Linoleate 9R-dioxygenase and allene oxide synthase activities of Aspergillus terreus

Oxygenation of linoleic acid by Aspergillus terreus was studied with LC-MS/MS. 9(R)-Hydroperoxy-10(E),12(Z)-octadecadienoic acid (9R-HpODE) was identified along with 10(R)-hydroxy-8(E),12(Z)-octadecadienoic acid and variable amounts of 8(R)-hydroxy-9(Z),12(Z)-octadecadienoic acid. 9R-HpODE was formed from [11S-²H]18:2n − 6 with loss of the deuterium label, suggesting antarafacial hydrogen abstraction and oxygenation. Two polar metabolites were identified as 9-hydroxy-10-oxo-12(Z)-octadecenoic acid (α-ketol) and 13-hydroxy-10-oxo-11(E)-octadecenoic acid (γ-ketol), likely formed by spontaneous hydrolysis of an unstable allene oxide, 9(R),10-epoxy-10,12(Z)-octadecadienoic acid. α-Linolenic acid and 20:2n − 6 were oxidized to hydroperoxy fatty acids at C-9 and C-11, respectively, but α- and γ-ketols of these fatty acids could not be detected. The genome of A. terreus lacks lipoxygenases, but contains genes homologous to 5,8-linoleate diol synthases and linoleate 10R-dioxygenases of aspergilli. Our results demonstrate that linoleate 9R-dioxygenase linked to allene oxide synthase activities can be expressed in fungi.     

Vector borne diseases on an urban environment: The effects of heterogeneity and human circulation

We study the effect of human circulation and host/vector heterogeneities on the onset of epidemics of arboviruses. From a meta-population dynamics based on the classical Bailey–Dietz model, we derive a multi-group model under three assumptions: (i) fast host sojourn time-scale; (ii) mosquitoes do not move; (iii) time homogeneity and strong connectivity of human circulation. Within this modelling framework, three different kinds of R₀ appear: (i) the “true” or “global” R₀—derived from the corresponding next generation matrix; (ii) the uniform R₀—obtained if the patches are taken homogeneous; (iii) the local R₀s—obtained if the patches are disconnected. We show that there is relevant epidemiological information associated to all of them. In particular, they can be used to understand the effects of changing the circulation on the value of the global R₀. We also present additional results on the effects on R₀ of different vector control policies, and a simulation with data from the city of Rio de Janeiro, Brazil.     

Precise measurement of diffusion coefficients using scanning fluorescence correlation spectroscopy

We have implemented scanning fluorescence correlation spectroscopy (sFCS) for precise determination of diffusion coefficients of fluorescent molecules in solution. The measurement volume where the molecules are excited, and from which the fluorescence is detected, was scanned in a circle with radius comparable to its size at frequencies 0.5-2 kHz. The scan radius R, determined with high accuracy by careful calibration, provides the spatial measure required for the determination of the diffusion coefficient D, without the need to know the exact size of the measurement volume. The difficulties in the determination of the measurement volume size have limited the application of standard FCS with fixed measurement volume to relative measurements, where the diffusion coefficient is determined by comparison with a standard. We demonstrate, on examples of several common fluorescent dyes, that sFCS can be used to measure D with high precision without a need for a standard. The correct value of D can be determined in the presence of weak photobleaching, and when the measurement volume size is modified, indicating the robustness of the method. The applicability of the presented implementation of sFCS to biological systems in demonstrated on the measurement of the diffusion coefficient of eGFP in the cytoplasm of HeLa cells. With the help of simulations, we find the optimal value of the scan radius R for the experiment.     

Precision of sodium dodecyl sulfate-polyacrylamide-gel electrophoresis for the molecular weight estimation of a membrane glycoprotein: studies on bovine rhodopsin.

Criteria for assessing the precision and accuracy of methods for estimation of molecular weight for proteins using sodium dodecyl sulfate-polyacrylamide-gel electrophoresis have been applied to rhodopsin from bovine visual cell outer segment membranes. Various methods of preparing this hydrophobic protein for electrophoresis differ in their ability to solubilize and disaggregate polypeptide constituents of the outer segment membrane, with resultant variations in the pattern of protein bands and the apparent molecular weight of rhodopsin. Even with optimal solubilization and disaggregation, the behavior of rhodopsin relative to a series of standard proteins is such that the apparent molecular weight decreases systematically from 40,400 to 34,500 as the acrylamide concentration increases from 4 to 10%. As demonstrated by Ferguson plots of logR_f vs gel concentration and split gel experiments, this discrepancy is explained by the fact that the extrapolated R_f for zero gel concentration (Y₀) for rhodopsin is significantly lower than the Y₀'s for the soluble proteins used as molecular weight standards. In such cases, a possibly more reliable molecular weight estimate is obtained by plotting the retardation coefficient (K_R) vs molecular weight. This method yields a value of 29,500 ± 1000 for bovine rhodopsin if only the errors in measurement of R_f are considered and a quadratic relationship between K_R and molecular weight is used. Using weighted linear regression for K_R vs molecular weight, we obtain a molecular weight estimate of 32,700 ± 5000 when the uncertainty in the calibration curve is considered. Because of uncertainties regarding the detergent-binding properties of rhodopsin and the relationship of its Stokes radius to its molecular weight by comparison with the soluble protein standards, these values must be viewed with caution.     

A Class of Pairwise Models for Epidemic Dynamics on Weighted Networks

In this paper, we study the SIS (susceptible–infected–susceptible) and SIR (susceptible–infected–removed) epidemic models on undirected, weighted networks by deriving pairwise-type approximate models coupled with individual-based network simulation. Two different types of theoretical/synthetic weighted network models are considered. Both start from non-weighted networks with fixed topology followed by the allocation of link weights in either (i) random or (ii) fixed/deterministic way. The pairwise models are formulated for a general discrete distribution of weights, and these models are then used in conjunction with stochastic network simulations to evaluate the impact of different weight distributions on epidemic thresholds and dynamics in general. For the SIR model, the basic reproductive ratio R ₀ is computed, and we show that (i) for both network models R ₀ is maximised if all weights are equal, and (ii) when the two models are ‘equally-matched’, the networks with a random weight distribution give rise to a higher R ₀ value. The models with different weight distributions are also used to explore the agreement between the pairwise and simulation models for different parameter combinations.     

Cytoplasm Resistivity of Mammalian Atrial Myocardium Determined by Dielectrophoresis and Impedance Methods

Many cardiac arrhythmias are caused by slowed conduction of action potentials, which in turn can be due to an abnormal increase of intracellular myocardial resistance. Intracellular resistivity is a linear sum of that offered by gap junctions between contiguous cells and the cytoplasm of the myocytes themselves. However, the relative contribution of the two components is unclear, especially in atrial myocardium, as there are no precise measurements of cytoplasmic resistivity, R_c. In this study, R_c was measured in atrial tissue using several methods: a dielectrophoresis technique with isolated cells and impedance measurements with both isolated cells and multicellular preparations. All methods yielded similar values for R_c, with a mean of 138 ± 5 Ω·cm at 23°C, and a Q₁₀ value of 1.20. This value is about half that of total intracellular resistivity and thus will be a significant determinant of the actual value of action potential conduction velocity. The dielectrophoresis experiments demonstrated the importance of including divalent cations (Ca²⁺ and Mg²⁺) in the suspension medium, as their omission reduced cell integrity by lowering membrane resistivity and increasing cytoplasm resistivity. Accurate measurement of R_c is essential to develop quantitative computational models that determine the key factors contributing to the development of cardiac arrhythmias.     

A study of cis-dichlorobis(methylamine)platinum(II): Crystal and molecular structures of two crystal forms

A new synthesis of cis-dichlorobis(methylamine)platinum(II) is described. It appears that during the crystallization process at least two types of crystals are formed. Form A is monoclinic with space group P2 ₁/n and unit cell dimensions a = 6.272, b = 15.726, c = 7.419Å, β = 99.86°, V = 721Å ³, Z = 4, R = 0.055. Form B is monoclinic, with space group P2 ₁/c and unit cell dimensions a = 16.078, b = 6.372, c = 21.459Å, β = 92.7°, V = 2196Å ³, Z = 12, R = 0.057. The two forms can be readily distinguished by IR spectroscopy.     

Identification of macromolecules by quantitative polyacrylamide gel electrophoresis and isoelectric focusing: a comparison of three approaches.

Identification of macromolecules by zone electrophoresis has usually been based on differences in migration distances under a single set of electrophoretic conditions. Classically, it has taken the form of coelectrophoresis on gel slabs. In “quantitative” polyacrylamide gel electrophoresis (PAGE), separation conditions were standardized sufficiently to allow for identification of macromolecules between experiments on the basis of their relative electrophoretic mobilities, R_f ± σ_Rf. More reliably, molecular identity or distinguishability have been based on several R_f values at several gel concentrations (%T) and the linear relationship between log R_f and %T, the Ferguson plot. The slope (retardation coefficient K_R of this plot is desoriptive of molecular size while the γ-intercept (Y₀) is a measure of net charge. The joint 95% confidence envelopes for K_R and Y₀ may be used as criteria for identification of molecules. Distinction between two molecular species depends on the size and position of the two confidence envelopes or ellipses. By pooling estimates of residual varlance (scatter areund the regression line for the Ferguson plot) for several proteins, it is possible to reduce the size of the ellipses and improve the sensitivity of the method to distinguish elesely related species. The sensitivity of this method depends on the size and reprodueibility of the 95% confidence envelopes, and on the limitatiens in the number of electrophoretic fractionations that one is reasonably willing to invest. Any molecular identification problem therefore raises the implieit question whether to base distinction on migration distance, on R_f, or on the joint 95% confidence envelopes for K_R and Y₀ and related statistical (F test) eriteria. Further, in the event of inconsistent answers to the question of molecular distinguishability from the three approaches, we need rational criteria to select the “best” answer. These problems and some solutions are illustrated by the present study which was designed to determine whether the enzymatic digestion products of human growth hormone produced by subtilisin-B are or are not the same as those obtained by digestion with plasmin. It appears that the joint 95% confidence envelopes of K_R and Y₀ provide at this time the most discriminating criteria of distinction, indicating significant differences between nearly all the products of plasmin and subtilisin digestion of hGH. However, the lower resolution provided by the R_f criteria has the advantage that it allows one to group the products of the partial hydrolysis of hGH into “families” which may be associated with different ranges of specific bioactivities.     

Samia cynthia versus Bombyx mori: comparative gene mapping between a species with a low-number karyotype and the model species of Lepidoptera

We performed gene-based comparative FISH mapping between a wild silkmoth, Samia cynthia ssp. with a low number of chromosomes (2n = 25-28) and the model species, Bombyx mori (2n = 56), in order to identify the genomic components that make up the chromosomes in a low-number karyotype. Mapping of 64 fosmid probes containing orthologs of B. mori genes revealed that the homologues of either two or four B. mori chromosomes constitute the S. c. ricini (Vietnam population, 2n = 27??/28??, Z0/ZZ) autosomes. Where tested, even the gene order was conserved between S. c. ricini and B. mori. This was also true for the originally autosomal parts of the neo-sex chromosomes in S. c. walkeri (Sapporo population, 2n = 26??/26??, neo-Wneo-Z/neo-Zneo-Z) and S. cynthia subsp. indet. (Nagano population, 2n = 25??/26??, neo-WZ₁Z₂/Z₁Z₁Z₂Z₂). The results are evidence for an internal stability of lepidopteran chromosomes even when all autosomes had undergone fusion processes to form a low-number karyotype.     

The structures of barium hexafluorosilicate and cesium hexafluororhenate(V)

The crystal structure of CsReF₆, together with a reinvestigation of that of BaSiF₆, is reported. Both have been determined from single crystal three-dimensional X-ray diffraction data. The structure of BaSiF₆ has been found to conform to the initially assigned space group R$\text{3}$m, contrary to the suggestions of other workers. The unit cell of BaSiF₆ has the dimensiona a_hex 7.189(1), c_hex 7.015(1) Å; Z = 3. Refinement by a least squares method gave R 0.0079 and R_w 0.0077. Crystals of CsReF₆ belong to the lower symmetry rhombohedral space group R$\text{3}$. The unit cell has the dimensions a_hex 7.853(1), c_hex 8.140(1) Å; Z = 3. Refinement gave R 0.031 and R_w 0.030. The lowering of symmetry is caused by rotation of the ReF₆^? octahedra about the 3-fold axis through each Re atom, causing CsReF₆ to have the KOsF₆ structure.     

Separating the contributions of vascular anatomy and blood viscosity to peripheral resistance and the physiological implications of interspecific resistance variation in amphibians

Amphibian pulmonary and systemic vascular circuits are arranged in parallel, with potentially important consequences for resistance (R) to blood flow. The contribution of the parallel anatomic arrangement to total vascular R (R _T), independent of blood viscosity, is unknown. We measured pulmonary (R _P) and systemic (R _S) vascular R with an in situ Ringer’s solution perfusion technique using anesthetized anuran and urodele species to determine: (1) relative contributions of vascular anatomy and blood viscosity to R _T; (2) distensibility index (%Δ flow kPa^?1) of the pulmonary and systemic vascular circuits; and (3) interspecific correlates of variation in these parameters with red blood cell size, cardiac power output, and aerobic capacities. R _P was lower than R _S in anurans, while R _P of the urodeles was greater than R _S and significantly greater than anuran R _P. Anuran R _T was lowest and did not vary interspecifically, whereas urodele R _T was significantly greater than anuran, and varied interspecifically. Pulmonary and systemic circuit distensibility differences may explain cardiac shunt patterns in toads with changes in cardiac output from rest to activity. When blood viscosity was taken into account, vascular resistance accounted for about 25 % of R _T while blood viscosity accounted for the remaining 75 %. Owing to lower R _T, terrestrial anuran species required lower cardiac power outputs when moving fluid through their vasculature compared to aquatic species. These results indicate that physical characteristics of the vasculature can account for interspecific differences in cardiovascular physiology and suggest a co-evolution of cardiac and vascular anatomy among amphibians.     

Bond valence sums and structural studies of antimony complexes containing Sb bonded only to O ligands

New R₀ values for Sb(III)-O of 1.955(13) Å and for Sb(V)-O of 1.912(12) Å were derived from a bond valence sum, or BVS, analysis of of 123 SbO_n fragments with n = 3-7. These R₀ values can be used to calculate the oxidation state, or OS, of Sb in complexes where Sb is bonded only to O ligands. If the OS of the Sb ion is uncertain, the average R₀ value of 1.934 Å can be used to decide between the +3 or +5 OS from the observed Sb-O bond distances without any assumptions. The Sb-O distances used in deriving the R₀ values for the +3 and +5 complexes are tabulated as a function of coordination number and have a wide range of values, but the average Sb-O distance reflects the requirement that the BVS must equal the OS. To supplement the Sb-O data, 2 new antimony tartrates were synthesized, and their crystal structures were determined. A single crystal structure determination of NaSb(OH)₆, an unexpected reaction product, gave Sb-O distances that were also included in our BVS analysis.     

Improved retrieval of Secchi depth for optically-complex waters using remote sensing data

Water transparency is one of the ecological indicators for describing water quality and the underwater light field which determines its productivity. In the European Water Framework Directive (WFD) as well as in the European Marine Strategy Framework Directive (MSFD) water transparency is used for ecological status classification of inland, coastal and open sea waters and it is regarded as an indicator for eutrophication in Baltic Sea management (HELCOM, 2007). We developed and compared different empirical and semi-analytical algorithms for lakes and coastal Nordic waters to retrieve Secchi depth (Z_SD) from remote sensing data (MERIS, 300 m resolution). The algorithms were developed in water bodies with high coloured dissolved organic matter absorption (a_CDOM(442) ranging 1.7–4.0 m⁻¹), Chl a concentration (0.5–73 mg m⁻³) and total suspended matter (0.7–37.5 g m⁻³) and validated against an independent data set over inland and coastal waters (0.6 m < Z_SD < 14.8 m). The results indicate that for empirical algorithms, using longer wavelengths in the visible spectrum as a reference band decreases the RMSE and increases the coefficient of determination (R²). The accuracy increased (R² = 0.75, RMSE = 1.33 m, n = 134) when Z_SD was retrieved via an empirical relationship between Z_SD and K_d(490). The best agreement with in situ data was attained when Z_SD was calculated via both the diffuse and the beam attenuation coefficient (R² = 0.89, RMSE = 0.77 m, n = 89). The results demonstrate that transparency can be retrieved with high accuracy over various optical water types by the means of ocean color remote sensing, improving both the spatial and temporal coverage. The satellite derived Z_SD product could be therefore used as an additional source of information for WFD and MSFD reporting purposes.     

Estimates of the basic reproduction number for rubella using seroprevalence data and indicator-based approaches

The basic reproduction number (R₀) of an infection determines the impact of its control. For many endemic infections, R₀ is often estimated from appropriate country-specific seroprevalence data. Studies sometimes pool estimates from the same region for settings lacking seroprevalence data, but the reliability of this approach is unclear. Plausibly, indicator-based approaches could predict R₀ for such settings. We calculated R₀ for rubella for 98 settings and correlated its value against 66 demographic, economic, education, housing and health-related indicators. We also trained a random forest regression algorithm using these indicators as the input and R₀ as the output. We used the mean-square error to compare the performances of the random forest, simple linear regression and a regional averaging method in predicting R₀ using 4-fold cross validation. R₀ was <5, 5–10 and >10 for 81, 14 and 3 settings respectively, with no apparent regional differences and in the limited available data, it was usually lower for rural than urban areas. R₀ was most correlated with educational attainment, and household indicators for the Pearson and Spearman correlation coefficients respectively and with poverty-related indicators followed by the crude death rate considering the Maximum Information Coefficient, although the correlation for each was relatively weak (Pearson correlation coefficient: 0.4, 95%CI: (0.24,0.48) for educational attainment). A random forest did not perform better in predicting R₀ than simple linear regression, depending on the subsets of training indicators and studies, and neither out-performed a regional averaging approach. R₀ for rubella is typically low and using indicators to estimate its value is not straightforward. A regional averaging approach may provide as reliable an estimate of R₀ for settings lacking seroprevalence data as one based on indicators. The findings may be relevant for other infections and studies estimating the disease burden and the impact of interventions for settings lacking seroprevalence data.     

Application of the Marcus theory for analysis of the temperature dependence of the reactions leading to photosynthetic water oxidation: results and implications

The temperature dependence of donor side reactions was analysed within the framework of the Marcus theory of nonadiabatic electron transfer. The following results were obtained for PS II membrane fragments from spinach: (1) the reorganisation energy of P680^+? reduction by Y_Z is of the order of 0.5?eV in samples with a functionally fully competent water oxidising complex (WOC); (2) destruction of the WOC by Tris-washing gives rise to a drastic increase of λ to values of the order of 1.6?eV; (3) the reorganisation energies of the oxidation steps in the WOC are dependent, on the redox states S _i with values of about 0.6?eV for the reactions Y_Z ^OX S ₀→Y_Z S ₁ and Y_Z ^OX S ₁→Y_Z S ₂, 1.6?eV for the reaction Y_Z ^OX S ₂→Y_Z S ₃ and 1.1?eV (above a characteristic temperature u_c of about 6??°C) for the reaction Y_Z ^OX S ₃→→Y_Z S ₀+O₂. Using an empirical rate constant-distance relationship, the van der Waals distance between Y_Z and P680 was found to be about 10?Å, independent of the presence or absence of the WOC, whereas the distance between Y_Z and the manganese cluster in the WOC was ≥15?Å. Based on the calculated activation energies the environment of Y_Z is inferred to be almost "dry" and hydrophobic when the WOC is intact but becomes enriched with water molecules after WOC destruction. Furthermore, it is concluded that the transition S ₂→S ₃ is an electron transfer reaction gated by a conformational change, i.e. it comprises significant structural changes of functional relevance. Measurements of kinetic H/D isotope exchange effects support the idea that none of these reactions is gated by the break of a covalent O-H bond. The implications of these findings for the mechanism of water oxidation are discussed.     

The potential of the satellite derived green chlorophyll index for estimating midday light use efficiency in maize, coniferous forest and grassland

Light use efficiency (LUE) is an important variable in carbon cycle and climate change research. We present an investigation of remotely estimating midday LUE using the green chlorophyll index (CI_green) derived from the cloud-free Moderate Resolution Imaging Spectroradiometer (MODIS) images in maize, coniferous forest and grassland. Similar temporal patterns are observed in both canopy chlorophyll content and midday LUE which indicates that the chlorophyll content in the maize canopy servers as a proxy of midday LUE (R² = 0.736, p < 0.001). Therefore, the CI_green, tested as a good indicator of canopy chlorophyll content (R² = 0.840, p < 0.001), has been demonstrated to be a reliable candidate in providing reasonable estimates of midday LUE with determination coefficient R² equals to 0.820 and a root mean square error (RMSE) of 0.002 mol CO₂ per mol incident photosynthetic photon flux density (PPFD). Further validation of the prediction model derived from the maize site demonstrates that the CI_green has potential to be applied in the coniferous forest and grassland ecosystems with RMSE of 0.005 and 0.004 mol CO₂ mol⁻¹ PPFD, respectively. A comparison analysis between different vegetation types is included and these results could be helpful in the development of future LUE and terrestrial models.