Base Cation and Nitrogen Budgets for a Mixed Hardwood Catchment in South-central Ontario

There is growing concern that available base cation pools in soil are declining in eastern North America and that some forests are approaching nitrogen (N) saturation due to the combined effects of acid deposition and harvesting. To assess these concerns, elemental mass balances for calcium (Ca), magnesium (Mg), potassium (K), and N were conducted over a 17-year period in a representative mixed hardwood forest (HP4) in the Muskoka-Haliburton region in central Ontario, Canada. On average, 76% of the N measured in bulk deposition, which is a conservative estimate of total N deposition, was retained in HP4, with tree uptake accounting for over half of the retained N. Year-to-year variations in annual NO₃ export were affected by climate variations, although the low annual NO₃-N concentrations (80–156 g/L) suggest that HP4 is not approaching N saturation. Losses of Ca, Mg, and K in stream export plus accumulation in trees (more than 12 cm in diameter at breast height) exceeded inputs in deposition by 296, 76.2, and 53.6 kg/ha, respectively, over the 17-year period. Inclusion of mineral weathering estimates obtained using PROFILE, zirconium (Zr) depletion, and total analysis correlation failed to balance Ca losses from HP4, and calculations indicate that between 98 and 145 kg/ha (depending on mineral weathering estimate) was lost from the soil exchangeable pool between 1983 and 1999. These losses were supported by repeated field measurements, which showed that the exchangeable Ca concentrations and soil pH decreased over the 17-year period, particularly in the upper soil horizons. When mineral weathering estimates are included, mass balance calculations generally indicated that there was no net loss of Mg and K from HP4, which was confirmed by our soil measurements. At present, there is sufficient Ca in the soil exchangeable pool to sustain forest growth at HP4; however, continued losses of Ca due to leaching and harvesting at the present rate may ultimately threaten the health and productivity of the forest within just a few decades.     

Free energy calculations for the relative binding affinity between DNA and lambda-repressor

The change in the binding free energy between DNA and lambda-repressor resulting from a base substitution, thymine (T)-->deoxyuracil (abbreviated as U), was evaluated by the free energy perturbation method on the basis of molecular dynamics simulations for the DNA-lambda-repressor complex in water with all degrees of freedom and including long-range Coulomb interactions. The binding free energy change that we calculated (1.47 +/- 0.40 kcal/mol) was in good agreement with an experimental value (1.8 kcal/mol). We clarified why the small difference between T and U (CH(3) in T is replaced with H in U) caused such a significant change in the binding free energy: The substitution of CH(3) in T with H in U lowered the dissociated-state free energy level due to the gain of the hydration free energy. Furthermore, the T-->U substitution raised the free energy level in the associated state due to the loss of the favored van der Waals (vdW) interactions with the lambda-repressor amino acid residues. In other words, the amino acid residues of lambda-repressor can recognize the CH(3) in T through the vdW interactions with the CH(3). This recognition is enhanced in a water environment, because the hydrophobic CH(3) prefers the amino acid residues of lambda-repressor to water molecules.     

Molecular evidence for a kdr-like pyrethroid resistance mechanism in the malaria vector mosquito Anopheles stephensi

The mosquito Anopheles stephensi Liston (Diptera: Culicidae) is the urban vector of malaria in several countries of the Middle East and Indian subcontinent. Extensive use of residual insecticide spraying for malaria vector control has selected An. stephensi resistance to DDT, dieldrin, malathion and other organophosphates throughout much of its range and to pyrethroids in the Middle East. Metabolic resistance mechanisms and insensitivity to pyrethroids, so-called knockdown resistance (kdr), have previously been reported in An. stephensi. Here we provide molecular data supporting the hypothesis that a kdr-like pyrethroid-resistance mechanism is present in An. stephensi. We found that larvae of a pyrethroid-selected strain from Dubai (DUB-R) were 182-fold resistant to permethin, compared with a standard susceptible strain of An. stephensi. Activities of some enzymes likely to confer pyrethroid-resistance (i.e. esterases, monooxygenases and glutathione S-transferases) were significantly higher in the permethrin-resistant than in the susceptible strain, but the use of synergists--piperonyl butoxide (PBO) to inhibit monooxygenases and/or tribufos (DEF) to inhibit esterases--did not fully prevent resistance in larvae (permethrin LC50 reduced by only 51-68%), indicating the involvement of another mechanism. From both strains of An. stephensi, we obtained a 237-bp fragment of genomic DNA encoding segment 6 of domain II of the para type voltage-gated sodium channel, i.e. the putative kdr locus. By sequencing this 237 bp fragment, we identified one point mutation difference involving a single A-T base change encoding a leucine to phenylalanine amino acid substitution in the pyrethroid-resistant strain. This mutation appears to be homologous with those detected in An. gambiae and other insects with kdr-like resistance. A diagnostic polymerase chain reaction assay using nested primers was therefore designed to detect this mechanism in An. stephensi.     

Thermodynamic characterization of the interaction of human cyclophilin 18 with cyclosporin A

Isothermal titration calorimetry (ITC) was used to investigate thermodynamic parameters of the cyclosporin A (CsA)-cyclophilin 18 (hCyp18) association reaction. We have calculated the thermodynamic parameters (enthalpy, entropy, heat capacity, and free energy of binding) of the CsA/hCyp18 complexation. All but two methods described in the literature underestimate the affinity to hCyp18 of CsA. We found that the association constant (1.1·10⁸ M⁻¹ at 10 °C) of CsA to hCyp18 is in close agreement with the reciprocal of the reported inhibitory constant of the peptidylprolyl cis/trans isomerase activity of hCyp18. Interpretation of the thermodynamic parameters in buffered solution of water, 30% glycerol and D₂O leads to the conclusion that the highly specific binding of CsA to hCyp18 is mainly mediated through hydrogen bonding and to a lesser degree through hydrophobic interaction. Furthermore, the pH dependence of the association constant was determined and analyzed according to a single proton linkage model, resulting in a pK_a value of 5.7 in free hCyp18 and below 4.5 in the CsA complexed form. Titration experiments using different single component buffers possessing different heats of ionization allowed us to estimate that statistically half a proton is transferred upon CsA binding from the binding interface of hCyp18 to the buffer at pH 5.5. No proton transfer was detected at pH 7.5. The thermodynamic results are discussed in relation to the published X-ray and NMR structure of the free and CsA complexed hCyp18.     

A survey of the year 2002 literature on applications of isothermal titration calorimetry

Isothermal titration calorimetry (ITC) is becoming widely accepted as a key instrument in any laboratory in which quantification of biomolecular interactions is a requisite. The method has matured with respect to general acceptance and application development over recent years. The number of publications on ITC has grown exponentially over the last 10 years, reflecting the general utility of the method. Here all the published works of the year 2002 in this area have been surveyed. We review the broad range of systems to which ITC is being directed and classify these into general areas highlighting key publications of interest. This provides an overview of what can be achieved using this method and what developments are likely to occur in the near future.     

A role for p53 in base excision repair

Wild-type p53 protein can markedly stimulate base excision repair (BER) in vitro, either reconstituted with purified components or in extracts of cells. In contrast, p53 with missense mutations either at hot-spots in the core domain or within the N-terminal transactivation domain is defective in this function. Stimulation of BER by p53 is correlated with its ability to interact directly both with the AP endonuclease (APE) and with DNA polymerase beta (pol beta). Furthermore, p53 stabilizes the interaction between DNA pol beta and abasic DNA. Evidence that this function of p53 is physiologically relevant is supported by the facts that BER activity in human and murine cell extracts closely parallels their levels of endogenous p53, and that BER activity is much reduced in cell extracts immunodepleted of p53. These data suggest a novel role for p53 in DNA repair, which could contribute to its function as a key tumor suppressor.     

Serine base exchange enzyme in porcine lyophilised platelets: enzyme properties and modulation by AIF4-and different types of heparin

Phosphatidylserine is one of the PKC modulators and thus it may play an important role in signal transduction. Regulation of the synthesis of this phospholipid is not yet clarified. The contrasting reports are possibly related to the existence of different enzymes which, in mammalian tissues, catalyse the exchange between free serine and the nitrogen base of a membrane phospholipid. This study demonstrates that serine base exchange reactions of commercially available lyophilised porcine platelets exhibit similar pH optima, temperature and Ca²⁺ dependence as observed in fresh tissues. Analysis of fatty acids composition of the three phospholipid classes involved in base exchange reactions also demonstrated a similarity with fresh platelets. Serine and ethanolamine base exchange enzyme activities were assayed in parallel in platelet lysate subjected to preincubation at various temperatures (30-60°C). When dithioerithrol was omitted from the incubation medium, the two base exchange reactions were inhibited with a similar temperature-dependent pattern. Addition of the reducing agent enhanced the sensitivity to preincubation only for the serine base exchange reaction which was inhibited by 80% after preincubation at 45°C. With respect to its regulation, porcine platelet serine base exchange enzyme(s) was inhibited by fluoroalluminate, a widely used G-protein activator, and stimulated by unfractionated heparin. Low mol. wt. heparin did not influence enzyme activity. Unfractionated heparin greatly stimulated SBEE activity assayed at pH 7.4, a pH value far from the optimal pH.     

NMR characterization of a pH-dependent equilibrium between two folded solution conformations of the pheromone-binding protein from Bombyx mori

NMR spectroscopic changes as a function of pH in solutions of the pheromone-binding protein of Bombyx mori (BmPBP) show that BmPBP undergoes a conformational transition between pH 4.9 and 6.0. At pH below 4.9 there is a single "acid form" (A), and a homogeneous "basic form" (B) exists at pH above 6.0. Between pH 5 and 6, BmPBP exists as a mixture of A and B in slow exchange on the NMR chemical shift time scale, with the transition midpoint at pH 5.4. The form B has a well-dispersed NMR spectrum, indicating that it represents a more structured, "closed" conformation than form A, which has a significantly narrower chemical shift dispersion. Conformational transitions of the kind observed here may explain heterogeneity reported for a variety of odorant-binding proteins, and it will be of interest to further investigate possible correlations with pH-dependent regulation of ligand binding and release in the biological function of this class of proteins.     

Photoinhibition as a function of the ambient redox potential in Tris-washed PS II membrane fragments

The mode of photoinhibition as a function of the ambient redox potential (E_ambient) in suspensions of Tris-washed PS II membrane fragments has been analyzed by monitoring flash-induced absorption changes at 830 nm. It was found: (a) the detectable initial amplitude, ΔA^total ₈₃₀, as a measure of the capacity to form the `stable' radical pair, P680^+ċ Q^−ċ _A, drastically decreases during a 10 min photoinhibition at E_ambient values below +350 mV; (b) conversely, the normalized extent of the 18 μs relaxation kinetics, ΔA^{18 μ s} ₈₃₀ as a measure of the electron transfer from Y_Z to P680^+ċ becomes highly susceptible to light stress when E_ambient exceeds values of about +350 mV; (c) effects of the ambient redox potentials are highly pronounced during light exposure under anaerobic conditions, while much smaller differences arise under aerobic conditions; (d) the extent of damage does not correlate with the total concentration of K₃[Fe(CN)₆] and K₄[Fe(CN)₆] in the suspension during photoinhibition but rather depends on the E_m-values; (e) qualitatively similar features are observed when the redox buffer system K₃[Fe(CN)₆]/Na₂S₂O₄ is replaced by K₂[IrCl₆]/Na₂S₂O₄; (f) the characteristic E_ambient-dependence of photoinhibition is observed only under anaerobic conditions. The results are discussed with respect to different redox components that might be involved, including brief comments on a possible role of Cyt b559. This revised version was published online in June 2006 with corrections to the Cover Date.     

Alkylcobalt chelates with Schiff bases derived from a β-diketone bearing both alkyl and aryl groups

Organocobalt(III) complexes with Schiff bases derived from a β-diketone bearing both an alkyl and an aryl group have been prepared. The template syntheses using benzoylacetone and ethylenediamine as complexing agents provide a route to alkylcobalt chelates with the corresponding tri- and tetradentate Schiff bases. However, if a β-diketone with two aryl groups, e.g. dibenzoylmethane, was employed as the starting ketoenol component, no organometallic products were detected; a new mixed-ligand ‘inorganic’ chelate of cobalt(II), [Co{O=C(Ph)CH=C(Ph)O}₂(en)], was isolated instead. Its structure as well as that of one of the alkylcobalt complexes with a tridentate Schiff base composed of benzoylacetone and ethylenediamine have been established by X-ray techniques. The current scope of the template synthesis of alkylcobalt complexes with Schiff bases is summarized.