Transition from octahedral to tetrahedral geometry causes the activation or inhibition by Zn<Superscript>2+</Superscript> of <Emphasis Type="Italic">Pseudomonas aeruginosa</Emphasis> phosphorylcholine phosphatase

Pseudomonas aeruginosa phosphorylcholine phosphatase (PchP) catalyzes the hydrolysis of phosphorylcholine, which is produced by the action of hemolytic phospholipase C on phosphatidylcholine or sphyngomielin, to generate choline and inorganic phosphate. Among divalent cations, its activity is dependent on Mg²⁺ or Zn²⁺. Mg²⁺ produced identical activation at pH 5.0 and 7.4, but Zn²⁺ was an activator at pH 5.0 and became an inhibitor at pH 7.4. At this higher pH, very low concentrations of Zn²⁺ inhibited enzymatic activity even in the presence of saturating Mg²⁺ concentrations. Considering experimental and theoretical physicochemical calculations performed by different authors, we conclude that at pH 5.0, Mg²⁺ and Zn²⁺ are hexacoordinated in an octahedral arrangement in the PchP active site. At pH 7.4, Mg²⁺ conserves the octahedral coordination maintaining enzymatic activity. The inhibition produced by Zn²⁺ at 7.4 is interpreted as a change from octahedral to tetrahedral coordination geometry which is produced by hydrolysis of the [ \textZn ²⁺ \textL ₂ ^{- 1} \textL ₂⁰ ( \textH ₂ \textO ) ₂ ] \left[ {{\text{Zn}}^{ 2+ } {\text{L}}_{ 2}^{ - 1} {\text{L}}_{ 2}^{0} \left( {{\text{H}}_{ 2} {\text{O}}} \right)_{ 2} } \right] complex.     

Parameterization of chlorophyll a-specific absorption coefficients and effects of their variations in a highly eutrophic lake: a case study at Lake Kasumigaura, Japan

The chlorophyll a-specific absorption coefficient ( a_\textph^* ( l) a_{\text{ph}}^{*} \left( \lambda \right) ) in a highly eutrophic lake can show characteristics distinct from that in the ocean due to the differences in the structure and composition of phytoplankton. In this study, investigated the variation of a_\textph^* ( l) a_{\text{ph}}^{*} \left( \lambda \right) in Lake Kasumigaura, a highly eutrophic lake in Japan, in association with the package effect and the effect of accessory pigments, and carried out the parameterization of a_\textph^* ( l) a_{\text{ph}}^{*} \left( \lambda \right) . Although a_\textph^* ( l) a_{\text{ph}}^{*} \left( \lambda \right) did not vary spatially, it did show significant temporal variation, with a particularly high value after spring-bloom. This high a_\textph^* ( l) a_{\text{ph}}^{*} \left( \lambda \right) in spring was attributed to a lower package effect and a higher proportion of carotenoid than the other samples. Although the value of a_\textph^* ( l) a_{\text{ph}}^{*} \left( \lambda \right) was correlated with the concentration of chlorophyll-a (Chl-a), the correlation coefficient was lower than those reported in the ocean. Some lake-water samples showed variations of the package effect and the effect of accessory pigments that were independent of the concentration of Chl-a, and these independent variations resulted in the weak correlation between a_\textph^* ( l) a_{\text{ph}}^{*} \left( \lambda \right) and the concentration of Chl-a. Together, these results suggest that the factors controlling a_\textph^* ( l) a_{\text{ph}}^{*} \left( \lambda \right) in highly eutrophic lakes are distinct from that in ocean samples.     

Interaction-induced electric (hyper)polarizability in the dihydrogen–neon pair: basis set and electron correlation effects

We investigated the interaction (hyper)polarizability of neon–dihydrogen pairs by performing high-level ab initio calculations with atom/molecule-specific, purpose-oriented Gaussian basis sets. We obtained interaction-induced electric properties at the SCF, MP2, and CCSD levels of theory. At the CCSD level, for the T-shaped configuration, around the respective potential minimum of 6.437 a₀, the interaction-induced mean first hyperpolarizability varies for 5?<? R/a₀?<?10 as

$$ \left[{\overline{\beta}}_{\mathrm{int}}(R)\hbox{-} {\overline{\beta}}_{\mathrm{int}}\left({R}_{\mathrm{e}}\right)\right]/{e}^3{a_0}^3{E_{\mathrm{h}}}^{-2}=-0.91\left(R\hbox{-} {R}_{\mathrm{e}}\right)+0.50{\left(R\hbox{-} {R}_{\mathrm{e}}\right)}^2\hbox{--} 0.13{\left(R\hbox{-} {R}_{\mathrm{e}}\right)}^3+0.01{\left(R\hbox{-} {R}_{\mathrm{e}}\right)}^4. $$

Again, at the CCSD level, but for the L-shaped configuration around the respective potential minimum of 6.572 a₀, this property varies for 5?<? R/a₀?<?10 as

$$ \left[{\overline{\beta}}_{\mathrm{int}}(R)\hbox{-} {\overline{\beta}}_{\mathrm{int}}\left({R}_{\mathrm{e}}\right)\right]/{e}^3{a_0}^3{E_{\mathrm{h}}}^{-2}=-1.33\left(R\hbox{-} {R}_{\mathrm{e}}\right)+0.75{\left(R\hbox{-} {R}_{\mathrm{e}}\right)}^2-0.20{\left(R\hbox{-} {R}_{\mathrm{e}}\right)}^3+0.02{\left(R\hbox{-} {R}_{\mathrm{e}}\right)}^4. $$

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Graphical Abstract Interaction-induced mean dipole polarizability (\( \overline{a} \)) for the T-shaped configuration of H₂–Ne calculated at the SCF, MP2, and CCSD levels of theory

     

13C spin relaxation measurements in RNA: Sensitivity and resolution improvement using spin-state selective correlation experiments

A set of new NMR pulse sequences has been designed for the measurement of ¹³C relaxation rate constants in RNA and DNA bases: the spin-lattice relaxation rate constant R(C_z), the spin-spin relaxation rate constant R(C₊), and the CSA-dipolar cross-correlated relaxation rate constant . The use of spin-state selective correlation techniques provides increased sensitivity and spectral resolution. Sensitivity optimised C-C filters are included in the pulse schemes for the suppression of signals originating from undesired carbon isotopomers. The experiments are applied to a 15% ¹³C-labelled 33-mer RNA–theophylline complex. The measured ratios indicate that ¹³C CSA tensors do not vary significantly for the same type of carbon (C₂, C₆, C₈), but that they differ from one type to another. In addition, conformational exchange effects in the RNA bases are detected as a change in the relaxation decay of the narrow ¹³C doublet component when varying the spacing of a CPMG pulse train. This new approach allows the detection of small exchange effects with a higher precision compared to conventional techniques.     

HNCA-TOCSY-CANH experiments with alternate <Superscript>13</Superscript>C-<Superscript>12</Superscript>C labeling: a set of 3D experiment with unique supra-sequential information for mainchain resonance assignment

Described here is a set of three-dimensional (3D) NMR experiments that rely on CACA-TOCSY magnetization transfer via the weak ³ \textJ_{\textCa\textCa} ^{ 3} {\text{J}}_{{{\text{C}}\alpha {\text{C}}\alpha }} coupling. These pulse sequences, which resemble recently described ¹³C detected CACA-TOCSY (Takeuchi et al. 2010) experiments, are recorded in ¹H₂O, and use ¹H excitation and detection. These experiments require alternate ¹³C-¹²C labeling together with perdeuteration, which allows utilizing the small ³ \textJ_{\textCa\textCa} ^{ 3} {\text{J}}_{{{\text{C}}\alpha {\text{C}}\alpha }} scalar coupling that is otherwise masked by the stronger ¹J_CC couplings in uniformly ¹³C labeled samples. These new experiments provide a unique assignment ladder-mark that yields bidirectional supra-sequential information and can readily straddle proline residues. Unlike the conventional HNCA experiment, which contains only sequential information to the ^{1 3} \textC^a ^{ 1 3} {\text{C}}^{\alpha } of the preceding residue, the 3D hnCA-TOCSY-caNH experiment can yield sequential correlations to alpha carbons in positions i−1, i + 1 and i−2. Furthermore, the 3D hNca-TOCSY-caNH and Hnca-TOCSY-caNH experiments, which share the same magnetization pathway but use a different chemical shift encoding, directly couple the ¹⁵N-¹H spin pair of residue i to adjacent amide protons and nitrogens at positions i−2, i−1, i + 1 and i + 2, respectively. These new experimental features make protein backbone assignments more robust by reducing the degeneracy problem associated with the conventional 3D NMR experiments.     

Genetic parameters and predicted selection responses for timber production traits in a Castanea sativa progeny trial: developing a breeding program

Total height, diameter, index volume, stem straightness, apical dominance, and survival were assessed at 8 years from seed in an open-pollinated progeny test of 36 families of European chestnut (Castanea sativa Miller) established at two sites in the Atlantic area of Galicia, Spain. Iterative spatial analysis was applied to eliminate the effect of the spatial dependence in the original data and to estimate accurately genetic parameters for evaluating the potential for selection of the measured trees. Spatial analysis was very beneficial for growth traits and survival, but less so if at all for form traits. Estimated individual heritabilities ranged from moderate to high for growth traits ([^(h)]_i² = 0.29 - 0.42 \widehat{h}_i^2 = 0.29 - 0.42 ) and stem straightness ([^(h)]_i² = 0.24 - 0.42 \widehat{h}_i^2 = 0.{24} - 0.{42} ). High coefficients of additive genetic variance were obtained for volume ( [^(\textC)]\textV_\textA = 36.5 - 41.5% \widehat{\text{C}}{{\text{V}}_{\text{A}}} = {36}.{5} - {41}.{5}\% ) and straightness ( [^(\textC)]\textV_\textA = 44.26 - 53.84% \widehat{\text{C}}{{\text{V}}_{\text{A}}} = {44}.{26} - {53}.{84}\% ). Phenotypic and estimated genetic correlations between growth traits were very high, and correlations between sites indicated that there was no important family × site interaction. No adverse correlations between traits were evident. The results indicate the ample potential for selection in the current progeny trial, where responses to within-family and combined selection for growth traits may be high. Accordingly, three selection scenarios were addressed with the aim to initiate the selection of individuals for implementing the Forest Breeding Plan of Galicia for European chestnut.     

Topological research on diamagnetic susceptibilities of organic compounds

A novel molecular connectivity index, , based on the adjacency matrix of molecular graphs and novel atomic valence connectivities, , for predicting the molar diamagnetic susceptibilities of organic compounds is proposed. The is defined as: , where and E_i are the atomic valence connectivity and the valence orbital energy of atom i, respectively. A good QSPR model for molar diamagnetic susceptibilities can be constructed from and using multivariate linear regression (MLR). The correlation coefficient r, standard error, and average absolute deviation of the MLR model are 0.9918, 5.56 cgs, and 4.26 cgs, respectively, for the 721 organic compounds tested (training set). Cross-validation using the leave-one-out method demonstrates that the MLR model is highly reliable statistically. Using the MLR model, the average absolute deviations of the predicted values of molar diamagnetic susceptibility of another 360 organic compounds (test set) is 4.34 cgs. The results show that the current method is more effective than literature methods for estimating the molar diamagnetic susceptibility of an organic compound. The MLR method thus provides an acceptable model for the prediction of molar diamagnetic susceptibilities of organic compounds. Figure Plot of calculated vs experimental values of molar diamagnetic susceptibilities using the multivariate linear regression (MLR) model (Eq. 8)     

Influence of {\text{NH - }}{{\text{S}}^\gamma } bonding interactions on the structure and dynamics of metallothioneins

Mammalian metallothioneins ( \textM₇^\textIIMTs {\text{M}}_7^{\text{IIMTs}} ) show a clustered arrangement of the metal ions and a nonregular protein structure. The solution structures of Cd₃-thiolate cluster containing β-domain of mouse β-MT-1 and rat β-MT-2 show high structural similarities, but widely differing structure dynamics. Molecular dynamics simulations revealed a substantially increased number of \textNH - \textS^g {\text{NH - }}{{\text{S}}^\gamma } hydrogen bonds in β-MT-2, features likely responsible for the increased stability of the Cd₃-thiolate cluster and the enfolding protein domain. Alterations in the \textNH - \textS^g {\text{NH - }}{{\text{S}}^\gamma } hydrogen-bonding network may provide a rationale for the differences in dynamic properties encountered in the β-domains of MT-1, -2, and -3 isoforms, believed to be essential for their different biological function.     

An Annular Plasmonic Lens Under Illumination of Circularly Polarized Light

In this paper, we consider a circular central aperture surrounded with annular depth-tuned grooves and investigate the beaming effect of the structure under illumination of a circularly polarized (CP) plane wave. As a CP plane wave is equivalent to the superposition of two linearly polarized plane waves (TM and TE) with a phase difference of π/2, the superposition of the electric field intensity, ( | E_x |² + | E_y |² ) \left( {{{\left| {E_x} \right|}^2} + {{\left| {E_y} \right|}^2}} \right) , is observed in the transmission field. In addition, two plasmonic modes are found at the resonant wavelengths λ ₁ and λ ₂ with each consisting of multiple wavelengths. At the wavelength λ ₁ = 420 nm, the significant near-field collimation is formed along the direction z, having a long propagation distance up to 1.75 μm (≈4λ) away from the exit plane of the new plasmonic lens.     

Long‐term isolation of the coastal plant Calystegia soldanella (Convolvulaceae) in ancient freshwater Lake Biwa,Japan

Lake Biwa is an ancient freshwater lake that was formed approximately 4 Mya and harbours many coastal plants that commonly inhabit the seashore. We used chloroplast DNA haplotype analysis using two spacer sequences and simple sequence repeat (SSR) analysis using eight nuclear microsatellite markers to detect genomic signatures indicating long‐term isolation of inland populations of Calystegia soldanella in Lake Biwa from coastal populations. We used 348 samples from 63 populations for haplotype analysis and 478 samples from 27 populations for SSR analysis covering the inland and coastal distribution of the species. We detected seven haplotypes, and the distribution pattern of these haplotypes was geographically highly structured between Lake Biwa and the coast. Nuclear SSR analysis also supported genetic differentiation between Lake Biwa and coastal populations (analyses of molecular variance, 43%), and the grouping of Lake Biwa and coastal populations by a Neighbour‐joining tree. In addition, genetic diversity of the inland populations (mean H_E = 0.153) was significantly lower than that of coastal populations (mean H_E = 0.328). These results suggested that inland populations at Lake Biwa have been isolated from coastal populations for a very long time. The inland populations most likely experienced a bottleneck effect, resulting in sufficient in situ genetic divergence to clearly distinguish them from coastal populations. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 51–66.     

Soil temperature and biotic factors drive the seasonal variation of soil respiration in a maize (Zea mays L.) agricultural ecosystem

The diurnal and seasonal variation of soil respiration (SR) and their driving environmental factors were studied in a maize ecosystem during the growing season 2005. The diurnal variation of SR showed asymmetric patterns, with the minimum occurring around early morning and the maximum around 13:00 h. SR fluctuated greatly during the growing season. The mean SR rate was 3.16 μmol CO₂ m⁻² s⁻¹, with a maximum of 4.87 μmol CO₂ m⁻² s⁻¹ on July 28 and a minimum of 1.32 μmol CO₂ m⁻² s⁻¹ on May 4. During the diurnal variation of SR, there was a significant exponential relationship between SR and soil temperature (T) at 10 cm depth: . At a seasonal scale, the coefficient α and β fluctuated because the biomass (B) increased α, and the net primary productivity (NPP) of maize markedly increased β of the exponential equation. Based on this, we developed the equation to estimate the magnitude of SR and to simulate its temporal variation during the growth season of maize. Most of the temporal variability (93%) in SR could be explained by the variations in soil temperature, biomass and NPP of maize. This model clearly demonstrated that soil temperature, biomass and NPP of maize combined to drive the seasonal variation of SR during the growing season. However, only taking into account the influence of soil temperature on SR, an exponential equation over- or underestimated the magnitude of SR and resulted in an erroneous representation of the seasonal variation in SR. Our results highlighted the importance of biotic factors for the estimation of SR during the growing season. It is suggested that the models of SR on agricultural sites should not only take into account the influence of soil temperature, but also incorporate biotic factors as they affect SR during the growing season.     

Studies on a continuous recycle reactor for a lipase-catalysed processing of ricebran oil

The authors have developed a continuous recycle reactor which efficiently performs emulsion type enzymatic reactions. The reactor column is filled with immobilised lipase and the reactions are effected by pumping the pre-prepared oil-water emulsion through the bottom of the reactor. A part of the product was recycled back and this type of recycling greatly improves the productivity of fatty acid compared to continuous once-through reactor without recycling. The recycle reactor could be continuously run for 35 days without decrease in conversions. The performance of the reactor was interpreted by a model and the theoretical conversion was compared with the experimental data.List of Symbols F _AO mol/min feed rate - K _M g/l Michaelis constant - R recycle ratio - r ₅ mol/(ml · min) reaction rate - S ₀ g/l initial substrate concentration - V _max mol/(ml · min) maximum reaction velocity - V _R l void volume of the reactor - x _s fractional conversion - Standard deviation      

Genetic diversity,genetic drift and mixed mating system in small subpopulations of <Emphasis Type="Italic">Dyckia ibiramensis</Emphasis>, a rare endemic bromeliad from Southern Brazil

Dyckia ibiramensis is a naturally rare, endemic and threatened bromeliad which occurs naturally on 4 km of rocky river outcroppings in Southern Brazil. For this study, subpopulations of the species were characterized based on size and genetics, to compile information for in situ and ex situ conservation strategies. A census of the rosettes was undertaken for each subpopulation and seven allozyme polymorphic loci were used to estimate genetic diversity and structure of adults and offspring and assess the mating system. In general, the subpopulations were small and most of the rosettes were aggregated into clumps. The species showed a high genetic diversity ([^(H)]_e = 0.219 \hat{H}_{e} = 0.219 ) and significant fixation index ([^(f)] = 0.642, \hat{f} = 0.642, P ≤ 0.05). The estimate of differentiation among all adult subpopulations indicate pronounced genetic structure ([^(G)]^￠_ST = 0.674 \hat{G}^{\prime}_{ST} = 0.674 ). D. ibiramensis has a mixed mating system and multilocus outcrossing rates [^(t)]_m \hat{t}_{m} were variable between subpopulations. This study demonstrates the importance of in situ preservation of all subpopulations for the maintenance of species diversity. For effective ex situ conservation, it would be necessary to collect seeds from 52 to 99 seed-rosettes, depending on the target population.     

Streptomyces daliensis sp. nov. from soil

A novel actinomycete strain YIM 31724^T was isolated from a soil sample collected from Dali, Yunnan Province, People’s Republic of China. The strain is characterized by white to yellow white aerial mycelia, spiral spore chains and smooth spore surface. The cell wall of strain YIM 31724^T contained LL-diaminopimelic acid (A₂pm) and traces of meso-A₂pm. Whole-cell hydrolysates contained mainly glucose and small amounts of galactose and xylose. The menaquinones were MK-9(H₆) (31%) and MK-9(H₈) (69%). Phosphatidylethanolamine was the diagnostic phospholipid. The DNA G+C content of strain YIM 31724^T was 67.2 mol%. Phylogenetic analysis indicated that the strain belongs to the genus Streptomyces, with highest similarity to Streptomyces rimosus subsp. rimosus JCM 4667^T (rRNA gene sequence similarity value of 98.9%) and Streptomyces erumpens DSM 40941^T (rRNA gene sequence similarity value of 98.7%). Based on its phenotypic and genotypic characteristics, including low DNA–DNA hybridization results, strain is proposed as the type strain of a novel species, Streptomyces daliensis sp. nov.     

Lake Biwa and the ocean: geochemical similarity and difference

The average composition of water, bottom sediments, manganese (Mn) crusts, and Mn concretions from Lake Biwa (the largest freshwater lake in Japan) are re-examined, in conjunction with those of seawater, oceanic pelagic clay, and deep-sea Mn nodules. The purpose is to gain additional insights into the geochemical behaviors of elements in Lake Biwa and the ocean, which are quite different in ionic strength (or salinity), pH, water residence times, sediment accumulation rates, carbon fluxes to sediments, and the redox potential in sediments. Excluding a few millimeters of oxic surface sediment, there is no appreciable accumulation of Mn in the Lake Biwa bottom sediments due to reducing condition there. Consequently, other B-type cations [such as iron (Fe), gallium (Ga), copper (Cu), lead (Pb), cobalt (Co), tin (Sn), and bismuth (Bi), with subshell valence electron configuration of d ¹⁻¹⁰] are also less concentrated in the lake sediments than in the oceanic pelagic clay. In turn, B-type cations have much higher dissolved concentrations in the lake water than in the ocean. The rare earth elements (REE) mainly form organic complexes in the lake water and carbonate complexes in the ocean. REE are mostly associated with detritus aluminosilicate phases in Lake Biwa sediments but with phosphate phases in deep-sea sediments. Fe and Mn oxide phases are clearly separated in marine Mn nodules and crusts but not in Mn crusts and concretions from Lake Biwa. Useful parameters such as the enrichment factor (E _Al) and logarithms of the distribution coefficient (log K _d) of elements between solid and liquid phases were estimated in both systems for further discussions.     

Effect of temperature on growth of the cyanobacterium Aphanizomenon flos-aquae in Lake Biwa and Lake Yogo

The water bloom‐forming cyanobacterium Aphanizomenon flos‐aquae Ralfs ex Bornet et Flahault (Nos‐tocales, Cyanophyceae) appeared in Lake Biwa and Lake Yogo in 1999 for the first time. The morphological characteristics were described using natural samples. In contrast to the other water bloom‐forming cyanobacteria such as Microcystis and Anabaena in Lake Biwa and Lake Yogo, the small summer population of A. flos‐aquae is apt to grow in winter, suggesting the low temperature preference or tolerance of this species. In order to clarify the effect of temperature on the growth, culture experiments were conducted using an axenic strain isolated from Lake Biwa. The strain could grow at above 8°C with an optimum temperature ranging from 23 to 29°C, and survived even at 5°C for at least 25days under low light conditions. Although these results confirmed the ability of the bloom formation during late autumn and winter, it is still unclear why the Aphanizomenon bloom occurred at temperatures of ca 10°C in December and not immediately after the disappearance of Microcystis and/or Anabaena bloom during autumn.