Determination of dissolved oxygen in water with leukoberbelin-blue I. A quick Winkler method. [Translation from: Z.analyt.Chem. 262 97-99, 1972.]

The reaction of Mn(II) with water-dissolved oxygen, to a higher manganese hydroxide in an alkaline medium, as with the longstanding classic Winkler method, is the first step in the method described here. The assumption for faultless results by the conventional and modified Winkler method is clean water, which contains no organic substances by Mn(III) or Mn(IV). In many cases, however, eg. in river and lake-water tests, it can be seen with the naked eye that after some time the originally brown-coloured precipitate of manganese hydroxide becomes more and more colourless. Oxygen content was analysed in the water samples and evaluated by raising the amount of the leuko-base and giving the corresponding dilution of the colouring matter solution formed still higher oxygen contents can be measured.

Investigations of DNA-mediated protein oxidation

DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt π-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA π-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]^3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.

Dps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.

Further work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)₂, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)₂ is substituted with poly(dAdT)₂, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.

We have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.

DNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.

While the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]^3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]³⁺ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.

In conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.

The effect of oxygen concentration in water on the growth and nitrogen metabolism in the fry of rainbow trout [Translation from: Rybnoe Khoziaistvo,V.33, 74-75, 1957]

To ascertain the effect of various concentrations of oxygen in water on the fry of rainbow trout experiments were made with aquaria at various concentrations of oxygen. The food supplied was chironomid larvae (Chironomus plumosus). A surplus of food was supplied to the fry. Indices are given of the reaction of the fry to different temperatures.

Nature of the radical intermediates in a substituted cyclopropylcarbiny-allylcarbinyl system

We have sought to determine the nature of the free-radical precursors to ring-opened hydrocarbon 5 and ring-closed hydrocarbon 6. Reasonable alternative formulations involve the postulation of hydrogen abstraction (a) by a pair of rapidly equilibrating classical radicals (the ring-opened allylcarbinyl-type radical 3 and the ring-closed cyclopropylcarbinyl-type 4), or (b) by a nonclassical radical such as homoallylic radical 7.

[Figure not reproduced.]

Entry to the radical system is gained via degassed thermal decomposition of peresters having the ring-opened and the ring-closed structures. The ratio of 6:5 is essentially independent of the hydrogen donor concentration for decomposition of the former at 125° in the presence of triethyltin hydrdride. A deuterium labeling study showed that the α and β methylene groups in 3 (or the equivalent) are rapidly interchanged under these conditions.

Existence of two (or more) product-forming intermediates is indicated (a) by dependence of the ratio 6:5 on the tin hydride concentration for decomposition of the ring-closed perester at 10 and 35°, and (b) by formation of cage products having largely or wholly the structure (ring-opened or ring-closed) of the starting perester.

Relative rates of hydrogen abstraction by 3 could be inferred by comparison of ratios of rate constants for hydrogen abstraction and ortho-ring cyclization:

[Figure not reproduced.]

At 100° values of k_a/k_r are 0.14 for hydrogen abstraction from 1,4-cyclohexadiene and 7 for abstraction from triethyltin hydride. The ratio 6:5 at the same temperature is ~0.0035 for hydrogen abstraction from 1,4-cyclohexadiene, ~0.078 for abstraction from the tin hydride, and ≥ 5 for abstraction from cyclohexadienyl radicals. These data indicate that abstraction of hydrogen from triethyltin hydride is more rapid than from 1,4-cyclohexadiene by a factor of ~1000 for 4, but only ~50 for 3.

Measurements of product ratios at several temperatures allowed the construction of an approximate energy-level scheme. A major inference is that isomerization of 3 to 4 is exothermic by 8 ± 3 kcal/mole, in good agreement with expectations based on bond dissociation energies. Absolute rate-constant estimates are also given.

The results are nicely compatible with a classical-radical mechanism, but attempted interpretation in terms of a nonclassical radical precursor of product ratios formed even from equilibrated radical intermediates leads, it is argued, to serious difficulties.

The roles played by hydrogen abstraction from 1,4,-cyclohexadiene and from the derived cyclohexadienyl radicals were probed by fitting observed ratios of 6:5 and 5:10 in the sense of least-squares to expressions derived for a complex mechanistic scheme. Some 30 to 40 measurements on each product ratio, obtained under a variety of experimental conditions, could be fit with an average deviation of ~6%. Significant systematic deviations were found, but these could largely be redressed by assuming (a) that the rate constant for reaction of 4 with cyclohexadienyl radical is inversely proportional to the viscosity of the medium (i.e., is diffusion-controlled), and (b) that k_a/k_r for hydrogen abstraction from 1,4-cyclohexadiene depends slightly on the composition of the medium. An average deviation of 4.4% was thereby attained.

Degassed thermal decomposition of the ring-opened perester in the presence of the triethyltin hydride occurs primarily by attack on perester of triethyltin radicals, presumably at the –O-O- bond, even at 0.01 M tin hydride at 100 and 125°. Tin ester and tin ether are apparently formed in closely similar amounts under these conditions, but the tin ester predominates at room temperature in the companion air-induced decomposition, indicating that attack on perester to give the tin ether requires an activation energy approximately 5 kcal/mole in excess of that for the formation of tin ester.

Preparation, characterization and gas sensing properties of high soluble metal (II) phthalocyanine thin films by spin-coating method

Three novel metal (II) phthalocyanine complexes were synthesized by cyclic tetramerisation reaction of a dicyano benzene component and different metal ions (Pd2+, Co2+, Zn2+). The structure of complexes was confirmed by elemental analysis, mass and IR spectrum. The excellent solubility of the complexes in benzene enabled us to obtain films by a spin-coating method. The films were characterized by IR, electronic spectral and AFM. The gas sensing properties to NO2 of the metal (II) phthalocyanine complex films were studied. In addition, the effects of different metal ions and the gas sensing temperature on the sensing properties were studied. (C) 2005 Elsevier B.V. All rights reserved.

Preparation and optical properties of Ag/PPy composite colloids

Ag/PPy (polypyrrole) composite colloids were prepared through the reaction of silver nitrate with pyrrole solution in DNIF either in the dark, or under the irradiation of femtosecond laser (fs) pulse or UV lamp. The UV-vis spectra of the nanocomposite colloid display an intense absorption band around 620 nm, accompanied by a weak one around 470 nm. The colors and optical absorption spectra of as-synthesized colloids can be reversibly tuned between blue and red, corresponding to absorption band of 620 urn and 526 urn, within few seconds by adding base and acid solutions or gases in turn into the composite colloid suspension. In addition, excess of H+ solution enhanced the absorption band around 470 nm and, at the same time, depressed that around 620 nm. The possible mechanism for the formation and optical absorption properties of the Ag/PPy composite colloid was proposed. (C) 2006 Elsevier B.V. All rights reserved.

Preliminary experiments to evaluate the relative efficiency of different natural baits in line fishing

A series of experimental hand-line fishing operations were conducted off the Madras coast employing five different types of natural fish baits. Based on the total catch of fish per day of fishing under each type of bait used, a comparative study on the catching efficiency of the different natural fish-baits was made. The reaction of the fish to particular bait appears to be the result of a complex process. Live baits have the maximum catching efficiency as seen from the fish landings when live prawns were employed as the bait. The procurement of live baits is a serious problem to the fishermen and as such suitable artificial fish lures can be profitably employed.

Effect of some environmental factors on the acute toxicity of deltamethrin to common carp: a laboratory study under aerobic condition

The toxicity of xenobiotic in aquatic ecosystems is influenced by many factors such as ambient temperature, water hardness, pond soil type, etc. In the present study, it was observed that air temperature, water hardness and soil sediment have profound influence on the toxicity of deltamethrin to common carp fry (ay. length 3.5 ± 0.5 cm, ay. weight 0.58 ± 0.25 g); 96h LC(sub)50 values for common carp at 38.07 ± 2.20°C maximum and 27.86 ± 1.22°C minimum air temperature in soft and very hard water were 0.102 and 0.495 µg lˉ¹, respectively. This value had increased significantly to 2.37 and 3.02 µg at 30.55 ± 1.21°C maximum and 26.04 ± 0.61°C minimum air temperature, respectively. When sediment was included, 96h LC(sub)50 at 38.07°C maximum temperature in very hard water was 1.808 µg 1ˉ¹ and this had increased to 8.073 µg 1ˉ¹ when tested at 30.55°C maximum temperature. Due to the 7.5°C increase in maximum and 1.7°C in minimum temperature, toxicity increased significantly. Lower toxicity in very hard water in comparison to soft water may be due to the lower solubility of deltarnethrin and high level of calcium. Adsorption reaction of deltamethrin with clay, humus, FeOOH, MnOOH and particulate organic carbon, and complexation reaction with dissolved organic carbon were responsible for the lowered toxicity in the experiment with sediment. Exposure time had no significant effect on acute toxicity of deltamethrin.

Effect of electric stimulation on heart beat and body muscle in fish

The effect of AC and DC electric stimulations on the heart-rate and the entire body of Heteropneustis fossillis, Tilapia mossambica and Macrobrachium rosenbergii were studied and presented in kymograph tracings. The reaction of spinal cord in Puntius ticto, Heteropneustis fossilis and Tilapia mossambica to D. C. field was observed to find out its role in electric shocks. A test-check of the electrical resistance of a few species was also conducted. The effect of D. C. and A.C. on the body muscle was found to be the same as that in the case of frog. Different degrees of cardiac slowing were observed in AC and DC. Unbalanced galvanotropic movements were also noticed in spinal fishes.

Validation of a lattice Boltzmann model for gas-solid reactions with experiments

A lattice Boltzmann method is used to model gas-solid reactions where the composition of both the gas and solid phase changes with time, while the boundary between phases remains fixed. The flow of the bulk gas phase is treated using a multiple relaxation time MRT D3Q19 model; the dilute reactant is treated as a passive scalar using a single relaxation time BGK D3Q7 model with distinct inter- and intraparticle diffusivities. A first-order reaction is incorporated by modifying the method of Sullivan et al. [13] to include the conversion of a solid reactant. The detailed computational model is able to capture the multiscale physics encountered in reactor systems. Specifically, the model reproduced steady state analytical solutions for the reaction of a porous catalyst sphere (pore scale) and empirical solutions for mass transfer to the surface of a sphere at Re=10 (particle scale). Excellent quantitative agreement between the model and experiments for the transient reduction of a single, porous sphere of Fe 2O 3 to Fe 3O 4 in CO at 1023K and 10 5Pa is demonstrated. Model solutions for the reduction of a packed bed of Fe 2O 3 (reactor scale) at identical conditions approached those of experiments after 25 s, but required prohibitively long processor times. The presented lattice Boltzmann model resolved successfully mass transport at the pore, particle and reactor scales and highlights the relevance of LB methods for modelling convection, diffusion and reaction physics. © 2012 Elsevier Inc.

Optical and structural properties of Er2O3 films grown by magnetron sputtering

The structural properties and the room temperature luminescence of Er 2O3 thin films deposited by magnetron sputtering have been studied. In spite of the well-known high reactivity of rare earth oxides towards silicon, films characterized by good morphological properties have been obtained by using a SiO2 interlayer between the film and the silicon substrate. The evolution of the properties of the Er2O3 films due to thermal annealing processes in oxygen ambient performed at temperatures in the range of 800-1200°C has been investigated in detail. The existence of well defined annealing conditions (rapid treatments at a temperature of 1100°C or higher) allowing to avoid the occurrence of extensive chemical reactions with the oxidized substrate has been demonstrated; under these conditions, the thermal process has a beneficial effect on both structural and optical properties of the film, and an increase of the photoluminescence (PL) intensity by about a factor of 40 with respect to the as-deposited material has been observed. The enhanced efficiency of the photon emission process has been correlated with the longer lifetime of the PL signal. Finally, the conditions leading to a reaction of Er2O3 with the substrate have been also identified, and evidences about the formation of silicate-like phases have been collected. © 2006 American Institute of Physics.

Tests of an adaptive QM/MM calculation on free energy profiles of chemical reactions in solution.

We present reaction free energy calculations using the adaptive buffered force mixing quantum mechanics/molecular mechanics (bf-QM/MM) method. The bf-QM/MM method combines nonadaptive electrostatic embedding QM/MM calculations with extended and reduced QM regions to calculate accurate forces on all atoms, which can be used in free energy calculation methods that require only the forces and not the energy. We calculate the free energy profiles of two reactions in aqueous solution: the nucleophilic substitution reaction of methyl chloride with a chloride anion and the deprotonation reaction of the tyrosine side chain. We validate the bf-QM/MM method against a full QM simulation, and show that it correctly reproduces both geometrical properties and free energy profiles of the QM model, while the electrostatic embedding QM/MM method using a static QM region comprising only the solute is unable to do so. The bf-QM/MM method is not explicitly dependent on the details of the QM and MM methods, so long as it is possible to compute QM forces in a small region and MM forces in the rest of the system, as in a conventional QM/MM calculation. It is simple, with only a few parameters needed to control the QM calculation sizes, and allows (but does not require) a varying and adapting QM region which is necessary for simulating solutions.

Genetic diversity: Geographical distribution and toxin profiles of Microcystis strains (Cyanobacteria) in China

Twenty strains of Microcystis Kutz were isolated from different freshwater bodies in China to analyze the diversity, geographical distribution and toxin profiles. Based on whole-cell polymerase chain reaction of cpcBA-IGS nucleotide sequence, the derived neighbor-joining (NJ) and maximum parsimony (MP) trees indicate that these strains of Microcystis can be divided into four clusters. The strains from south, middle and north region of China formed distinct lineages, suggesting high diversity and a geographical distribution from south to north locations. Moreover, the results being indicating high variable genotypes of the strains of the Microcystis strains from the same lake show that there is high diversity of Microcystis within a water bloom population. Comparing the results of the present study with those reported for compared with 43 strains of Microcystis from other locations, also reveals Chinese strains have high similarity with those from regions in the North Hemispherical. This suggests that the Microcystis strains in the world might have a geographical distribution. Analysis of 30 strains using the primers MCF/TER and TOX2P/TOX2M showed that there was no correlation between the gene of cpcBA-IGS and the presence of mcy. Toxic strains were founded to be predominant in different water bodies throughout China.

Identification and characterization of Bacillus anthracis by multiplex PCR on DNA chip

Bacillus anthracis can be identified by detecting virulence factor genes located on two plasmids, pXO1 and pXO2. Combining multiplex PCR with arrayed anchored primer PCR and biotin-avidin alkaline phosphatase indicator system, we developed a qualitative DNA chip method for characterization of B. anthracis, and simultaneous confirmation of the species identity independent of plasmid contents. The assay amplifies pag gene (in pXO1), cap gene (in pXO2) and Ba813 gene (a B. anthracis specific chromosomal marker), and the results were indicated by an easy-to-read profile based on the color reaction of alkaline phosphatase. About 1 pg of specific DNA fragments on the chip wells could be detected after PCR. With the proposed method, the avirulent (pXO1(+)/2(-), pXO1(-)/2(+) and pXO1(-)/2(-)) strains of B. anthracis and distinguished 'anthrax-like' strains from other B. cereus group bacteria were unambiguously identified, while the genera other than Bacillus gave no positive signal. (C) 2004 Elsevier B.V. All rights reserved.

Large-scale synthesis of single-phase, high-quality GaN nanocrystallites

Large-scale synthesis of high-quality GaN nano-crystallites has been achieved by direct reaction of a 4:1 molar Ga/Ga2O3 mixture with ammonia at 950degreesC. X-ray diffraction, transmission electron microscopy, selected-area electron diffraction and high-resolution transmission electron microscopy revealed that the produced GaN nanocrystallites were single hexagonal wurtzite structure with an average particle size around 45 nm. A sharp near band edge emission peak and a blue light emission peak were observed in photoluminescence spectroscopy. The synthesis approach is simple and easy to be commercialized.