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.

Primary culture and characteristic morphologies of medulla terminalis neurons in the eyestalks of Chinese shrimp, Fenneropenaeus chinensis

A method for culturing medulla terminalis (MT) neurons in the eyestalk of Chinese shrimp, Fenneropenaeus chinensis, was first established. The neurons showed immediate outgrowth in the culture medium supplemented with glutamine, glucose and antibiotics. The cells grew for about 2-7 days and then sustained for a week or more. At least six types of neurons were distinguished on the basis of size and form of soma and outgrowth pattern of cells. (C) 2003 Elsevier Science B.V. All rights reserved.

Cross-Ocean distribution of Rhodobacterales bacteria as primary surface colonizers in temperate coastal marine waters

Bacterial surface colonization is a universal adaptation strategy in aquatic environments. However, neither the identities of early colonizers nor the temporal changes in surface assemblages are well understood. To determine the identities of the most common bacterial primary colonizers and to assess the succession process, if any, of the bacterial assemblages during early stages of surface colonization in coastal water of the West Pacific Ocean, nonnutritive inert materials (glass, Plexiglas, and polyvinyl chloride) were employed as test surfaces and incubated in seawater off the Qingdao coast in the spring of 2005 for 24 and 72 h. Phylogenetic analysis of the 16S rRNA gene sequences amplified from the recovered surface-colonizing microbiota indicated that diverse bacteria colonized the submerged surfaces. Multivariate statistical cluster analyses indicated that the succession of early surface-colonizing bacterial assemblages followed sequential steps on all types of test surfaces. The Rhodobacterales, especially the marine Roseobacter clade members, formed the most common and dominant primary surface-colonizing bacterial group. Our current data, along with previous studies of the Atlantic coast, indicate that the Rhodobacterales bacteria are the dominant and ubiquitous primary surface colonizers in temperate coastal waters of the world and that microbial surface colonization follows a succession sequence. A conceptual model is proposed based on these findings, which may have important implications for understanding the structure, dynamics, and function of marine biofilms and for developing strategies to harness or control surface-associated microbial communities.

Seasonal and interannual variability of primary and export production in the South China Sea: a three-dimensional physical-biogeochemical model study

To investigate the seasonal and interannual variations in biological productivity in the South China Sea (SCS), a Pacific basin-wide physical - biogeochemical model has been developed and used to estimate the biological productivity and export flux in the SCS. The Pacific circulation model, based on the Regional Ocean Model Systems (ROMS), is forced with daily air-sea fluxes derived from the NCEP (National Centers for Environmental Prediction) reanalysis between 1990 and 2004. The biogeochemical processes are simulated with a carbon, Si(OH)(4), and nitrogen ecosystem (CoSiNE) model consisting of silicate, nitrate, ammonium, two phytoplankton groups (small phytoplankton and large phytoplankton), two zooplankton grazers (small micrograzers and large mesozooplankton), and two detritus pools. The ROMS-CoSiNE model favourably reproduces many of the observed features, such as ChI a, nutrients, and primary production (PP) in the SCS. The modelled depth-integrated PP over the euphotic zone (0-125 m) varies seasonally, with the highest value of 386 mg C m (-2) d (-1) during winter and the lowest value of 156 mg C m (-2) d (-1) during early summer. The annual mean value is 196 mg C m (-2) d (-1). The model-integrated annual mean new production (uptake of nitrate), in carbon units, is 64.4 mg C m (-2) d (-1) which yields an f-ratio of 0.33 for the entire SCS. The modelled export ratio (e-ratio: the ratio of export to PP) is 0.24 for the basin-wide SCS. The year-to-year variation of biological productivity in the SCS is weaker than the seasonal variation. The large phytoplankton group tends to dominate over the smaller phytoplankton group, and likely plays an important role in determining the interannual variability of primary and new production.

Analysis of primary aromatic amines using precolumn derivatization by HPLC fluorescence detection and online MS identification

2-(2-Phenyl-1H-phenanthro-[9,10-d]imidazole-1-yl)-acetic acid (PPIA) and 2-(9-acridone)-acetic acid (AAA), two novel precolumn fluorescent derivatization reagents, have been developed and compared for analysis of primary aromatic amines by high performance liquid chromatographic fluorescence detection coupled with online mass spectrometric identification. PPIA and AAA react rapidly and smoothly with the aromatic amines on the basis of a condensation reaction using 1-ethyl-3-(3dimethylaminopropyl)-carbodiimide (EDC) as dehydrating catalyst to form stable derivatives with emission wavelengths at 380 and 440 nm, respectively. Taking six primary aromatic amines (aniline, 2-methylaniline, 2-methoxyaniline, 4-methylaniline, 4-chloroaniline, and 4-bromoaniline) as testing compounds, derivatization conditions such as coupling reagent, basic catalyst, reaction temperature and time, reaction solvent, and fluorescent labeling reagent concentration have also been investigated. With the better PPIA method, chromatographic separation of derivatized aromatic amines exhibited a good baseline resolution on an RP column. At the same time, by online mass spectrometric identification with atmospheric pressure chemical ionization (APCI) source in positive ion mode, the PPIA-labeled derivatives were characterized by easy-to-interpret mass spectra due to the prominent protonated molecular ion m/z [M + H](+) and specific fragment ions (MS/MS) m/z 335 and 295. The linear range is 24.41 fmol-200.0 pmol with correlation coefficients in the range of 0.9996-0.9999, and detection limits of PPIA-labeled aromatic amines are 0.12-0.21 nmol/L (S/N = 3). Method repeatability, precision, and recovery were evaluated and the results were excellent for the efficient HPLC analysis. The most important argument, however, was the high sensitivity and ease-of-handling of the PPIA method. Preliminary experiments with wastewater samples collected from the waterspout of a paper mill and its nearby soil where pollution with aromatic amines may be expected show that the method is highly validated with little interference in the chromatogram.

Net primary productivity and spatial distribution of vegetation in an alpine wetland, Qinghai-Tibetan Plateau

To initially describe vegetation structure and spatial variation in plant biomass in a typical alpine wetland of the Qinghai-Tibetan Plateau, net primary productivity and vegetation in relationship to environmental factors were investigated. In 2002, the wetland remained flooded to an average water depth of 25 cm during the growing season, from July to mid-September. We mapped the floodline and vegetation distribution using GPS (global positioning system). Coverage of vegetation in the wetland was 100%, and the vegetation was zonally distributed along a water depth gradient, with three emergent plant zones (Hippuris vulgaris-dominated zone, Scirpus distigmaticus-dominated zone, and Carex allivescers-dominated zone) and one submerged plant zone (Potamogeton pectinatus-dominated zone). Both aboveground and belowground biomass varied temporally within and among the vegetation zones. Further, net primary productivity (NPP) as estimated by peak biomass also differed among the vegetation zones; aboveground NPP was highest in the Carex-dominated zone with shallowest water and lowest in the Potamogeton zone with deepest water. The area occupied by each zone was 73.5% for P. pectinatus, 2.6% for H. vulgaris, 20.5% for S. distigmaticus, and 3.4% for C. allivescers. Morphological features in relationship to gas-transport efficiency of the aerial part differed among the emergent plants. Of the three emergent plants, H. vulgaris, which dominated in the deeper water, showed greater morphological adaptability to deep water than the other two emergent plants.

Modeling gross primary production of alpine ecosystems in the Tibetan Plateau using MODIS images and climate data

The eddy covariance technique provides measurements of net ecosystem exchange (NEE) Of CO2 between the atmosphere and terrestrial ecosystems, which is widely used to estimate ecosystem respiration and gross primary production (GPP) at a number Of CO2 eddy flux tower sites. In this paper, canopy-level maximum light use efficiency, a key parameter in the satellite-based Vegetation Photosynthesis Model (VPM), was estimated by using the observed CO2 flux data and photosynthetically active radiation (PAR) data from eddy flux tower sites in an alpine swamp ecosystem, an alpine shrub ecosystem and an alpine meadow ecosystem in Qinghai-Tibetan Plateau, China. The VPM model uses two improved vegetation indices (Enhanced Vegetation Index (EVI), Land Surface Water Index (LSWI)) derived from the Moderate Resolution Imaging Spectral radiometer (MODIS) data and climate data at the flux tower sites, and estimated the seasonal dynamics of GPP of the three alpine grassland ecosystems in Qinghai-Tibetan Plateau. The seasonal dynamics of GPP predicted by the VPM model agreed well with estimated GPP from eddy flux towers. These results demonstrated the potential of the satellite-driven VPM model for scaling-up GPP of alpine grassland ecosystems, a key component for the study of the carbon cycle at regional and global scales. (c) 2006 Elsevier Inc. All rights reserved.

Seasonal patterns of gross primary production and ecosystem respiration in an alpine meadow ecosystem on the Qinghai-Tibetan Plateau

We measured the net ecosystem CO2 exchange (NEE) in an alpine meadow ecosystem (latitude 37degrees29'-45'N, longitude 101degrees12'-23'E, 3250 m above sea level) on the Qinghai-Tibetan Plateau throughout 2002 by the eddy covariance method to examine the carbon dynamics and budget on this unique plateau. Diurnal changes in gross primary production (GPP) and ecosystem respiration (R-e) showed that an afternoon increase of NEE was highly associated with an increase of R-e. Seasonal changes in GPP corresponded well to changes in the leaf area index and daily photosynthetic photon flux density. The ratio of GPP/R-e was high and reached about 2.0 during the peak growing season, which indicates that mainly autotrophic respiration controlled the carbon dynamics of the ecosystem. Seasonal changes in mean GPP and R-e showed compensatory behavior as reported for temperate and Mediterranean ecosystems, but those of GPP(max) and R-emax were poorly synchronized. The alpine ecosystem exhibited lower GPP (575 g C m(-2) y(-1)) than, but net ecosystem production (78.5 g C m(-2) y(-1)) similar to, that of subalpine forest ecosystems. The results suggest that the alpine meadow behaved as a CO2 sink during the 1-year measurement period but apparently sequestered a rather small amount of C in comparison with similar alpine ecosystems.

Formulation of a basal medium for primary cell culture of the marine sponge Hymeniacidon perleve

Marine sponge cell culture is a potential route for the sustainable production of sponge-derived bioproducts. Development of a basal culture medium is a prerequisite for the attachment, spreading, and growth of sponge cells in vitro. With the limited knowledge available on nutrient requirements for sponge cells, a series of statistical experimental designs has been employed to screen and optimize the critical nutrient components including inorganic salts (ferric ion, zinc ion, silicate, and NaCl), amino acids (glycine, glutamine, and aspartic acid), sugars (glucose, sorbitol, and sodium pyruvate), vitamin C, and mammalian cell medium (DMEM and RPMI 1640) using MTT assay in 96-well plates. The marine sponge Hymeniacidon perleve was used as a model system. Plackett-Burman design was used for the initial screening, which identified the significant factors of ferric ion, NaCl, and vitamin C. These three factors were selected for further optimization by Uniform Design and Response Surface Methodology (RSM), respectively. A basal medium was finally established, which supported an over 100% increase in viability of sponge cells.