Thermodynamics and kinetics of the helix-coil transition of oligomers containing GC base pairs

Absorbance-temperature profiles have been determined for the following self-complementary oligonucleotides or equimolar paris of complementary oligonucleotides containing GC base pairs: A₂GCU₂, A₃GCU₃, A₄GCU₄, A₆CG + CGU₆, A₈CG + CGU₈, A₄G₂ + C₂U₄, A₅G₂ + C₂U₅, A₄G₃ + C₃U₄, and A₅G₃ + C₃U₅. In all cases cooperative melting transitions indicate double-helix formation. As was found previously, the stability of GC containing oligomer helices is much higher than that of AU helices of corresponding length. Moreover, helices with the same length and base composition but different sequences also have quite different stabilites. The melting curves were andlyzed using a zipper model and the thermodynamic parameters for the AU pairs determined previously. The effect of single-strand stacking was considered separately. According to this model, the formation of a GC pair from unstacked single strands is associated with an ethalpy change of ?15 kcal/mole. Due to the high degree of single-strand stacking at room temperature the enthalpy change for the formation of GC pairs from unstacked single strands is only ?5 to ?6 kcal/mole. (The corresponding parameters for AU pairs are ?10.7 kcal/mole and ?5 to ?6 kcal/mole.) The sequence dependence of helix stability seems to be primarily entropic since no differences in ΔH were seen among the sequence isomers. The kinetics of helix formation was investigated for the same molecules using the temperature jump technique. Recombination of strands is second order with rate constants in the range of 10⁵ to 10⁷M^?1 sec^?1 depending on the chain length and the nucleotide sequence. Within a series of oligomers of a given type, the rates of recombination decrease with increasing chain length. Oligomers with the sequence A_nGCU_n recombine six to eight times slower than the other oligomers of corresponding chain length. The experimental enthalpies of activation of 6 to 9 kcal/mole suggest a nucleation length of one or two GC base pairs. The helix dissociation process has rate constants between 0.5 and 500 sec^?1 and enthalpies of activation of 25 to 50 kcal/mole. An increase of chain length within a given nucleotide series leads to decreased rates of dissociation and increased enthalpies of activation. An investigation of the effect of ionic strength on A_nGCU_n helix formation showed that the rates of recombination increase considerably with increased ionic strength.     

Static and dynamic properties of mid-size liquid n- alkanes,C12∼C400: a molecular dynamics simulation study

ABSTRACT

In this paper, we have extended our previous study of the static and dynamic properties (self-diffusion coefficient D_self and friction coefficient ζ) of liquid n-alkane systems up C₄₀₀ at several temperatures (～2300?K) using molecular dynamics (MD) simulations in the canonical ensembles. For the small n-alkanes with n?≤?120 (n: the chain length), the chains are clearly ?R² _ee?/6?R² _g? ≥ 1 (1.06 ～ 1.44), which leads to the conclusion that the liquid n-alkanes are far away from the ideal chain regime. But for the n-alkanes of n?≥?160, the chains are ?R² _ee?/6?R² _g? ≈ 1, indicating that they are Gaussian. It is found that the long chains of these n-alkanes at high temperatures show abnormalities in density and friction coefficient. We observed a clear transition in the power law dependence of n-alkane self-diffusion coefficient on the molecular weight (M) of n-alkane, D_self ～ M^?γ, occurs in the range C₁₂₀～C₁₆₀ at temperatures of 318, and 618?K, corresponding to a crossover from the ‘oligomer’ to the ‘Rouse’ regime. The entanglement lengths (N_e) are calculated by the Z1 code and discussed shortly.     

Annual nitrous oxide emissions from open-air and greenhouse vegetable cropping systems in China

Aims

A field experiment was conducted to quantify annual nitrous oxide (N₂O) fluxes from control and fertilized plots under open-air and greenhouse vegetable cropping systems in southeast China. We compiled the reported global field annual N₂O flux measurements to estimate the emission factor of N fertilizer for N₂O and its background emissions from vegetable fields.

Methods

Fluxes of N₂O were measured using static chamber-GC techniques over the 2010–2011 annual cycle with multiple cropping seasons.

Results

The mean annual N₂O fluxes from the controls were 46.1?±?2.3 μg N₂O-N m^?2 hr^?1 and 68.3?±?4.1 μg N₂O-N m^?2 hr^?1 in the open-air and greenhouse vegetable systems, respectively. For the plots receiving 900 kg?N?ha^?1, annual N₂O emissions averaged 90.6?±?8.9 μg N₂O-N m^?2 hr^?1 and 106.4?±?6.6 μg N₂O-N?m^?2 hr^?1 in the open-air and greenhouse vegetable systems, respectively. By pooling published field N₂O flux measurements taken over or close to a full year, the N₂O emission factor for N fertilizer averaged 0.63?±?0.09 %, with a background emission of 2.67?±?0.80 kg N₂O-N ha^?1 in Chinese vegetable fields. Annual N₂O emissions from Chinese vegetable systems were estimated to be 84.7 Gg N₂O-N yr^?1, consisting of 72.5 Gg N₂O-N yr^?1 and 12.2 Gg N₂O-N yr^?1 in the open-air and greenhouse vegetable systems, respectively.

Conclusions

While N₂O emissions from the greenhouse vegetable cropping system tended to be slightly higher compared to the open-air system in our experiment, the synthesis of literature data suggests that N₂O emissions would be greater at low N-rates but smaller at high N-rates in greenhouse systems than in open-air vegetable cropping systems. The estimates of this study suggest that vegetable cropping systems covering 11.4 % in national total cropping area, contributed 21–25 % to the total N₂O emission from Chinese croplands.     

Helix-coil transition of poly-gamma-N-carbobenzoxy-L-alpha, gamma-diaminobutyrate and poly-delta-N-carbobenzoxy-L-ornithine

The helix–coil transition of poly-γ-N-carbobenzoxy-L -α,γ-diaminobutyrate (PCLB) and poly-δ-N-carbobenzoxy-L -ornithine (PCLO) in chloroform–dichloroacetic acid mixtures was followed by optical rotatory dispersion. PCLB displays a “normal” temperature-induced transition, but PCLO an “inverse” one. The thermodynamic parameters for helix formation of the two polymers were determined using the Zimm-Bragg theory. The enthalpy for adding an amide residue to a helical region, ΔH, and the initiation factor σ were ΔH = ?180 cal/mole and σ = 9.2 × 10^?5 for PCLB and ΔH = +490 cal/mole and σ = 1.9 × 10^?5 for PCLO.     

Phase-transition properties of glycerol-monopalmitate lipid bilayers investigated by molecular dynamics simulation: influence of the system size and force-field parameters

Phase-transition properties of glycerol-1-monopalmitate (GMP) bilayers are investigated using explicit-solvent molecular dynamics (MD) simulations, initiated from structures appropriate for the gel (GL) or liquid crystal (LC) phases, and carried out at different hydration levels and temperatures. Building up on a previous study and based on 600 ns simulations, the influence of the system size and of the force field on the equilibrium thermodynamic and dynamic parameters of the bilayers in the GL and LC phases, as well as on the temperature T_m and properties of the GL ? LC phase transition, are analysed. Qualitatively speaking, the results agree with the available experimental data for the area per lipid in the two phases and for the phase-transition temperatures at the three hydration levels irrespective of the selected model parameters. They also suggest that the total number of hydrogen bonds formed between a lipid headgroup and its environment is essentially constant, amounting to about four in both the LC and the GL phases. Quantitatively speaking, the dependence of T_m on the hydration level is found to be non-systematic across the different combinations of model parameters. This results in part from a sensitivity of the results on the system size and force-field parameters but also from the limited accuracy of the bracketing approach employed here to estimate T_m. Finally, a simple kinetic model is proposed to account for the timescales of the transitions. This model involves enthalpy and entropy increases of about 26 kJ mol^? 1 and 83 J mol^? 1 K^? 1 per lipid, upon going from the GL to the LC phase. The transition state is associated with activation parameters corresponding to 13% and 11%, respectively, of these values along the GL → LC transition, resulting in an activation free energy of about 0.3 kJ mol^? 1 per lipid at T_m.     

Polymer concentration effects on helix–coil transition widths

A theoretical study of effects of excluded volume intermolecular interactions on the sharpness of helix–coil transitions in solutions of polyamino acids or simple proteins indicates that the transition width may vary appreciably as a function of polymer concentration. The analysis is based on a second virial approximation for the excess free energy of mixing of a solution of polymers of varying degrees of helicity. The virial coefficients involved are roughly estimated on the basis of gross polymer geometry. For large N (degree of polymerization) the transition is found, typically to sharpen with increasing concentration, becoming second order and then first order at sufficiently high concentrations. The critical polymer concentration is found to be roughly of the order N^?1.2 ??₀^?1 for an “all or none” model and of order σ^1/2 N^?0.2 ??₀^?1 for a model with continuously variable degree of helicity (??₀ is the volume of a single helical molecule and σ^1/2 the normalized statistical weight of a helix–coil interface). In the second case for N ～ 10³ and σ ～ 10^?2–10^?4, the predicted critical concentration is in the range 10^?1–10^?3 g/cm.³ Comparison is made with experiments on solutions of poly(γ-benzyl-L glutamate).     

Improved enzymatic two-phase biotransformation for (R)-phenylacetylcarbinol: Effect of dipropylene glycol and modes of pH control

An octanol/aqueous two-phase process for the enzymatic production of (R)-phenylacetylcarbinol (PAC) has been investigated further with regard to optimal pH control and replacement of 2.5?M MOPS buffer by a low cost solute. The specific rate of PAC production in the 2.5?M MOPS system controlled at pH?7 was 0.60?mg?U^?1?h^?1 (reaction completed at 34?h), a 1.6 times improvement over the same 2.5?M MOPS system without pH control (0.39?mg?U^?1?h^?1 at 49?h). An improved stability of PDC was evident at the end of biotransformation for the pH-controlled system with 84% residual carboligase activity, while 23% of enzyme activity remained in the absence of pH control. Lowering the MOPS concentration to 20?mM resulted in a lower benzaldehyde concentration in the aqueous phase with a major increase in the formation of by-product acetoin and three times decreased PAC production (0.21?mg?U^?1?h^?1). Biotransformation with 20?mM MOPS and 2.5?M DPG as inexpensive replacement of high MOPS concentrations provided similar aqueous phase benzaldehyde concentrations compared to 2.5?M MOPS and resulted in a comparable PAC concentration (92.1?g?L^?1 in the total reaction volume in 47?h) with modest formation of acetoin.     

The critical swimming speed of Iberian barbel Barbus bocagei in relation to size and sex

The swimming capacity of Barbus bocagei was measured with the critical swimming speed (U_crit) standard test in a modified Bla?ka‐type swim tunnel. Sixty B. bocagei were tested and they exhibited a mean ±s .d . U_crit of 0·81 ± 0·11 m s^?1 or 3·1 ± 0·86 total lengths per second (L_T s^?1). Sex had no effect on U_crit but significant differences were found between the swimming performance of fish with distinct sizes.     

Production,extraction, and thermodynamics protease partitioning from Aspergillus tamarii Kita UCP1279 using PEG/sodium citrate aqueous two-phase systems

Abstract

The protease from Aspergillus tamarii Kita UCP1279 extraction by aqueous two-phase PEG-Citrate (ATPS) systems, using a factorial design 2⁴, was investigated. Then, the variables studied were polyethylene glycol (PEG) molar mass (M_PEG), concentrations of PEG (C_PEG) and citrate (C_CIT), and pH. The responses analyzed were the partition coefficient (K), activity yield (Y) and purification factor (PF). The thermodynamic parameters of the ATPS partition were estimated as a function of temperature. ATPS was able to pre-purify the protease (PF = 1.6) and obtained 84% activity yield. The thermodynamic parameters ΔG°_m (?10.89?kJ mol^?1), ΔH_m (?5.0?kJ?mol^?1) and partition ΔS_m (19.74?J mol^?1 K^?1) showed that the preferential migration of almost all protein contaminants of the crude extract to the salt-rich phase, while the preferred protease was the PEG rich phase. The extracted enzyme presents optimum temperature and pH at range of 40–50?°C and 9.0–11.0, respectively. Moreover, the enzyme was identified as serine protease based on inhibition profile. ATPS showed the satisfactory performance as the first step for Aspergillus tamarii Kita UCP1279 protease pre-purification.     

Trace gas flux and the influence of short-term soil water and temperature dynamics in Australian sheep grazed pastures of differing productivity

Temperate pastures are often managed with P fertilizers and N₂-fixing legumes to maintain and increase pasture productivity which may lead to greater nitrous oxide (N₂O) emissions and reduced methane (CH₄) uptake. However, the diel and inter-daily variation in N₂O and CH₄ flux in pastures is poorly understood, especially in relation to key environmental drivers. We investigated the effect of pasture productivity, rainfall, and changing soil moisture and temperature upon short-term soil N₂O and CH₄ flux dynamics during spring in sheep grazed pasture systems in southeastern Australia. N₂O and CH₄ flux was measured continuously in a High P (23 kg P ha^?1 yr^?1) and No P pasture treatment and in a sheep camp area in a Low P (4 kg P ha^?1 yr^?1) pasture for a four week period in spring 2005 using an automated trace gas system. Although pasture productivity was three-fold greater in the High P than No P treatment, mean CH₄ uptake was similar (?6.3?±?SE 0.3 to ?8.6?±?0.4 μg C m^?2 hr^?1) as were mean N₂O emissions (6.5 to 7.9?±?0.8 μg N m^?2 hr^?1), although N₂O flux in the No P pasture did not respond to changing soil water conditions. N₂O emissions were greatest in the Low P sheep camp (12.4 μg?±?1.1 N m^?2 hr^?1) where there were also net CH₄ emissions of 5.2?±?0.5 μg C m^?2 hr^?1. There were significant, but weak, relationships between soil water and N₂O emissions, but not between soil water and CH₄ flux. The diel temperature cycle strongly influenced CH₄ and N₂O emissions, but this was often masked by the confounding covariate effects of changing soil water content. There were no consistently significant differences in soil mineral N or gross N transformation rates, however, measurements of substrate induced respiration (SIR) indicated that soil microbial processes in the highly productive pasture are more N limited than P limited after >20 years of P fertilizer addition. Increased productivity, through P fertilizer and legume management, did not significantly increase N₂O emissions, or reduce CH₄ uptake, during this 4 week measurement period, but the lack of an N₂O response to rainfall in the No P pasture suggests this may be evident over a longer measurement period. This study also suggests that small compacted and nutrient enriched areas of grazed pastures may contribute greatly to the overall N₂O and CH₄ trace gas balance.     

Swimming performance of two Iberian cyprinids: the Tagus nase Pseudochondrostoma polylepis (Steindachner, 1864) and the bordallo Squalius carolitertii (Doadrio, 1988)

The main purpose of this study was to gather swimming performance information for two endemic cyprinids of the Iberian Peninsula to contribute to the optimization of fish ways. Critical swimming speed (U_crit) was determined for the Tagus nase Pseudochondrostoma polylepis (Steindachner, 1864) and for the bordallo Squalius carolitertii (Doadrio, 1988) in a swimming tunnel. From a total of 80 P. polylepis tested, the mean (± SD) U_crit observed was 0.78 ± 0.15 ms^?1 (c. 3.74 ± 0.93 BL s^?1); the 68 S. carolitertii tested presented an U_crit of 0.54 ± 0.1 ms^?1 (c. 4.43 ± 0.74 BL s^?1). Significant interspecific differences were found between the U_crit of the tested cyprinids. Intraspecific comparisons between the U_crit and the variables of size, sex, condition factor and gonado‐somatic index were also made. No sex‐or gonad maturation‐related differences between the U_crit were identified, but the robust P. polylepis were found to be stronger swimmers. Water velocities in fish ways for P. polylepis and S. carolitertii should aim, on average, for lower than 0.7 and 0.5 ms^?1, respectively.     

Sequestration of organometallic compounds by synthetic and naturally occurring polycarboxylate ligands. Binding of monomethylmercury(II) by polyacrylic and alginic acids

Abstract

The sequestering capacity of synthetic and naturally occurring polycarboxylate ligands towards mono-methylmercury(II) was evaluated by stability quantitative data on the interaction of CH₃Hg⁺ with different molecular weight synthetic polyacrylates (2 and 20kDa average M.wt) and alginate (70–100 kDa) extracted from brown algae Macrocystis pyrifera. The influence of ionic medium was evaluated by measurements on the CH₃Hg⁺-polyacrylate systems in NaNO₃ medium at different ionic strengths (0.10, 0.25, 0.50 and 0.75 mol L^?1), and a Debye-HiJckel type equation was used for the dependence of complex formation constants on ionic strength. Measurements on the CH3Hg⁺ - alginate system were carried out at l = 0.10 mol L^?1 in NaNO₃ medium. By using the stability data, the sequestering capacity of both ligands towards monomethylmercury(II) was determined at different pH values. Results obtained show that the binding ability of polyacrylic ligands (PAA) is stronger than the alginate (AA), following the trend PAA (20 kDa)> PAA (2kDa)>AA.     

Effects of age and size on critical swimming speed of juvenile Chinese sturgeon Acipenser sinensis at seasonal temperatures

Changes in the critical swimming speed (U_crit, cm s^?1) with ontogeny of 2·5–12·5 month‐old juvenile anadromous Chinese sturgeon Acipenser sinesis were measured in a modified Blazka‐type swimming tunnel. The absolute U_crit increased with length, mass and age; the relative U^′_crit (body lengths, s^?1), however, decreased. Juvenile A. sinesis did not display a parr–smolt transformation at the length or age threshold to tolerate full‐strength seawater.     

Proton transfer and polarizability of hydrogen bonds formed between cysteine and lysine residues

(L -Cys)_n + N-base systems and (L -Cys)_n + (L -Lys)_n systems were studied by ir spectroscopy. It is shown that in the water-free systems, SH ?N ? S^? ?H⁺N hydrogen bonds are formed. With the (L -Cys)_n + N-base systems, both proton-limiting structures in the SH ?N ? S^? ?H⁺N bonds have equal weight when the pK_a of the protonated N-base is 2 pK_a units larger than that of (L -Cys)_n. The same is true with the water-free (L -Cys)_n + (L -Lys)_n system. Thus, with regard to the type of proton potentials present, these hydrogen bonds are proton-transfer hydrogen bonds showing very large proton polarizabilities. This is confirmed by the occurrence of continua in the ir spectra. Small amounts of water open these hydrogen bonds and increase the transfer of the proton to (L -Lys)_n. In the (L -Lys)_n + N-base systems, with increasing proton transfer the backbone of (L -Cys)_n changes from antiparallel β-structure to coil. In (L -Cys)_n + (L -Lys)_n, the conformation is determined by the (L -Lys)_n conformation and changes depending on the chain length of (L -Lys)_n. Finally, the reactivity increase in the active center of fatty acid synthetase, which should be caused by the shift of a proton, is discussed on the basis of the great proton polarizability of the cysteine–lysine hydrogen bonds.     

Polyelectroyte behavior of a bacterial polysaccharide from Xanthomonas campestris: Comparison with carboxymethylcellulose

The main physicochemical properties of the polysaccharide called Xanthan produced by Xanthomonas compestris are discussed: the activity coefficient of the counter-ion, the pK(α), and the ionic selectivity are investigated and compared to those of a carboxymetholcellulose. The weight-average molecular weight (M _w = 2 × 10⁶), the intrinsic viscosity and the constant of sedimentation are determined as a function of the ionic strength. It is proved that in dilute solution, there is no intermolecular association, whatever the ionic strength. The conformation is proposed to be a rigid rodlike molecule whose length is 6000 Å, independent of ionic strength > 10^?2N.     

Nitrous oxide emissions during establishment of eight alternative cellulosic bioenergy cropping systems in the North Central United States

Greenhouse gas (GHG) emissions from soils are a key sustainability metric of cropping systems. During crop establishment, disruptive land‐use change is known to be a critical, but under reported period, for determining GHG emissions. We measured soil N₂O emissions and potential environmental drivers of these fluxes from a three‐year establishment‐phase bioenergy cropping systems experiment replicated in southcentral Wisconsin (ARL) and southwestern Michigan (KBS). Cropping systems treatments were annual monocultures (continuous corn, corn–soybean–canola rotation), perennial monocultures (switchgrass, miscanthus, and poplar), and perennial polycultures (native grass mixture, early successional community, and restored prairie) all grown using best management practices specific to the system. Cumulative three‐year N₂O emissions from annuals were 142% higher than from perennials, with fertilized perennials 190% higher than unfertilized perennials. Emissions ranged from 3.1 to 19.1 kg N₂O‐N ha^?1 yr^?1 for the annuals with continuous corn > corn–soybean–canola rotation and 1.1 to 6.3 kg N₂O‐N ha^?1 yr^?1 for perennials. Nitrous oxide peak fluxes typically were associated with precipitation events that closely followed fertilization. Bayesian modeling of N₂O fluxes based on measured environmental factors explained 33% of variability across all systems. Models trained on single systems performed well in most monocultures (e.g., R² = 0.52 for poplar) but notably worse in polycultures (e.g., R² = 0.17 for early successional, R² = 0.06 for restored prairie), indicating that simulation models that include N₂O emissions should be parameterized specific to particular plant communities. Our results indicate that perennial bioenergy crops in their establishment phase emit less N₂O than annual crops, especially when not fertilized. These findings should be considered further alongside yield and other metrics contributing to important ecosystem services.     

Polynucleotides. XI. Thermodynamics of (A) N -2(U) infinity from the dependence of T m N on oligomer length

The variation in the helix-coil transition temperature, T_m^N, with oligomer length, N, for the system ((I)) has been examined. The results for N = 4-13, measured in 0.2M Na+, have been analyzed in terms of the expression of Blake (1972): ((II)) where c_m is the free oligomer concentration at T_m^N, and V_r^f is the thermodynamic free volume available to a helical base-triplet residue. The correlation coefficient for the fit to expression (II) of data obtained over a 50° temperature range is 0.997 when ΔH_r = ?12.6 kcal/mole of base-triplets (independent of oligomer length (N ? 4) or temperature), the value previously obtained from both calorimetry of (A)_∞·2(U)_∞ and (A)₄ concentration dependence of T_m. It is found that V_r^f = 8.0 × 10^?4 1/mole (± 30%) or 1.33 ų per helical base-triplet, and is constant with temperature. A maximum value for V_r^f of 21.0 × 10^?4 1/M (± 1.3%), equivalent to 3.54 ų per helical basetriplet is obtained by the same treatment of the helix-coil transition data for the three-stranded helix formed by adenosine (N = 1) and 2(U)_∞ obtained by Davies and Davidson (1971).     

Effects on Mitochondrial K Flux of pH,K Concentration,and N-Ethyl Maleimide

Based on published evidence that cation transport in mitochondria is not significantly dependent on a membrane potential, it is suggested that the process of mitochondrial cation transport may be nonelectrogenic. These experiments focused on the possibility that K⁺ flux into rat liver mitochondria may be directly coupled, via an energy-linked carrier mechanism, to OH^? influx or H⁺ efflux. The dependence of the unidirectional K⁺ influx on the external K⁺ concentration indicates involvement of a saturable mechanism. Increasing the external pH from 7.0 to 8.0 increases the apparent V_max of the K⁺ influx without significantly altering the apparent K_m for K⁺. The pH dependence is greater in the presence of N-ethyl maleimide, a known inhibitor of the mitochondrial P_i/OH^? exchange mechanism. N-Ethyl maleimide decreases the apparent V_max at pH 7.0 and increases it at pH 8.0. Evidence indicates that both N-ethyl maleimide and a high external P_i concentration may stimulate the K⁺ influx at alkaline external pH (8.0) by preventing net exchanges between endogenous P_i and external OH^?. An apparent first-order dependence of the K⁺ influx on the external OH^? concentration is observed in the presence of N-ethyl maleimide. These results are consistent with a possible role of external OH^? as a cosubstrate of the K⁺ transport mechanism.