Analysis of the energies of the triple base triplets

Sixty-four sets of three-dimensional models of DNA triplex base triplets (TBT) were built up based on codons by homologous modeling method and their energies were minimized. According to sequence of TBT and orientation of the third ODN strand third, the energies of monomers and water-K+-TBT ternary complexes of TBT were analyzed. The results showed: (i) The energies of the symmetric parallel monomers are generally lower than those of the symmetric anti-parallel monomers of TBT, but the energies of the symmetric parallel ternary complexes are higher than those of the symmetric anti-parallel ternary complexes of TBT. (ii) No matter TBTs are monomers or ternary complexes, the energies of asymmetric parallel TBTs are generally lower than those of the asymmetric anti-parallel ones. (iii) Although the energies of the parallel TBTs are correlated with those of the anti-parallel ones, the energy differences are significant between them. The results here suggest the sequences of TBTs and the orientations of the third ODN strands are two of the key factors that can influence the formation and stability of TBT. (C) 2002 Elsevier Science B.V. All rights reserved.

The comparative analysis of the energies of conjugated triple base triplets and their applications

We built 64 sets of 3D models of DNA triplex base triplets (TBT) and minimized their energies. The TBTs were divided into 32 pairs of conjugated ones on the basis of their sequence characteristic, and the energies of each pair of them were compared and analyzed, the results showed: (i) The duplex DNA of which any strand contains at least a couple of A or T, has a preference for selecting the oligodeoxyribonucleic acid (ODN) strand containing abundant T to form TBT. (ii) The duplex DNA of which any strand contains at least a couple of G or C has a preference for selecting ODN containing abundant G to form symmetric antiparallel TBT, but selecting ODN containing abundant C to form asymmetric parallel TBT. (iii) The duplex DNA of which any strand contains only one of A, T, G or C has a preference for selecting ODN containing abundant pyrimidines (T or C) to form antiparallel TBT. Additionally, two examples of TBTs applications, in designing ODN to form triplex with duplex were presented. The energy calculation result revealed that 15-TCG is the best ligand of the HIV PPT duplex. The comparative analysis of energies of the conjugated TBTs provides directive significance for designing ODN strand that is easy to form triplex in theory. (C) 2002 Elsevier Science B.V. All rights reserved.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

The identification and quantification of highly stable 'common hairpin' in the dynamic process of co-transcriptional mRNA folding

In our studies, 88 human mRNA samples were collected from the Integrated Sequence-Structure database and then the dynamic process in co-transcriptional mRNA folding was simulated using the RNAstructure version 4.1 program. Through statistical analyses of the frequencies of occurrence of hairpins, a group of special folding structures-the 'common hairpins'-were identified. These 'common hairpins' have lower energies and occur in all the subsequent folding units that formed in the dynamic folding process. By applying the formulas (1)-(4) of the 'common hairpins' statistical model, 163 'common hairpins' were found, to make up about 7% of the total of 2286 hairpins. Classified studies further show that the 'common hairpins' that were studied may oscillate in the dynamic folding process. However, the hairpin loops of the 'common hairpins' and stems proximal to those 'common hairpins' loops maintain topologically stable structures, while other loops and stems distal to the 'common hairpins' loops are shown to be alterable structures. Strikingly, further studies indicate that the stable structures of these 'common hairpins' may have unbeknown effects on controlling the formation of protein structures in the translation process (unpublished results). (c) 2005 Elsevier B.V. All rights reserved.

Exploring consensus mRNA secondary (folding) structure units by stochastic sampling and folding simulation

It is extremely difficult to explore mRNA folding structure by biological experiments. In this report, we use stochastic sampling and folding simulation to test the existence of the stable secondary structural units of-mRNA, look for the folding units, and explore the probabilistic stabilization of the units. Using this method, We made simulations for all possible local optimum secondary structures of a single strand mRNA within a certain range, and searched for the common parts of the secondary structures. The consensus secondary structure units (CSSUs) extracted from the above method are mainly hairpins, with a few single strands. These CSSUs suggest that the mRNA folding units could be relatively stable and could perform specific biological function. The significance of these observations for the mRNA folding problem in general is also discussed. (c) 2004 Elsevier B.V. All rights reserved.

Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

Effects of ytterbium ion on the growth, metabolism and membrane fluidity of Tetrahymena thermophila

Power-time curves and metabolic properties of Tetrahymena thermophila BF5 exposed to different Yb3+ stop levels were studied by ampoule method of isothermal calorimetry at 28 degrees C. Metabolic rate (r) decreased significantly while peak time (PT) increased with the increase of Yb3+ stop. These results were mainly due to the inhibition of cell growth, which corresponded to the decrease of cell number obtained by cell counting. Compared with cell counting, calorimetry was sensible, easy to use and convenient for monitoring the toxic effects of Yb3+ stop on cells and freshwater ecosystem. It was also found that cell membrane fluidity decreased significantly under the effects of Yb3+ stop, which indicated that Yb3+ could be membrane active molecules with its effect on cell membranes as fundamental aspect of its toxicity.

Microcalorimetry as a possible tool for phylogenetic studies of Tetrahymena

Using isothermal microcalorimetry, the growth power-time curves of three strains of Tetrahymena were determined at 28 degrees C. Their Euclidean distances and cluster analysis diagram were obtained by using two thermokinetic parameters (r and Q(log)), which showed that T. thermophila BF1 and T. thermophila BF5 had a closer relationship. Compared with the single molecular biomarker (ITS1) method, microcalorimetry wasmaybe a simpler, more sensitive andmore economic technique in the phylogenetic studies of Tetrahymena species.

Application of polyurethane foam units and calorimetry to microbial monitoring in Lake Donghu

Combined with the national standard biomonitoring method (polyurethane foam units method), calorimetry was applied to study the metabolic activities of PFU microbial communities in fresh water to determine the effects of anthropotgenic stresses on the activity of the microbial community. Comparisons were made at four sampling stations with different eutrophic status in Lake Donghu. Water quality variables, species number of protozoa, abundances of microorganisms, biomass, heterotrophy indexes and diversity indexes are reported. The heat rate-time curves of the native and concentrated PFU microbial communities were determined at 28 degrees C. Growth rate, measured maximum power output and total heat were calculated from the heat rate-time curves. The values of metabolic variables are higher at the more eutrophic stations, which suggests that organic pollution increases the activity of PFU microbial communities. The metabolic variables are in good agreement with chemical and biotic variables. And calorimetry will be useful for biomonitoring of the PFU microbial community. (C) 2005 Elsevier B.V. All rights reserved.

Dissolution of kaolinite induced by citric, oxalic, and malic acids

Kaolinite is a dominant clay mineral in the soils in tropical and Subtropical regions, and its dissolution has an influence on a variety of soil properties. In this work, kaolinite dissolution induced by three kinds of low-molecular-weight organic acid, i.e., citric, oxalic, and malic acids, was evaluated under far-from-equilibrium conditions. The rates of kaolinite dissolution depended on the kind and concentration of organic acids, with the sequence R-oxalate > R-citrate > R-malate. Chemical calculation showed the change in concentration of organic ligand relative to change in concentration of organic acid in suspensions of kaolinite and organic acid. The effect of organic acid on kaolinite dissolution was modeled by species of organic anionic ligand. For oxalic acid, L-oxalic(2-) and HLoxalic- jointly enhanced the dissolution of kaolinite, but for malic and citric acids, HLmalic- and H2Lcitric- made a higher contribution to the total dissolution rate of kaolinite than L-malic(2-) and L-citric(3-), respectively. For oxalic acid, the proposed model was R-Si = 1.89 x 10(-12) x [(25x)/(1+25x)] + 1.93 x 10(-12) x [(1990x(1))/(1+1990x(1))] (R-2 = 0.9763), where x and x(1) denote the concentrations of HLoxalic and L-oxalic, respectively, and x(1) = 10(-3.81) x x/[H+]. For malic acid, the model was R-Si =4.79 x 10(-12) x [(328-v)/(1+328x)] + 1.67 x 10(-13) x [(1149x(1))/(1+1149x(1))] (R-2 =0.9452), where x and x(1) denote the concentrations of HLmalic and L-malic, respectively, and x(1) = 10(-5.11) x x/[H+], and for citric acid, the model was R-Si = 4.73 x 10(-12) x [(845x)/(1+845x)] +4.68 x 10(-12) x [(2855x(1))/(1+2855x(1))] (R-2 =0.9682), where x and x(1) denote the concentrations of H2Lcitric and L-citric, respectively, and x(1) = 10(-11.16) x x/[H+](2). (c) 2005 Elsevier Inc. All rights reserved.

High-dimensional assembly depending on polyoxoanion templates, metal ion coordination geometries, and a flexible bis(imidazole) ligand

By introducing the flexible 1,1'-(1,4-butanediyl)bis(imidazole) (bbi) ligand into the polyoxovanadate system, five novel polyoxoanion-templated architectures based on [As8V14O42](4-) and [V16O38Cl](6-) building blocks were obtained: [M(bbi)(2)](2)[As8V14O42(H2O)] [M = Co (1), Ni (2), and Zn (3)], [Cu(bbi)](4)[As8V14O42(H2O)] (4), and [Cu(bbi)](6)[V16O38Cl] (5). Compounds 1-3 are isostructural, and they exhibit a binodal (4,6)-connected 2D structure with Schlafli symbol (3(4)center dot 4(2))(3(4)center dot 4(4)center dot 5(4)center dot 6(3))(2), in which the polyoxoanion induces a closed four-membered circuit of M-4(bbi)(4). Compound 4 exhibits an interesting 3D framework constructed from tetradentate [As8V14O42](4-) cluster anions and cationic ladderlike double chains. There exists a bigger M-8(bbi)(6)O-2 circuit in 4. The 3D extended structure of 5 is composed of heptadentate [V16O38Cl](6-) anions and flexural cationic chains; the latter consists of six Cu(bbi) segments arranged alternately. It presents the largest 24-membered circuit of M-24(bbi)(24) so far observed made of bbi molecules and transition-metal cations. Investigation of their structural relations shows the important template role of the polyoxoanions and the synergetic interactions among the polyoxoanions, transition-metal ions, and flexible ligand in the assembly process.

Phenomenon of micro-droplets formation on metals during the deliquescence of salt particles in atmosphere

CORROSION; MECHANISM; WATER; ZINC

Enrichment of the hydrogen-producing microbial community from marine intertidal sludge by different pretreatment methods

To determine the effects of pretreatment on hydrogen production and the hydrogen-producing microbial community, we treated the sludge from the intertidal zone of a bathing beach in Tianjin with four different pretreatment methods, including acid treatment, heat-shock, base treatment as well as freezing and thawing. The results showed that acid pretreatment significantly promoted the hydrogen production by sludge and provided the highest efficiency of hydrogen production among the four methods. The efficiency of the hydrogen production of the acid-pretreated sludge was 0.86 +/- 0.07 mol H-2/mol glucose (mean +/- S.E.), whereas that of the sludge treated with heat-shock, freezing and thawing, base method and control was 0.41 +/- 0.03 mol H-2/mol glucose, 0.17 +/- 0.01 mol H-2/mol glucose, 0.11 +/- 0.01 mol H-2/mol glucose and 0.20 +/- 0.04 mol H-2/mol glucose, respectively. The result of denaturing gradient gel electrophoresis (DGGE) showed that pretreatment methods altered the composition of the microbial community that accounts for hydrogen production. Acid and heat pretreatments were favorable to enrich the dominant hydrogen-producing bacterium, i.e. Clostridium sp., Enterococcus sp. and Bacillus sp., However, besides hydrogen-producing bacteria, much non-hydrogen-producing Lactobacillus sp. was also found in the sludge pretreated with base, freezing and thawing methods. Therefore, based on our results, we concluded that, among the four pretreatment methods using acid, heat-shock, base or freezing and thawing, acid pretreatment was the most effective method for promoting hydrogen production of microbial community. (C) 2009 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.

Fermentative hydrogen production by the new marine Pantoea agglomerans isolated from the mangrove sludge

A new fermentative hydrogen-producing bacterium was isolated from mangrove sludge and identified as Pantoea agglomerans using light microscopic examination, Biolog test and 16S rRNA gene sequence analysis. The isolated bacterium, designated as P. agglomerans BH-18, is a new strain that has never been optimized as a potential hydrogen-producing bacterium. In this study, the culture conditions and the hydrogen-producing ability of P. agglomerans BH-18 were examined. The strain was a salt-tolerant facultative anaerobe with the initial optimum pH value at 8.0-9.0 and temperature at 30 degrees C on cell growth. During fermentation, hydrogen started to evolve when cell growth entered late-exponential phase and was mainly produced in the stationary phase. The strain was able to produce hydrogen over a wide range of initial pH from 5 to 10, with an optimum initial pH of 6. The level of hydrogen production was affected by the initial glucose concentration, and the optimum value was found to be 10 g glucose/l. The maximum hydrogen-producing yield (2246 ml/l) and overall hydrogen production rate (160 ml/l/h) were obtained at an initial glucose concentration of 10 g/l and an initial pH value of 7.2 in marine culture conditions. In particular, the level of hydrogen production was also affected by the salt concentration. Hydrogen production reached a higher level in fresh culture conditions than in marine ones. In marine conditions, hydrogen productivity was 108 ml/l/h at an initial glucose concentration of 20 g/l and pH value of 7.2, whereas, it increased by 27% in fresh conditions. In addition, this strain could produce hydrogen using glucose and many other carbon sources such as fructose, sucrose, sorbitol and so on. As a result, it is possible that P. agglomerans BH-18 is used for biohydrogen production and biological treatment of mariculture wastewater and marine organic waste. (C) 2008 International Association for Hydrogen Energy. Published by Elsevier Ltd. All rights reserved.

Photocatalytic degradation of CI Acid Blue 80 in aqueous suspensions of titanium dioxide under sunlight

The dye C.I. Acid Blue 80 (AB80) was easily degraded by TiO2-P25 assisted photocatalysis in aqueous dispersion under irradiation of sunlight. The optimal reaction conditions were [TiO2] = 2.0 g/L, pH = 10, [H2O2] = 5 mmol/L. The photocatalytic reaction followed pseudo-first order kinetics. The adsorption of AB80 onto TiO2 was in accord with Langmuir equation.