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.     

Times to exhaustion at 100% of velocity at [(V)\dot]\textO\text2 \dot V{\text{O}}_{\text{2}} max and modelling of the time-limit / velocity relationship in elite long-distance runners

The aim of this study was to measure running times to exhaustion (Tlim) on a treadmill at 100% of the minimum velocity which elicits _{max max} in 38 elite male long - distance runners _max = 71.4 ± 5.5 ml.kg^–1.min^–1 and _max = 21.8 ± 1.2 km.h^–1). The lactate threshold (LT) was defined as a starting point of accelerated lactate accumulation around 4 mM and was expressed in _max. Tlim value was negatively correlated with _max (r = -0.362, p< 0.05) and _max (r = –0.347, p< 0.05) but positively with LT (%v _max) (r = 0.378, p < 0.05). These data demonstrate that running time to exhaustion at _max in a homogeneous group of elite male long-distance runners was inversely related to _max and experimentally illustrates the model of Monod and Scherrer regarding the time limit-velocity relationship adapted from local exercise for running by Hughson et al. (1984) .     

Effects of common soil anions and pH on the uptake and accumulation of perchlorate in lettuce

A mechanistic understanding of perchlorate () entry into plants is important for establishing the human health risk associated with consumption of contaminated produce and for assessing the effectiveness of phytoremediation. To determine whether common soil anions affect uptake and accumulation in higher plants, a series of competition experiments using lettuce (Lactuca sativa L.) were conducted between (50 nM) and (4–12 mM), (1–10 mM), or Cl⁻ (5–15 mM) in hydroponic solution. The effects of (0–5 mM) and pH (5.5–7.5) on uptake were also examined. Increasing in solution significantly reduced the amount of taken up by green leaf, butter head, and crisphead lettuces. Sulfate and Cl⁻ had no significant effects on uptake in lettuce over the concentrations tested. Increasing pH significantly reduced the amount of taken up by crisphead and green leaf lettuces, whereas increasing significantly reduced uptake in butter head lettuce. The inhibition by across all lettuce genotypes suggests that may share an ion carrier with , and the decrease in uptake with increasing pH or provides macroscopic evidence for cotransport across the plasma membrane.     

Chronic nitrate additions dramatically increase the export of carbon and nitrogen from northern hardwood ecosystems

A long-term field experiment was initiated to simulate chronic atmospheric N deposition, a widespread phenomenon in industrial regions of the world. Eight years of experimental nitrate ( ) additions (3 g -N m^–2 per year) to four different northern hardwood forests located along a 500 km geographic gradient dramatically increased leaching losses of -N, dissolved organic carbon (DOC), and dissolved organic nitrogen (DON). During the last two water years, the average increase in solution -N and DON leaching from the -amended plots was 2.2 g N m^–2, equivalent to 72% of the annual experimental N addition. Results indicate that atmospheric N deposition may rapidly saturate some northern hardwood ecosystems across an entire biome in the upper Great Lakes Region of the USA. Changes in soil C and N cycling induced by chronic N deposition have the potential in this landscape to significantly alter the flux of DOC and DON from upland to aquatic ecosystems. Michigan Gradient study site characteristics are similar to those of European forests most susceptible to N saturation.     

A method for the destruction and analysis of biogenic silicon in two Antarctic diatom species:<Emphasis Type="Italic"> Thalassiosira</Emphasis> sp. and<Emphasis Type="Italic"> Chaetoceros brevis</Emphasis>

Diatoms in the Southern Ocean are limited by iron and light, and therefore produce little biomass. Sufficient biomass for analysis under these conditions requires large sample volumes, and diatom samples are therefore often pre-concentrated on a filter. A method for the digestion of diatom cells on polycarbonate filters, that is also suitable for trace metal analysis, is described here. Additional analysis by inductively coupled plasma-optical emission spectroscopy (ICP-OES) is used for the determination of biogenic silicon. Although several procedures were tested, the method of Hauptkorn et al., which uses tetramethylammonium hydroxide for the destruction of silicon is adapted here [Hauptkorn et al. (2001) Fres J Anal Chem 370:246–250]. Additional nitric acid is added to destroy the polycarbonate filters. The described method results in clear digests and a good correlation between cell numbers and silicon content. Using this procedure, the cellular silicon content for Chaetoceros brevis was determined as 86 ± 4 fmol cell⁻¹. For Thalassiosira sp. a sensitivity effect was observed, and silicon content was determined as . The obtained cellular silicon contents are in good agreement with values presented in the literature.     

Phy-X/ZeXTRa: a software for robust calculation of effective atomic numbers for photon,electron, proton,alpha particle,and carbon ion interactions

The purpose of the present work is robust calculation of effective atomic numbers ($${Z}_{\text{eff}}$$s) for photon, electron, proton, alpha particle and carbon ion interactions through the newly developed software, Phy-X/ZeXTRa (Zeff of materials for X-Type Radiation attenuation). A pool of total mass attenuation and energy absorption coefficients (for photons) and total mass stopping powers (for charged particles) for elements was constructed first. Then, a matrix of interaction cross sections for elements Z = 1–92 was constructed. Finally, effective atomic numbers were calculated for any material by interpolating adjacent cross sections through a linear logarithmic interpolation formula. The results for $${Z}_{\text{eff}}$$ for photon interaction were compared with those calculated through Mayneord’s formula, which suggests a single-valued $${Z}_{\text{eff}}$$ for any material for low-energy photons for which photoelectric absorption is the dominant interaction process. The single-valued $${Z}_{\text{eff}}$$ was found to agree well with that obtained by other methods, in the low-energy region. In addition, $${Z}_{\text{eff}}$$ values of various materials of biological interest were compared with those obtained experimentally at 59.54 keV. In general, the agreement between values calculated with Phy-X/ZeXTRa and Auto-Zeff and those measured were satisfactory. A comparison of $${Z}_{\text{eff}}$$ values for photon energy absorption calculated with Phy-X/ZeXTRa and literature values for a nucleotide base, adenine, was made, and the relative difference (RD) in $${Z}_{\text{eff}}$$ between Phy-X/ZeXTRa and literature values was found to be 2% < RD < 11%, at low photon energies (1–100 keV), while it was less than 1% at energies higher than 100 keV. Highest $${Z}_{\text{eff}}$$ values were observed at low photon energies, where photoelectric absorption dominates photon interaction. For electrons, corresponding RD(%) values in $${Z}_{\text{eff}}$$ were found to be in the range 0.4 ≤ RD(%) ≤ 1.7, while for heavy charged particle interactions it was 2.4 ≤ RD(%) ≤ 4.2 for total proton interaction and 0 ≤ RD(%) ≤ 8 for total alpha particle interaction. In view of the importance of $${Z}_{\text{eff}}$$ for identifying and differentiating tissues in diagnostic imaging as well as for estimating accurate dose in radiotherapy and particle-beam therapy, Phy-X/ZeXTRa could be used for fast and accurate calculation of $${Z}_{\text{eff}}$$ in a wide energy range for both photon and charged particle (electrons, protons, alpha particles and C ions) interactions.     

Energy requirements of Adélie penguin (Pygoscelis adeliae) chicks

Summary The energy requirements of Adélie penguin (Pygoscelis adeliae) chicks were analysed with respect to body mass (W, 0.145–3.35 kg, n=36) and various forms of activity (lying, standing, minor activity, locomotion, walking on a treadmill). Direct respirometry was used to measure O₂ consumption ( ) and CO₂ production. Heart rate (HR, bpm) was recorded from the ECG obtained by both externally attached electrodes and implantable HR-transmitters. The parameters measured were not affected by hand-rearing of the chicks or by implanting transmitters. HR measured in the laboratory and in the field were comparable. Oxygen uptake ranged from in lying chicks to at maximal activity, RQ=0.76. Metabolic rate in small wild chicks (0.14–0.38 kg) was not affected by time of day, nor was their feeding frequency in the colony (Dec 20–21). Regressions of HR on were highly significant (p< 0.0001) in transmitter implanted chicks (n=4), and two relationships are proposed for the pooled data, one for minor activities ( ), and one for walking ( ). Oxygen consumption, mass of the chick (2–3 kg), and duration of walking (T, s) were related as , whereas mass-specific O₂ consumption was related to walking speed (S, m·s^-1) as .Abbreviations bpm beats per minute - D distance walked (m) - ECG electrocardiogram - HR heart rate (bpm) - ns number of steps - RQ respiratory quotient - S walking speed (m·s^-1) - T time walked (s) - W body mass (kg)     

Determination of heteronuclear three-bond J-coupling constants in peptides by a simple heteronuclear relayed E.COSY experiment

Summary A simple heteronuclear relayed E.COSY pulse sequence with a minimum number of pulses is proposed for the quantitative determination of heteronuclear three-bond J-coupling constants in uniformly ¹³C-enriched polypeptide samples. Numerous heteronuclear three-bond coupling constants, including , , , and , can be determined for each residue from a single heteronuclear relayed E.COSY spectrum. Couplings relevant for stereospecific assignments as well as for the determination of dihedral angles in the amino acid backbone and in side chains are obtained. The method is demonstrated on the uniformly ¹³C-enriched decapeptide antamanide (-Val¹-Pro²-Pro³-Ala⁴-Phe⁵-Phe⁶-Pro⁷-Pro⁸-Phe⁹-Phe¹⁰-).     

High groundwater nitrate concentrations inhibit eutrophication of sulphate-rich freshwater wetlands

During the last 60 years, pollution of the groundwater with has greatly increased in many parts of Europe, as a consequence of excessive use of manure and synthetic fertilisers. Monitoring of groundwater-fed wetlands indicated that sediments with high concentrations had the lowest Fe and concentrations in the pore water. A comparison of two restored open water fens, differing in supply via the groundwater, indicated that the redox potential and the sulphate ( ) reduction rate were lower when the groundwater contained not only but also high concentrations. The lower reduction rates in the -rich open water fen were associated with lower concentrations and the presence of plant species characteristic of clear water. In contrast, the higher reduction rates in the -poor open water fen were associated with very high concentrations and massive development of plant species characteristic of eutrophic environments. Investigations at -rich seepage sites in black alder carrs, showed that high concentrations in the pore water caused chlorosis in the alder carr vegetation, due to lower availability of Fe in the pore water and less Fe uptake by the plants. Experimental desiccation of sediments proved that the -rich seepage sites contained no oxidisable FeS _x , contrary to -poor locations, which became acidified and mobilised extremely high amounts of due to FeS _x oxidation. A laboratory experiment showed that addition to sediments led to reduced releases of Fe, and S^2–, very likely due to the oxidation of reduced Fe and S compounds. Overall, the results confirmed that is an energetically more favourable electron acceptor in anaerobic sediments than Fe and , and that high loads function as a redox buffer, preventing reduction of Fe and . Limited reduction prevents S^2– -mediated mobilisation of from Fe- complexes. At a higher redox potential, reduced Fe, including FeS _x , was oxidised, increasing the content of Fe(III) capable of binding . This prevented increased availability and the concomitant massive development of plant species characteristic of eutrophic environments.     

Factors characterizing phosphate oxygen isotope ratios in river water: an inter-watershed comparison approach

Limnology - We compared the oxygen isotope ratio of dissolved phosphate $$\left( {\delta^{{{18}}} {\text{O}}_{{{\text{PO}}_{{4}} }} } \right)$$ in two rivers with different land-cover and...     

The mechanism and kinetics of decomposition of 5-aminotetrazole

The pathway and ab initio direct kinetics of the decomposition 5-aminotetrazole (5-ATZ) to HN₃ and NH₂CN was investigated. Reactant, products and transition state were optimized with MP2 and B3LYP methods using 6–311G** and aug-cc-pVDZ basis sets. The intrinsic reaction coordinate curve of the reaction was calculated using the MP2 method with 6–311G** basis set. The energies were refined using CCSD(T)/6–311G**. Rate constants were evaluated by conventional transition-state theory (CVT) and canonical variational transition-state theory (TST), with tunneling effect over 300 to 2,500 K. The results indicated that the tunneling effect and the variational effect are small for the calculated rate constants. The fitted three-parameter expression calculated using the CVT and TST methods are and , respectively. Figure The mechanism of the decomposition process of 5-ATZ to HN₃ and NH₂CN     

Bioaccumulation of Heavy Metals by Green Algae

The biosorption of metal ions (Cr⁺³, , Cu⁺², and Ni⁺²) on two algal blooms (designated HD-103 and HD-104) collected locally was investigated as a function of the initial metal ion concentration. The main constituent of HD-103 is Cladophora sp., while Spirulina sp. is present significantly in the bloom HD-104. Algal biomass HD-103 exhibited the highest Cu⁺² uptake capacity (819 mg/g). This bloom adsorbed Ni⁺² (504 mg/g), Cr⁺³ (347 mg/g), and (168 mg/g). Maximum of Ni⁺² (1108 mg/g) is taken by HD-104. This species takes up 306, 202, and 576 mg/g Cr⁺³, , and Cu⁺², respectively. Equilibrium data fit very well to both the Langmuir and the Freundlich isotherm models. The sorption process followed the Freundlich model better. Pseudo-first-order kinetic model could describe the kinetic data. Infrared (IR) spectroscopic data were employed to identify the site(s) of bonding. It was found that phosphate and peptide moieties participate in the metal uptake by bloom HD-103. In the case of bloom HD-104, carboxylate and phosphate are responsible for the metal uptake. The role of protein in metal uptake by HD-103 was investigated using polyacrylamide gel electrophoresis.     

Growth yields and saturation constant of Desulfovibrio vulgaris in chemostat culture

Desulfovibrio vulgaris (strain Marburg) was grown on H₂ and sulfate as sole energy source in a chemostat limited by the sulfate supply. The biomass concentration and the sulfate concentration in the culture were determined as a function of the dilution rate. From the data a K _S (saturation constant) for sulfate of 10 M, a _max of 0.23 h^–1, and a of 13 g/mol were calculated. The organism was also grown in chemostat culture on H₂ and sulfite, H₂ and thiosulfate, and pyruvate (without sulfate). was found to be 35 g/mol, 36 g/mol, and Y _pyr ^max 10 g/mol. The growth yields are discussed with respect to ATP gains in dissimilatory sulfate reduction.     

Larmor frequency selective model free analysis of protein NMR relaxation

Summary The Lipari-Szabo dynamical formalism is extended by setting the time constants of the Lorentzian terms to and . This analysis is compared to the earlier proposed three-parameter extended model free formalism with regard to the range of equivalence and the advantages of the simplified two-parameter (S _inff ^sup2 ,S _infH ^sup2 ) and (S _inff ^sup2 ,S _infN ^sup2 ) representations. Spectral density components are calculated and compared to those obtained from the spectral density analysis formalism. Protein relaxation data, commonly analyzed in terms of the two-parameter representation, may correspond to a dynamically heterogeneous behaviour that is more appropriately represented in terms of a fast limit order parameter and a second, lower frequency order parameter.     

Long-term changes in nutrient concentrations of the Changjiang River and principal tributaries

We present long-term nutrient data on the Changjiang River (Yangtze River) at six hydrological stations and eight principal tributaries during the period 1958–1985. Three patterns of temporal changes were observed in nitrate and nitrite : minimal variations in the upper catchment area, rapid increases in the middle watershed towards the end of the 1970s, and a gradual increase in the lower drainage basin. Prior to the 1970s, the level of throughout the Changjiang River system remained fairly constant. In the 1980s, however, this changed, with the lowest values in the upper Changjiang changing rapidly to the highest in the middle reaches and then declining slowly but steadily in the lower courses. Compared to and ammonium and soluble reactive phosphorus (SRP) showed smaller increases or no long-term variations, while dissolved silica (DSi) concentration generally decreased at most stations. These three patterns of and changes in the Changjiang River system were reflective of the difference in chemical fertilizer use and landscape features (e.g., slope, soil type and water body area) of the drainage basins of the primary tributaries. The decreases in DSi were most likely attributed to a reduction in suspended sediment loading due to dam constructions and increasing diatom consumption. The increase in and with a reduction in DSi concentrations in the Changjiang River could have significant effects on the stoichiometric balance of nutrients delivered to the East China Sea and the ecosystem in this dynamic region.     

Secondary production,calcification and CO<Subscript>2</Subscript> fluxes in the cirripedes <Emphasis Type="Italic">Chthamalus montagui</Emphasis> and <Emphasis Type="Italic">Elminius modestus</Emphasis>

Calcification, a process common to numerous marine taxa, has traditionally been considered to be a significant source of CO₂ in tropical waters only. A number of relatively recent studies, however, have shown that significant amounts of CO₂ are also produced in temperate waters, although none of these studies was carried out on rocky shores, which are considered to be very productive systems. We compared the CO₂ fluxes due to respiration and calcification in two temperate species, the cirripedes Chthamalus montagui and Elminius modestus. The population dynamics of both species were estimated at two sites during a 1-year experimental period in order to establish mean organic (ash-free dry weight) and CaCO₃ (dry shell weight) production. Based on these parameters, we estimated the CO₂ fluxes due to respiration and calcification. CaCO₃ production was estimated to be 481.0 and at each site, representing 3.4 and respectively, of released CO₂. These fluxes represent each 47% of the CO₂ released as a result of respiration and calcification. The production of CaCO₃ at the high-density site was: (1) among the highest values obtained for temperate organisms, and (2) comparable to the estimated CO₂ fluxes for coral reefs. As calcifying organisms are well represented in temperate ecosystems in terms of both density and biomass, our results provide clear evidence that calcification of temperate organisms should not be underestimated. Additional studies on other rocky shore taxa are needed before the relative importance of calcification in rocky intertidal carbon budgets can be generalized.     

Minimal Functional Unit of Lactate Dehydrogenase

The tetrameric heart isozyme of lactate dehydrogenase (H₄) is modified by p-chloromercuribenzoate (PCMB) to produce the inactive tetramer and then hybridized with native tetrameric muscle isozyme (M₄). The hybrid mixture was isolated by polyacrylamide gel electrophoresis (PAGE) and then stained for enzyme activity and with Coomassie brilliant blue. Only three bands were found on the gels in either case. The hybrid enzymes as isolated by PAGE have half the specific activity of the native muscle enzyme. The electrophoresis properties of HM₃ are very similar to those of HM₃, while the electrophoresis properties of are very similar to those of H₂M₂. The above results strongly suggest that the tetramer having enzymatic activity contains at least two native subunits, and the di-subunit in the tetrameric enzyme is the minimal functional unit.     

Nitrate reductase in needles,roots and trunk wood of spruce trees [Picea abies (L.) Karst.]

Summary Nitrate reductase (EC 1.6.6.2) activity (NRA), as measured by an in vivo assay, is present in needle leaves and mycorrhizal fine root tips of adult Norway spruce [Picea abies (L.) Karst.] in at least equal amounts on a fresh weight basis, in both adult and 5-year-old trees. NRA could also be demonstrated in trunk wood of deroted trees after fertilization with 5 mM , exhibiting a longitudinal profile in the trunk. Inducibility in needles can more efficiently be achieved by NO₂ (100 g·m^-3) than by 5 mM nitrate, which is effective only in root-amputated trees. A remarkably high level of needle-NRA in unfertilized trees, which are characterized by a very low level of nitrate in the xylem sap, suggests that NRA in spruce needles may in part be constitutive. Organic-N is a major nitrogen source for the needles even in root-amputated trees, indicating pronounced exchange processes between ray parenchyma and trunk xylem, which in turn are modified by the nitrogen source fed to the trunk stump. Intact trees exhibit a very similar amino acid composition of the xylem sap, regardless of whether or has been fed. The amino acid pattern of the needles is not thrown out of balance by flooding with and , which occurs in fertilized derooted trees. This indicates a distinct potential for homoeostasis of nitrogen entrance-metabolism (i.e. NRA and glutamine synthetase activity) in the needles. In the ectomycorrhiza/fine root-system (EMC), marked differences in NRA were observed depending on root-tip diameter and along the longitudinal profile of the fine roots. EMC-nitrate reductase is strongly enhanced by . Needle-NRA exhibits a circannual rhythm. An early summer maximum is followed by a December minimum. This activity pattern matches well the transitory increase of soluble nitrogen in spring and the total protein maximum in winter. In an indirect way assimilatory NRA may well contribute to nitrogen overfertilization (by consumption of NO_X) as one possible cause of the contemporary decline of spruce populations.     

(H)NCAHA and (H)CANNH experiments for the determination of vicinal coupling constants related to the ϕ-torsion angle

Summary A set of three-dimensional triple-resonance experiments is described which provide , , and coupling constants. The pulse sequences generate E.COSY-like multiplet patterns and comprise a magnetization transfer from the amide proton to the α-proton or vice versa via the directly bound heteronuclei. For residues with the ¹H^α spin resonating close to the H₂O signal, a modified HNCA experiment can be employed to measure the vicinal ¹H^N,¹H^α couplings. Ambiguities associated with the conversion of values into ϕ-angle constraints for protein structure determination can be resolved with the knowledge of the heteronuclear ³J-couplings. In favourable cases, stereospecific assignments of glycine α-protons can be obtained by employing the experiments described here in combination with NOE data. The methods are applied to flavodoxin from Desulfovibrio vulgaris.