36 to 0.55. These hyperbranched poly(ester-amide)s contain configurational isomers observed by C-13 and DEPT C-13 NMR spectroscopy, possess high molecular weights with broad distributions and display glass-transition temperatures (T(g)s) between 7 and 96 degreesC.

Synergistic extraction of zinc(II) and cadmium(II) with mixtures of primary amine N1923 and neutral organophosphorous derivatives

Synergistic extraction of zinc(IT) and cadmium(11) from hydrochloric acid solution with primary amine N1923 and neutral organophosphorus derivatives Cyanex 923 and Cyanex 925 is the focus of this paper. Extraction mechanisms are discussed as well as how the acidity of the aqueous phase, the composition of the organic phase, and the experimental temperature affect the rates of extraction of metal ions. Differences between synergistic efficiency of Zn(II) and Cd(II) with mixtures of primary amines N1923 and either Cyanex 923 or Cyanex 925 are observed. The equilibrium constants, the composition, and the formation constants of the extracted complexes as well as the values of the thermodynamic functions are calculated. According to the synergy coefficient formula, the synergy effect on the extraction of Zn(II) is in the following order:N1923 + Cyanex 925 > N1923 + Cyanex 923 This order is reversed in the case of cadmium(II). For the same synergistic system, the extraction rate follows the order: Zn(II) > Cd(II). Furthermore, the stereochemical structures of the various extractants and their effect on metal ion extraction rate are also investigated.

Extraction of zinc(II) and cadmium(II) by using mixtures of primary amine N1923 and organophosphorus acids

The extraction of zinc(II) and cadmium(II) from a chloride medium by mixtures of primary amine N1923 and organophosphorus acids [di-(2-ethylhexyl)-phosphoric acid, 2-ethylhexylphosphonic acid mono-2-ethylhexyl ester (HEH/EHP), isopropyl phosphonic acid 1-hexyl-4-ethyloctyl ester, bis(2,4,4-trimethylpentyl) phosphinic acid, bis(2,4,4-trimethylpentyl) monothiophosphinic acid, and bis(2,4,4-trimethylpentyl) dithiophosphinic acid] has been studied in the present paper. Results show that only the mixtures of N1923 + HEH/EHP and N1923 + Cyanex272 have synergistic effects on zinc(II), but the other mixtures have no evident synergistic effects. All six mixtures have no evident synergistic effects on cadmium(H). A possible explanation of the different extraction abilities is given based on the structure of the extractants. Furthermore, the possibilities of separating zinc(II) and cadmium(II) with these mixtures are investigated according to the extractabilities. It is possible to separate Zn2+ from bulk cadmium with N1923 and HEH/EHP mixtures and separate Cd2+ from bulk zinc with N1923 and Cyanex301 mixtures.

Enthalpy/entropy compensation: Influence of DNA flanking sequence on the binding of 7-amino actinomycin D to its primary binding site in short DNA duplexes

The effect of the context of the flanking sequence on ligand binding to DNA oligonucleotides that contain consensus binding sites was investigated for the binding of the intercalator 7-amino actinomycin D. Seven self-complementary DNA oligomers each containing a centrally located primary binding site, 5'-A-G-C-T-3', flanked on either side by the sequences (AT)(n) or (AA)(n) (with n = 2, 3, 4) and AA(AT)(2), were studied. For different flanking sequences, (AA)(n)-series or (AT)(n)-series, differential fluorescence enhancements of the ligand due to binding were observed. Thermodynamic studies indicated that the flanking sequences not only affected DNA stability and secondary structure but also modulated ligand binding to the primary binding site. The magnitude of the ligand binding affinity to the primary site was inversely related to the sequence dependent stability. The enthalpy of ligand binding was directly measured by isothermal titration calorimetry, and this made it possible to parse the binding free energy into its energetic and entropic terms.

Synthesis and characterization of hyperbranched poly(ester-amide)s from commercially available dicarboxylic acids and multihydroxyl primary amines

A new method for syntheses of hyperbranched poly(ester-amide)s from commercially available A(2) and CBx type monomers has been developed on the basis of a series of model reactions. The aliphatic and semiaromatic hyperbranched poly(ester-amide)s with multihydroxyl end groups are prepared by in situ thermal polycondensation of intermediates obtained from dicarboxylic acids (A(2)) and multihydroxyl primary amines (CBx) in N,N-dimethylformamide. Analyses of FTIR, H-1 NMR, and C-13 NMR spectra revealed the structures of the polymers obtained. The MALDI-TOF MS of the polymers indicated that cyclization side reactions occurred during polymerization. The hyperbranched poly(ester-amide) s contain configurational isomers observed by C-13 and DEPT C-13 NMR spectroscopy. The DBs of the polymers were determined to be 0.38-0.62 by H-1 NMR or quantitive C-13 NMR and DEPT 135 spectra. These polymers exhibit moderate molecular weights, with broad distributions determined by size exclusion chromatography ( SEC), and possess excellent solubility in a variety of solvents such as N, N- dimethylacetamide, dimethyl sulfoxide, tetrahydrofuran, and ethanol, and display glass-transition temperatures (T(g)s) between -2.3 and 53.2 degrees C, determined by DSC measurements.

Synergistic extraction of zinc(II) by mixtures of primary amine N1923 and Cyanex272

The extraction of zinc(II) and cadmium(II) from chloride solution by mixtures of primary amine N1923 and Cyanex272 (HA) was studied. The synergistic effect was observed for the extraction of zinc(II) while no synergistic effect for cadmium(II), which makes it possible to separate zine(II) and cadmium(II) with the mixtures. The results showed that zinc(II) was extracted as (RNH3Cl)(3) . ZnCIA instead of ZnA(2) . 2HA which was extracted by Cyanex272 alone. The extraction mechanism was discussed and the formation constants and thermodynamic functions were determined. The separation factors between zinc(II) and cadmium(II) were calculated.

Graphical representation and the similarity of DNA primary sequences

In this article, graphical representations of DNA primary sequences were generated. Topological indices and molecular connectivity indices were calculated and used for the comparison of similarities among eight different DNA segments. The satisfactory results were achieved by this analysis.

Gas-phase ion - Molecule reactions of neutral C-60 with the plasmas of alkyl methyl ethers and primary alcohols

The gas-phase ion-molecule reactions of C-60 with the methoxymethyl ion [CH3O=CH2](+) and the 1-hydroxyethyl ion [CH3CH=OH](+) generated under the self-chemical-ionization (self-CI) conditions of alkyl methyl ethers and primary alcohols were studied in the ion source of a mass spectrometer. The adduct ions [C60C2H5O](+) and protonated molecules [C60H](+) were observed as the major products of C-60 with the plasma of alkyl methyl ethers. On the contrary, the reactions of C-60 With the plasmas of primary alcohols produced few corresponding adduct ions. The AM1 semiempirical molecular orbital calculations were carried out on 14 possible structures. The calculated results showed that the most stable structure among the possible isomers of [C60C2H5O](+) is the [3+2] cycloadduct. According to experimental and theoretical results, the pathway for the formation of the adduct was presented.

Studies on synergistic extraction of rare earths(III) with HBTMPTP and primary amine N1923

The synergistic extraction of rare earths(III) with binary systems containing HBTMPTP and primary amine N1923 from sulfuric acid medium was observed, The syner gistic extraction factor(R) decreased with increasing atomic number of lanthanides. Through the methods of slope analysis, constant mole and saturation titration, the synergistic extraction stoichiometry was obtained, The thermodynamic function was calculated, The IR spectra of the saturated synergistic extraction completely confirmed the mechanism.

Protective immunity induced by CpG ODNs against white spot syndrome virus (WSSV) via intermediation of virus replication indirectly in Litopenaeus vannamei

The worldwide shrimp culture is beset with diseases mainly caused by white spot syndrome virus (WSSV) and suffered huge economic losses, which bring out an urgent need to develop the novel strategies to better protect shrimps against WSSV. In the present study, CpG-rich plasmid pUC57-CpG, plasmid pUC57 and PBS were employed to pretreat shrimps comparatively to evaluate the protective effects of CpG ODNs on shrimps against WSSV. The survival rates, WSSV copy numbers, and antiviral associated factors (Dicer, Argonaute, STAT and ROS) were detected in Litopenaeus vannamei. There were higher survival proportion, lower WSSV copy numbers, and higher mRNA expression of Dicer and STAT in pUC57-CpG-pretreatment shrimps than those in pUC57- and PBS-pretreatment shrimps after WSSV infection. The Argonaute mRNA expression in pUC57-CpG-, pUC57- and PBS-pretreatment shrimps after WSSV infection was significantly higher than that of shrimps post PBS stimulation on the first day. The ROS levels in pUC57-CpG-pretreatment shrimps post secondary stimulation of PBS were significantly higher than those post WSSV infection on the first day. These results together demonstrated that pUC57-CpG induced partial protective immunity in shrimps against WSSV via intermediation of virus replication indirectly and could be used as a potential candidate in the development of therapeutic agents for disease control of WSSV in L. vannamei. (C) 2009 Elsevier Ltd. All rights reserved.