Growth of Wolinella succinogenes with polysulphide as terminal acceptor of phosphorylative electron transport

Polysulphide was formed according to reaction (1), when tetrathionate was (1) $${\text{S}}_4 {\text{O}}_6^{2 - } + {\text{HS}}^ - \to 2{\text{S}}_2 {\text{O}}_3^{2 - } + {\text{S(O)}} + {\text{H}}^ + $$ added to an anaerobic buffer (pH 8.5) containing excess sulphide. S(O) denotes the zero oxidation state sulphur in the polysulphide mixture S _infn ^sup2- . The addition of formate to the polysulphide solution in the presence of Wolinella succinogenes caused the reduction of polysulphide according to reaction (2). The bacteria grew in a medium containing formate and sulphide, (2) $${\text{HCO}}_2^ - + {\text{S(O)}} + {\text{H}}2{\text{O}} \to {\text{HCO}}_3^ - + {\text{HS}}^ - + {\text{H}}^ + $$ when tetrathionate was continuously added. The cell density increased proportional to reaction (3) which represents the sum of reactions (1) and (3) $${\text{HCO}}_2^ - + {\text{S}}_{\text{4}} {\text{O}}_6^{2 - } + {\text{H}}2{\text{O}} \to {\text{HCO}}_3^ - + 2{\text{S}}_{\text{2}} {\text{O}}_3^{2 - } + 2{\text{H}}^ + $$ (2). The cell yield per mol formate was nearly the same as during growth on formate and elemental sulphur, while the velocity of growth was greater. The specific activities of polysulphide reduction by formate measured with bacteria grown with tetrathionate or with elemental sulphur were consistent with the growth parameters. The results suggest that W. succinogenes grow at the expense of formate oxidation by polysulphide and that polysulphide is an intermediate during growth on formate and elemental sulphur.     

The effects of temperature and exercise training on swimming performance in juvenile qingbo (Spinibarbus sinensis)

To investigate the effects of temperature and exercise training on swimming performance in juvenile qingbo (Spinibarbus sinensis), we measured the following: (1) the resting oxygen consumption rate $ \left( {{\dot{\text{M}}\text{O}}_{{ 2 {\text{rest}}}} } \right) $ , critical swimming speed (U _crit) and active oxygen consumption rate $ \left( {{\dot{\text{M}}\text{O}}_{{ 2 {\text{active}}}} } \right) $ of fish at acclimation temperatures of 10, 15, 20, 25 and 30 °C and (2) the $ \dot{M}{\text{O}}_{{ 2 {\text{rest}}}} $ , U _crit and $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ of both exercise-trained (exhaustive chasing training for 14 days) and control fish at both low and high acclimation temperatures (15 and 25 °C). The relationship between U _crit and temperature (T) approximately followed a bell-shaped curve as temperature increased: U _crit = 8.21/{1 + [(T ? 27.2)/17.0]²} (R ² = 0.915, P < 0.001, N = 40). The optimal temperature for maximal U _crit (8.21 BL s^?1) in juvenile qingbo was 27.2 °C. Both the $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ and the metabolic scope (MS, $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} - \dot{M}{\text{O}}_{{ 2 {\text{rest}}}} $ ) of qingbo increased with temperature from 10 to 25 °C (P < 0.05), but there were no significant differences between fish acclimated to 25 and 30 °C. The relationships between $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ or MS and temperature were described as $ {\dot{\text{M}}\text{O}}_{{ 2 {\text{active}}}} = 1,214.29/\left\{ {1 + \left[ {\left( {T - 28.8} \right)/10.6} \right]^{2} } \right\}\;\left( {R^{2} = 0.911,\;P < 0.001,\;N = 40} \right) $ and MS = 972.67/{1 + [(T ? 28.0)/9.34]²} (R ² = 0.878, P < 0.001, N = 40). The optimal temperatures for $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ and MS in juvenile qingbo were 28.8 and 28.0 °C, respectively. Exercise training resulted in significant increases in both U _crit and $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ at a low temperature (P < 0.05), but training exhibited no significant effect on either U _crit or $ \dot{M}{\text{O}}_{{ 2 {\text{active}}}} $ at a high temperature. These results suggest that exercise training had different effects on swimming performance at different temperatures. These differences may be related to changes in aerobic metabolic capability, arterial oxygen delivery, available dissolved oxygen, imbalances in ion fluxes and stimuli to remodel tissues with changes in temperature.     

Release of non-exchangeable {}^{{{\text{15}}}}{\text{NH}}^{{\text{ + }}}_{{\text{4}}} from subgrade, decomposed granite substrates and uptake by non-mycorrhizal and mycorrhizal California native annual grass, Vulpia microstachys

Release rates of recently fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ from non-exchangeable interlayer sites in 2:1 silicate minerals were determined for decomposed granite (DG) saprolites from three locations in California, USA. Recently-fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release from the DG substrate was quantified by extracting diffused $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with H-resin, as well as a native, annual grass Vulpia microstachys. The $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release data varied with via the method of extraction, which included H-resin pre-treatments (Na⁺ or H⁺) and V. microstachys uptake (mycorrhizal inoculated or uninoculated). After 6 weeks (1008 h), more $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ was recovered from fixed interlayer positions by the H-resins as compared to uptake by V. microstachys. The H⁺ treated H-resins recovered more released $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ (≈94 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{1} $ or (12%) of total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ) in two of the three DG samples as compared to the Na⁺ treated resins, (which recovered ≈70–78 mg ${\text{NH}}^{{\text{ + }}}_{{\text{4}}} - {\text{N}}\;{\text{kg}}^{{{\text{ - 1}}}} $ (or 9–10%) of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ ). The V. microstachys assimilated 8–9% of the total fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ with mycorrhizal inoculum as compared to only 2% without a mycorrhizal inoculum, over the same time period. The fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release kinetics from the H-resin experiments were most accurately described by first order and power function models, and can be characterized as biphasic using a heterogeneous diffusion model. Uptake of both the ¹⁵N and ambient, unlabelled N from the soils was closely related to plant biomass. There was no significant difference in percent of N per unit of biomass between the control and mycorrhizal treatments. The findings presented here indicate that observed, long-term $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ release rates from DG in studies utilizing resins, may overestimate the levels of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ made available to plants and microorganisms. Additionally, the study suggested that mycorrhizae facilitate the acquisition and plant uptake of fixed $ {\text{NH}}^{{\text{ + }}}_{{\text{4}}} $ , resulting in markedly increased plant biomass production.     

Retention of Dissolved Inorganic Nitrogen by Foliage and Twigs of Four Temperate Tree Species

Nitrogen (N) retention by tree canopies is believed to be an important process for tree nutrient uptake, and its quantification is a key issue in determining the impact of atmospheric N deposition on forest ecosystems. Due to dry deposition and retention by other canopy elements, the actual uptake and assimilation by the tree canopy is often obscured in throughfall studies. In this study, ¹⁵N-labeled solutions ( $ ^{15} {\text{NH}}_{4}^{ + } $ and $ ^{15} {\text{NO}}_{3}^{ - } $ ) were used to assess dissolved inorganic N retention by leaves/needles and twigs of European beech, pedunculate oak, silver birch, and Scots pine saplings. The effects of N form, tree species, leaf phenology, and applied $ {\text{NO}}_{3}^{ - } $ to $ {\text{NH}}_{4}^{ + } $ ratio on the N retention were assessed. Retention patterns were mainly determined by foliar uptake, except for Scots pine. In twigs, a small but significant ¹⁵N enrichment was detected for $ {\text{NH}}_{4}^{ + } $ , which was found to be mainly due to physicochemical adsorption to the woody plant surface. The mean $ {{^{15} {\text{NH}}_{4}^{ + } } \mathord{\left/ {\vphantom {{^{15} {\text{NH}}_{4}^{ + } } {^{15} {\text{NO}}_{3}^{ - } }}} \right. \kern-0em} {^{15} {\text{NO}}_{3}^{ - } }} $ retention ratio varied considerably among species and phenological stadia, which indicates that the use of a fixed ratio in the canopy budget model could lead to an over- or underestimation of the total N retention. In addition, throughfall water under each branch was collected and analyzed for $ ^{15} {\text{NH}}_{4}^{ + } $ , $ ^{15} {\text{NO}}_{3}^{ - } $ , and all major ions. Net throughfall of $ ^{15} {\text{NH}}_{4}^{ + } $ was, on average, 20 times higher than the actual retention of $ ^{15} {\text{NH}}_{4}^{ + } $ by the plant material. This difference in $ ^{15} {\text{NH}}_{4}^{ + } $ retention could not be attributed to pools and fluxes measured in this study. The retention of $ ^{15} {\text{NH}}_{4}^{ + } $ was correlated with the net throughfall of K⁺, Mg²⁺, Ca²⁺, and weak acids during leaf development and the fully leafed period, while no significant relationships were found for $ ^{15} {\text{NO}}_{3}^{ - } $ retention. This suggests that the main driving factors for $ {\text{NH}}_{4}^{ + } $ retention might be ion exchange processes during the start and middle of the growing season and passive diffusion at leaf senescence. Actual assimilation or abiotic uptake of N through leaves and twigs was small in this study, for example, 1–5% of the applied dissolved ¹⁵N, indicating that the impact of canopy N retention from wet deposition on forest productivity and carbon sequestration is likely limited.     

Longitudinal distribution of nitrate δ15N and δ18O in two contrasting tropical rivers: implications for instream nitrogen cycling

The longitudinal variations in the nitrogen (δ¹⁵N) and oxygen (δ¹⁸O) isotopic compositions of nitrate (NO₃ ^?), the carbon isotopic composition (δ¹³C) of dissolved inorganic carbon (DIC) and the δ¹³C and δ¹⁵N of particulate organic matter were determined in two Southeast Asian rivers contrasting in the watershed geology and land use to understand internal nitrogen cycling processes. The $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ became higher longitudinally in the freshwater reach of both rivers. The $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ also increased longitudinally in the river with a relatively steeper longitudinal gradient and a less cultivated watershed, while the $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ gradually decreased in the other river. A simple model for the $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ and the $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ that accounts for simultaneous input and removal of NO₃ ^? suggested that the dynamics of NO₃ ^? in the former river were controlled by the internal production by nitrification and the removal by denitrification, whereas that in the latter river was significantly affected by the anthropogenic NO₃ ^? loading in addition to the denitrification and/or assimilation. In the freshwater-brackish transition zone, heterotrophic activities in the river water were apparently elevated as indicated by minimal dissolved oxygen, minimal δ¹³C_DIC and maximal pCO₂. The δ¹⁵N of suspended particulate nitrogen (PN) varied in parallel to the $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ there, suggesting that the biochemical recycling processes (remineralization of PN coupled to nitrification, and assimilation of NO₃ ^?-N back to PN) played dominant roles in the instream nitrogen transformation. In the brackish zone of both rivers, the $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ displayed a declining trend while the $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ increased sharply. The redox cycling of NO₃ ^?/NO₂ ^? and/or deposition of atmospheric nitrogen oxides may have been the major controlling factor for the estuarine $ \delta^{15} {\text{N}}_{{{\text{NO}}_{3} }} $ and $ \delta^{18} {\text{O}}_{{{\text{NO}}_{3} }} $ , however, the exact mechanism behind the observed trends is currently unresolved.     

Estimation of viscosity from passage time of liquids flowing through a microchannel array

Recently, a microchannel flow analyzer (MC-FAN) has been used to study the flow properties of blood. However, the correlation between blood passage time measured by use of the MC-FAN and hemorheology has not been clarified. In this study, a simple model is proposed for estimation of liquid viscosity from the passage time t _p of liquids. The t _p data for physiological saline were well represented by the model. According to the model, the viscosity of Newtonian fluids was estimated reasonably well from the t _p data. For blood samples, although the viscosity $ \eta_{\text{mc}} $ estimated from t _p was shown to be smaller than the viscosity $ \eta_{{450{\text{s}}^{ - 1} }} $ measured by use of a rotatory viscometer at a shear rate of 450 s^?1, $ \eta_{\text{mc}} $ was correlated with $ \eta_{{450{\text{s}}^{ - 1} }} $ . An empirical equation for estimation of $ \eta_{{450{\text{s}}^{ - 1} }} $ from $ \eta_{\text{mc}} $ of blood samples is proposed.     

Long-term analysis of Hubbard Brook stable oxygen isotope ratios of streamwater and precipitation sulfate

In response to decreasing atmospheric emissions of sulfur (S) since the 1970s there has been a concomitant decrease in S deposition to watersheds in the Northeastern U.S. Previous study at the Hubbard Brook Experimental Forest, NH (USA) using chemical and isotopic analyzes ( $ \delta^{34} {\text{S}}_{{{\text{SO}}_{4} }} $ ) combined with modeling has suggested that there is an internal source of S within these watersheds that results in a net loss of S via sulfate in drainage waters. The current study expands these previous investigations by the utilization of δ¹⁸O analyzes of precipitation sulfate and streamwater sulfate. Archived stream and bulk precipitation samples at the Hubbard Brook Experimental Forest from 1968–2004 were analyzed for stable oxygen isotope ratios of sulfate ( $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ ). Overall decreasing temporal trends and seasonally low winter values of $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ in bulk precipitation are most likely attributed to similar trends in precipitation $ \delta^{18} {\text{O}}_{{{\text{H}}_{2} {\text{O}}}} $ values. Regional climate trends and changes in temperature control precipitation $ \delta^{18} {\text{O}}_{{{\text{H}}_{2} {\text{O}}}} $ values that are reflected in the $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values of precipitation. The significant relationship between ambient temperature and the $ \delta^{18} {\text{O}}_{{{\text{H}}_{2} {\text{O}}}} $ values of precipitation is shown from a nearby site in Ottawa, Ontario (Canada). Although streamwater $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values did not reveal temporal trends, a large difference between precipitation and streamwater $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values suggest the importance of internal cycling of S especially through the large organic S pool and the concomitant effect on the $ \delta^{18} {\text{O}}_{{{\text{SO}}_{4} }} $ values in drainage waters.     

Quantifying the risk of mis-estimating correlation significance of climate–tree growth relationships

In dendroecology, sampling effort has a strong influence of both regional chronology properties and climate–tree growth relationships assessment. Recent studies evidenced that decreasing sample size leads to a weakening of the bootstrapped correlation coefficients ( ${\text{BCC}}$ BCC ). The present analysis focused on the risk of mis-estimating the significance of population ${\text{BCC}}\,\left( {{\text{BCC}}_{\text{POP}} } \right)$ BCC ( BCC POP ) from a sample of N trees, and then proposed an approach to detect and correct mis-estimations using the properties of the sample. The sample size effect and the limits of the correction were illustrated from 840 individual growth chronologies of Corsican pine (Pinus nigra Arnold ssp. laricio Poiret var. Corsicana) sampled in Western France. The 840 trees were used to assess the population characteristics, and the effect of sampling effort was investigated through a simulation approach based on a resampling procedure of N trees amongst 840 (N ? [5; 50]). Our results evidenced that the risk strongly varied amongst the climatic regressors. The highest risks were evidenced for significant ${\text{BCC}}_{\text{POP}}$ BCC POP , with a percentage of mis-estimation ranging from 25 to 80. On the contrary, small samples allowed providing an reliable estimation of the significance of non-significant ${\text{BCC}}_{\text{POP}}$ BCC POP . To a lesser extent, the risk slightly decreased with increasing N, according to a negative exponential trend. The detection and correction method was found relevant to detect mis-estimation only for significant ${\text{BCC}}_{\text{POP}}$ BCC POP ; otherwise, the ${\text{BCC}}_{\text{POP}}$ BCC POP significance was generally overestimated.     

Stress fermentation strategies for the production of hyperthermostable superoxide dismutase from Thermus thermophilus HB27: effects of ions

In this study, we explored how ammonium and metal ion stresses affected the production of recombinant hyperthermostable manganese superoxide dismutase (Mn-SOD). To improve Mn-SOD production, fed-batch culture in shake flasks and bioreactor fermentation were undertaken to examine the effects of $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ feeding. Under the optimized feeding time and concentrations of $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺, the maximal SOD activity obtained from bioreactor fermentation reached some 480 U/ml, over 4 times higher than that in batch cultivation (113 U/ml), indicating a major enhancement of the concentration of Mn-SOD in the scale-up of hyperthermostable Mn-SOD production. In contrast, when the fed-batch culture with appropriate $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ feeding was carried out in the same 5-L stirred tank bioreactor, a maximal SOD concentration of some 450 U/ml was obtained, again indicating substantial increase in SOD activity as a result of $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ feeding. The isoelectric point (pI) of the sample was found to be 6.2. It was highly stable at 90 °C and circular dichroism measurements indicated a high α-helical content of 70 % as well, consistent with known SOD properties. This study indicates that $ {\text{NH}}_{ 4}^{{^{ + } }} $ and Mn²⁺ play important roles in Mn-SOD expression. Stress fermentation strategies established in this study are useful for large-scale efficient production of hyperthermostable Mn-SOD and may also be valuable for the scale-up of other extremozymes.     

Litterfall and litter nutrient dynamics under cocoa ecosystems in lowland humid Ghana

There have been few studies quantifying litterfall, standing litterstock and gross litter decomposition following forest conversion to plantation crops such as cocoa. Additionally, an assessment of changing processes occurring in forest floor litter systems with plantation age is lacking. We investigated litterfall production, standing litter changes and litter decomposition along a chronosequence of shaded cocoa farm fields (secondary forest, 3, 15 and 30-year-old) in the moist semi-deciduous forest belt in the Ashanti Region of Ghana in West Africa over 24 months. Mean annual litterfall production differed significantly among study sites and ranged from 5.0 to 10.4 Mg DM ha^?1. Similarly, standing litter differed significantly between land-use /plot ages. The results showed significant differences in quality between litter from forest and litter from cocoa plantations. Litterfall from forests had higher concentrations of nitrogen and lower concentration of soluble polyphenols and lignin compared to litter from cocoa systems. Monthly decomposition coefficients (k) estimated as $ k = {{\left( {{\text{A}} - \left( {{\text{L}}_1 - {\text{L}}_0 } \right)} \right)} \mathord{\left/ {\vphantom {{\left( {{\text{A}} - \left( {{\text{L}}_1 - {\text{L}}_0 } \right)} \right)} {\left( {{{\left( {{\text{L}}_1 + {\text{L}}_0 } \right)} \mathord{\left/ {\vphantom {{\left( {{\text{L}}_1 + {\text{L}}_0 } \right)} 2}} \right. } 2}} \right)}}} \right. } {\left( {{{\left( {{\text{L}}_1 + {\text{L}}_0 } \right)} \mathord{\left/ {\vphantom {{\left( {{\text{L}}_1 + {\text{L}}_0 } \right)} 2}} \right. } 2}} \right)}} $ , where A is litterfall production during the month, L₀ is the standing litterstock at the beginning of the month and L₁ is the standing litterstock at the end of the month. Annual decomposition coefficients (k _L ) were similar in cocoa systems (0.221–0.227) but higher under secondary forests (0.354). Correlations between litter quality parameters and the decomposition coefficient showed nitrogen and lignin concentrations as well as ratios that include nitrogen are the best predictors of decomposition for the litters studied. Our results confirm the hypothesis that decomposition decreases following forest conversion to shaded cocoa systems because of litter quality changes and that decomposition rates correlate to litter quality differences between forest and cocoa ecosystems. The study also showed that standing litter pools and litterfall production in recently converted cocoa plantations are low compared to secondary forests or mature cocoa systems. Management strategies involving the introduction of upper canopy species during plantation development with corresponding replacement of tree mortality with diverse fast growing species will provide high quality and quantity litter resources.     

Interaction of ascorbate with photosystem I

Ascorbate is one of the key participants of the antioxidant defense in plants. In this work, we have investigated the interaction of ascorbate with the chloroplast electron transport chain and isolated photosystem I (PSI), using the EPR method for monitoring the oxidized centers \( {\text{P}}_{700}^{ + } \) and ascorbate free radicals. Inhibitor analysis of the light-induced redox transients of P₇₀₀ in spinach thylakoids has demonstrated that ascorbate efficiently donates electrons to \( {\text{P}}_{ 7 0 0}^{ + } \) via plastocyanin. Inhibitors (DCMU and stigmatellin), which block electron transport between photosystem II and Pc, did not disturb the ascorbate capacity for electron donation to \( {\text{P}}_{700}^{ + } \) . Otherwise, inactivation of Pc with CN^? ions inhibited electron flow from ascorbate to \( {\text{P}}_{700}^{ + } \) . This proves that the main route of electron flow from ascorbate to \( {\text{P}}_{700}^{ + } \) runs through Pc, bypassing the plastoquinone (PQ) pool and the cytochrome b ₆ f complex. In contrast to Pc-mediated pathway, direct donation of electrons from ascorbate to \( {\text{P}}_{700}^{ + } \) is a rather slow process. Oxidized ascorbate species act as alternative oxidants for PSI, which intercept electrons directly from the terminal electron acceptors of PSI, thereby stimulating photooxidation of P₇₀₀. We investigated the interaction of ascorbate with PSI complexes isolated from the wild type cells and the MenB deletion strain of cyanobacterium Synechocystis sp. PCC 6803. In the MenB mutant, PSI contains PQ in the quinone-binding A₁-site, which can be substituted by high-potential electron carrier 2,3-dichloro-1,4-naphthoquinone (Cl₂NQ). In PSI from the MenB mutant with Cl₂NQ in the A₁-site, the outflow of electrons from PSI is impeded due to the uphill electron transfer from A₁ to the iron-sulfur cluster F_X and further to the terminal clusters F_A/F_B, which manifests itself as a decrease in a steady-state level of \( {\text{P}}_{700}^{ + } \) . The addition of ascorbate promoted photooxidation of P₇₀₀ due to stimulation of electron outflow from PSI to oxidized ascorbate species. Thus, accepting electrons from PSI and donating them to \( {\text{P}}_{700}^{ + } \) , ascorbate can mediate cyclic electron transport around PSI. The physiological significance of ascorbate-mediated electron transport is discussed.     

Theoretical study of the reaction of CH2XO (X = F, Cl, Br) radicals with the NO radical

In this paper, we focus on the multiple-channel reactions of CH₂XO (X = F, Cl, Br) radicals with the NO radical by means of direct dynamic methods. All structures of the stationary points were obtained at the MP2/6-311+G(d,p) level and vibrational frequency analysis was also performed at this level of theory. The minimum energy path (MEP) was obtained via the intrinsic reaction coordinate (IRC) theory at the MP2/6-311+G(d,p) level, and higher-level energetic information was refined by the MC-QCISD method. The rate constants for the three hydrogen abstraction reaction channels over the temperature range 200–1,500 K were calculated by the improved canonical variational transition state theory (ICVT) with a correction for small-curvature tunneling (SCT). The rate constants calculated in this manner were in good agreement with the available experimental data, and the three-parameter rate–temperature formulae for the temperature range 200–1,500 K were $ {k_{1{\text{a}} }}(T)=0.32\times {10^{-18 }}{T^{1.83 }}\exp \left( {1748.54/T} \right) $ , $ {k_{2{\text{a}} }}(T)=0.22\times {10^{-19 }}{T^{2.19 }}\exp \left( {1770.19/T} \right) $ , $ {k_{3{\text{a}} }}(T)=0.88\times {10^{-20 }}{T^{2.20 }}\exp \left( {1513.82/T} \right) $ (in units of cm³ molecule^?1?s^?1).     

Can the positive aromatic ring be as ��-electron donor in ��-halogen bond? A MP2 theoretical investigation on the unusual ��-halogen bond interaction between three-membered ring \left( {\hbox{BNN}} \right)_3^{+} and X1X2 (X1, X2?=?F, Cl, Br)

The unusual ??-halogen bond interactions are investigated between $ \left( {\hbox{BNN}} \right)_3^{+} $ and X1X2 (X1, X2?=?F, Cl, Br) employing MP2 at 6-311?+?G(2d) and aug-cc-pVDZ levels according to the ??CP (counterpoise) corrected potential energy surface (PES)?? method. The order of the ??-halogen bond interactions and stabilities of the complexes are obtained to be $ \left( {\hbox{BNN}} \right)_3^{+} \ldots {{\hbox{F}}_2} < \left( {\hbox{BNN}} \right)_3^{+} \ldots {\hbox{ClF < }}\left( {\hbox{BNN}} \right)_3^{+} \ldots {\hbox{C}}{{\hbox{l}}_2} < \left( {\hbox{BNN}} \right)_3^{+} \ldots {\hbox{BrCl}}\quad { < }\quad \left( {\hbox{BNN}} \right)_3^{+} \ldots {\hbox{B}}{{\hbox{r}}_2}\quad { < }\quad \left( {\hbox{BNN}} \right)_3^{+} \ldots {\hbox{BrF}}{.} $ at MP2/aug-cc-pVDZ level. The analyses of the Mulliken charge transfer, natural bond orbital (NBO), atoms in molecules (AIM) theory and electron density shifts reveal that the nature of the ??-halogen bond interaction in the complexes of ClF, BrF and BrCl might partly be charge transfer from the delocalized ??-HOMO orbital of $ \left( {\hbox{BNN}} \right)_3^{+} $ to X1X2. This result suggests that the positive aromatic ring $ \left( {\hbox{BNN}} \right)_3^{+} $ might act as a ??-electron donor to form the ??-halogen bond.

Relative CO2/NH3 Permeabilities of Human RhAG, RhBG and RhCG

Mammalian glycosylated rhesus (Rh) proteins include the erythroid RhAG and the nonerythroid RhBG and RhCG. RhBG and RhCG are expressed in multiple tissues, including hepatocytes and the collecting duct (CD) of the kidney. Here, we expressed human RhAG, RhBG and RhCG in Xenopus oocytes (vs. H₂O-injected control oocytes) and used microelectrodes to monitor the maximum transient change in surface pH (ΔpH_S) caused by exposing the same oocyte to 5 % CO₂/33 mM HCO₃ ^? (an increase) or 0.5 mM NH₃/NH₄ ⁺ (a decrease). Subtracting the respective values for day-matched, H₂O-injected control oocytes yielded channel-specific values (*). $({\Updelta {\text{pH}}_{\text{S}}^{*} })_{{{\text{CO}}_{ 2} }}$ and $({ - \Updelta {\text{pH}}_{\text{S}}^{*} })_{{{\text{NH}}_{ 3} }}$ were each significantly >0 for all channels, indicating that RhBG and RhCG—like RhAG—can carry CO₂ and NH₃. We also investigated the role of a conserved aspartate residue, which was reported to inhibit NH₃ transport. However, surface biotinylation experiments indicate the mutants RhBG_D178N and RhCG_D177N have at most a very low abundance in the oocyte plasma membrane. We demonstrate for the first time that RhBG and RhCG—like RhAG—have significant CO₂ permeability, and we confirm that RhAG, RhBG and RhCG all have significant NH₃ permeability. However, as evidenced by $({\Updelta {\text{pH}}_{\text{S}}^{*} })_{{{\text{CO}}_{ 2} }} /({ - \Updelta {\text{pH}}_{\text{S}}^{*} })_{{{\text{NH}}_{ 3} }}$ values, we could not distinguish among the CO₂/NH₃ permeability ratios for RhAG, RhBG and RhCG. Finally, we propose a mechanism whereby RhBG and RhCG contribute to acid secretion in the CD by enhancing the transport of not only NH₃ but also CO₂ across the membranes of CD cells.     

On the page number of RNA secondary structures with pseudoknots

Let ${\mathcal {S}}$ denote the set of (possibly noncanonical) base pairs {i, j} of an RNA tertiary structure; i.e. ${\{i, j\} \in \mathcal {S}}$ if there is a hydrogen bond between the ith and jth nucleotide. The page number of ${\mathcal {S}}$ , denoted ${\pi(\mathcal {S})}$ , is the minimum number k such that ${\mathcal {S}}$ can be decomposed into a disjoint union of k secondary structures. Here, we show that computing the page number is NP-complete; we describe an exact computation of page number, using constraint programming, and determine the page number of a collection of RNA tertiary structures, for which the topological genus is known. We describe an approximation algorithm from which it follows that ${\omega(\mathcal {S}) \leq \pi(\mathcal {S}) \leq \omega(\mathcal {S}) \cdot \log n}$ , where the clique number of ${\mathcal {S}, \omega(\mathcal {S})}$ , denotes the maximum number of base pairs that pairwise cross each other.     

Phosphoenolpyruvate synthetase inMethanobacterium thermoautotrophicum

The thermophilic autotrophMethanobacterium thermoautotrophicum assimilates CO₂ via a novel pathway rather than via the Calvin cycle. The central intermediate of this pathway is acetyl CoA which is reductively carboxylated to pyruvate. Cell extracts of the organism contained phosphoenolpyruvate synthetase with a specific activity of 100 nmol min^-1 mg^-1 protein (65°C). Pyruvate kinase and pyruvate, phosphate dikinase were not detected. Phosphoenolpyruvate synthetase was partially purified (50-fold) and the following reaction stoichiometry was established: $${\text{Pyruvate + ATP + H}}_{\text{2}} {\text{O }} \to {\text{ Phosphoenolpyruvate + AMP + P}}_{\text{i}} $$ The enzyme activity was depedent on free Mg²⁺ ions, NH ₄ ⁺ or K⁺ ions, and SH-groups. Mn²⁺, but not Ca²⁺, could partially substitute for Mg²⁺; Na⁺ could not substitute for K⁺ or NH ₄ ⁺ . The pH-optima,V _max-values and the apparentK _M-values for the substrates of the enzyme in both directions were determined. Thermodynamic, kinetic and regulatory features indicate that, in vivo, the enzyme functions in the direction of phosphoenolpyruvate synthesis from pyruvate. Not only is the synthesis of phosphoenolpyruvate via the PEP synthetase reaction energetically favorable; the enzyme also catalyzed this synthesis 100 times faster than the reverse reaction, the apparentK _M value for pyruvate (40 μM) being low and the apparentK _M value for phosphate (100 mM) being high. Furthermore, AMP, ADP, PP and α-ketoglutarate were inhibitors of PEP synthesis, indicating that the enzyme activity may be controlled in vivo. The role of phosphoenolpyruvate synthetase in autotrophic CO₂ assimilation pathway ofMethanobacterium, as expected from previous labelling studies, is confirmed.     

Dynamical systems under constant organization I. Topological analysis of a family of non-linear differential equations —A model for catalytic hypercycles

The paper presents a qualitative analysis of the following systems ofn differential equations: \(\dot x_i = x_i x_j - x_i \sum\nolimits_r^n { = 1} x_r x_s {\mathbf{ }}(j = i - 1 + n\delta _{i1} {\mathbf{ }}and{\mathbf{ }}s = r - 1 + n\delta _{r1} )\) , which show cyclic symmetry. These dynamical systems are of particular interest in the theory of selforganization and biological evolution as well as for application to other fields.     

Age structure, growth and mortality estimates of an endemic Ptychobarbus dipogon (Regan, 1905) (Cyprinidae: Schizothoracinae) in the Lhasa River, Tibet

Ptychobarbus dipogon is an endemic fish in the Yarlung Tsangpo River, but its biology is poorly known. We sampled 582 specimens (total length, TL, between 70.6 and 593.0 mm) from April 2004 to August 2006 in the Lhasa River, Tibet. We estimated ages based on the counts of alternating opaque and translucent zones (annuli) in thin transverse sections of lapilli otoliths. Ages ranged from 1⁺ to 23⁺ years for males and 1⁺ to 44⁺ for females. The observed 44⁺ years was the oldest reported for schizothoracine fishes. Females attained a larger size than males. The TL–weight relationship was W?=?7.12?×?10^?6 TL ^3.006 for combined sexes. The growth parameters fitted von Bertalanffy growth functions were $L_\infty = 598.66\,{\text{mm}}$ , k?=?0.0898 year^?1, t ₀?=??0.7261 year and $W_\infty = 1585.38\;{\text{g}}$ for females and $L_\infty = 494.23{\text{ mm}}$ , k?=?0.1197 year^?1, t ₀?=??0.7296 year and $W_\infty = 904.88{\text{ g}}$ for males. The longevities of 32.7 year for females and 24.3 year for males were similar to the observed ages. Using an empirical model we estimated the instantaneous rate of total mortality (Z) at 0.28 per year in the lower reaches. Z in the upper and middle stocks was close to the M because of unexploited or lightly exploited stock. Protracted longevity, slow growth, low natural mortality and large body size were typical characteristics of P. dipogon. The current declining trend of P. dipogon could be prevented by altering fishing regulations.