A new viewpoint to understand the response of leaf dark respiration to elevated CO<Subscript>2</Subscript> concentration

By investigating the R _D-C _a (dark respiration rate-atmospheric CO₂ concentration) and P _N (net photosynthetic rate)-C _a curves of bamboo (Fargesia denudata) and poplar (Populus cathayanna), we found that: (1) the minimal R _D was close to ambient CO₂ concentration, and the elevated or decreased atmospheric CO₂ concentration enhanced the R _D of both species; (2) the response curves of R _D-C _a were simulated well by quadratic function. This phenomenon might be an inherent property of leaf R _D of F. denudata and P. cathayanna. If this was true, it implies that effect of CO₂ on R _D could be interpreted with the relationship of R _D-C _a curves and the quadratic function.     

Brownian Dynamics Simulations of Colloidal Liquids: Hydrodynamics and Stress Relaxation

Abstract

We describe the statistical mechanics background and additional algorithmic features of a recently proposed simple mean-field Brownian Dynamics algorithm formulated to include many-body hydrodynamics, using a local density approximation for the friction coefficient. We show that the equations of motion satisfy the incompressibility of phase space. We make further developments to the model, computing the hydrodynamic effects on the shear stress relaxation function. We show that stress relaxation takes place over two well-defined regimes, in both cases with and without mean field hydrodynamics, MFH. At short times ta ²/D ₀ < 10^?3, where a is the radius of the colloidal particle and D ₀ is the self-diffusion coefficient at infinite dilution, decay of the stress autocorrelation function, C_s(t) is essentially independent of volume fraction and does not fit to a simple analytic form. At longer times than ta ²/D ₀ < 10^?2 the decay has the fractional exponential form ～exp(-t ^β) with β ? 1. The transition between these two regimes coincides with a rapid fall in the time-dependent diffusion coefficient from the so-called short-time to long-time values. We do not find any evidence for power law decay in the C_s(t) as predicted by recent mode-coupling based analytical expansions.     

Characterization of photosynthesis of Populus euphratica grown in the arid region

Net photosynthetic rate (P _N), stomatal conductance (g _s), intercellular CO₂ concentration (C _i), transpiration rate (E), water use efficiency (WUE), and stomatal limitation (L_s) of Populus euphratica grown at different groundwater depths in the arid region were measured. g _s of the trees with groundwater depth at 4.74 m (D₄) and 5.82 m (D₅) were lower and a little higher than that at 3.82 m (D₃), respectively. Compared with C _i and L_s of the D₃ trees, C _i decreased and L_s increased at 4.74 m, however, Ci increased and L_s decreased at D₅. Hence photosynthetic reduction of P. euphratica was attributed to either stomatal closure or non-stomatal factors depending on the groundwater depths in the plant locations. P _N of the D₃ trees was significantly higher than those at D₄ or D₅. The trees of D₄ and D₅ did not show a significant difference in their P _N, indicating that there are mechanisms of P. euphratica tolerance to mild and moderate drought stress.     

Regulation of biosynthesis of pesticidal metabolic complexes inStreptomyces griseus

The complex of pesticidal metabolites produced byStreptomyces griseus LKS-1 consists of a peptide antibiotic (A), nonactic acids (B), macrotetrolides (C), pyrrolizines (D), and of cycloheximide. The latter unwanted phytotoxic compound was eliminated by treatment with mutagens. Combined approaches, including both genetic and physiological manipulations, resulted in the following alterations in the biosynthetic capacity: (1) A more than 80-fold increase in the production of C under a substantial decrease in the yields ofA, B andD, the ratio of the components ofC being steered toward the required more active ones; (2) a more than 300-fold increase in the production ofB under suppression of the formation ofA andC: (3) a 10-fold increase in the yields ofD under suppression ofA andC; (4 a significant increase in the yields ofA with eliminatingB, C andD. The level of inorganic phosphate in fermentation media and the sensitivity of the organism to carbon catabolite repression were important factors participating in the regulation of the above biosynthetic processes.     

Studies in the Synthesis and Biosynthesis of C-Nucleosides

Abstract

The naturally occurring C-nucleosides show marked antiturnour and antiviral properties. We have developed, over a period of years, a general synthetic route to C-nucleosides by way of acetylenic intermediates. Tri-O-benzyl-D-ribofuranose (1) reacts with acetylenic Grignard reagents to give mixtures of D-allo and D-altro diols. The latter, on ring closure by means of toluene-p-sulphonyl chloride in pyridine, gives derivatives, (2) or (3), of β-D-ribofuranosylethyne in ～50% yield from (1).     

Acetylcholinesterase/Butyrylcholinesterase inhibition activity of some new carbacylamidophosphate deriviatives

Eight newly synthesized carbacylamidophosphates with the general formula RC(O)NHP(O)Cl₂ with R = pCl–C₆H₄ 1a, pBr–C₆H₄ 2a, C₆H₅ 3a, and pMe–C₆H₄ 4a and RC(O)NHP(O)(NC₄H₈O)₂ R = pCl–C₆H₄ 1b, pBr–C₆H₄ 2b, C₆H₅ 3b, pMe–C₆H₄ 4b, were selected to compare the inhibition kinetic parameters, IC₅₀, K_i, k_p and K_D, on human erythrocyte acetylcholinesterase (hAChE) and bovine serum butyrylcholinesterase (BuChE), Also, the in vivo inhibition potency of compound 2a, 2b and 3a, were studied. The data demonstrates that compound 2a and compound 2b are the potent sensitive as AChE and BuChE inhibitors respectively, and the inhibition of hAChE is about 10-fold greater than that of BuChE.     

A new visualization scheme of chemical energy density and bonds in molecules

Covalent bond describes electron pairing in between a pair of atoms and molecules. The space is partitioned in mutually disjoint regions by using a new concept of the electronic drop region R_D, atmosphere region R_A, and the interface S (Tachibana in J Chem Phys 115:3497–3518, 2001). The covalent bond formation is then characterized by a new concept of the spindle structure. The spindle structure is a geometrical object of a region where principal electronic stress is positive along a line of principal axis of the electronic stress that connects a pair of the R_Ds of atoms and molecules. A new energy density partitioning scheme is obtained using the Rigged quantum electrodynamics (QED). The spindle structure of the stress tensor of chemical bond has been disclosed in the course of the covalent bond formation. The chemical energy density visualization scheme is applied to demonstrate the spindle structures of chemical bonds in H₂, C₂H₆, C₂H₄ and C₂H₂ systems.Figure Field theory of the energy density.     

Lipid composition of halophilic species of Dunaliella from the dead sea

The lipid patterns of six halophilic Dunaliella species from the Dead Sea (C₉, D_11a, D_11b, D₁₃, F_20a and D. viridis) were found to be generally similar to those of halotolerant Dunaliella species previously examined, except for the presence in the halphilic Dunaliella of small to trace amounts of one or more (up to five) unidentified glycolipids. The lipids of two of the halophilic algae, species C₉ and D_11b, were studied in detail and were found to be similar in composition. Glycolipids were the major group (55.0 and 53.2 mol % for C₉ and D_11b, respectively), followed by neutral lipids (mainly triacyglycerols: 21.3 mol %; 24.6 mol %), whereas phospholipids were a much smaller fraction (6.5 mol %; 5.8 mol %). Monogalactosyldiacylglycerol was the largest component (22.0 mol %; 24.3 mol %) but digalactosyldiacylglycerol (18.7 mol %; 14.9 mol %) and sulfoquinovosyldiacylglycerol (14.3 mol %; 14.0 mol %) were also present in high concentrations. All phospholipids were present at low concentrations: phosphatidylglycerol (4.4 mol %; 3.1 mol %); phosphatidylethanolamine (1.1 mol %; 0.7 mol %); phosphatidylcholine (0.9 mol %; 1.9 mol %); and phosphatidylinositol (traces). Diacylglyceryl-O-(N,N,N-trimethyl)homoserine was present in C₉ and D_11b (3.3 mol %; 9.3 mol %) and in all the other species examined. Fatty acid composition of the individual lipid components of C₉ and D_11b showed characteristic differences between glycolipids and phospholipids, in a similar pattern for both algae. The major fatty acids detected in all species examined were -linolenic, linoleic, palmitic, oleic and a polyunsaturated sixteen carbon acid.     

Effects of elevated atmospheric [CO2] on instantaneous transpiration efficiency at leaf and canopy scales in Eucalyptus saligna

Rising atmospheric concentrations of CO₂ (C_a) can reduce stomatal conductance and transpiration rate in trees, but the magnitude of this effect varies considerably among experiments. The theory of optimal stomatal behaviour predicts that the ratio of photosynthesis to transpiration (instantaneous transpiration efficiency, ITE) should increase in proportion to C_a. We hypothesized that plants regulate stomatal conductance optimally in response to rising C_a. We tested this hypothesis with data from young Eucalyptus saligna Sm. trees grown in 12 climate‐controlled whole‐tree chambers for 2 years at ambient and elevated C_a. Elevated C_a was ambient + 240 ppm, 60% higher than ambient C_a. Leaf‐scale gas exchange was measured throughout the second year of the study and leaf‐scale ITE increased by 60% under elevated C_a, as predicted. Values of leaf‐scale ITE depended strongly on vapour pressure deficit (D) in both CO₂ treatments. Whole‐canopy CO₂ and H₂O fluxes were also monitored continuously for each chamber throughout the second year. There were small differences in D between C_a treatments, which had important effects on values of canopy‐scale ITE. However, when C_a treatments were compared at the same D, canopy‐scale ITE was consistently increased by 60%, again as predicted. Importantly, leaf and canopy‐scale ITE were not significantly different, indicating that ITE was not scale‐dependent. Observed changes in transpiration rate could be explained on the basis that ITE increased in proportion to C_a. The effect of elevated C_a on photosynthesis increased with rising D. At high D, C_a had a large effect on photosynthesis and a small effect on transpiration rate. At low D, in contrast, there was a small effect of C_a on photosynthesis, but a much larger effect on transpiration rate. If shown to be a general response, the proportionality of ITE with C_a will allow us to predict the effects of C_a on transpiration rate.     

Flow-induced forces on free-floating macrophytes

Free-floating macrophytes have buoyant petioles and unanchored roots; certain species are highly invasive, owing to characteristics such as high growth rates and the formation of dense floating mats that drift on wind and water currents. Water hyacinth (Eichhornia crassipes) is one example; its invasion of tropical and subtropical freshwater systems worldwide harms native ecosystems and impedes human activities. This research examines flow-induced forces and biomechanical properties of E. crassipes to better understand flow interactions and transport mechanisms. Drag forces were measured in a flume and a wind tunnel for varying approach velocities and raft configurations; from this data, drag coefficients in water (C _D^w) and air (C _D^a) were developed. Over similar Reynolds number (Re _b ) regimes, C _D^w decrease as Re _b increases while C _D ^a are invariant. For the same raft tested in air and water, water drag exceeds air drag and the value of C _D^w approaches C _D^a at high Re _b . Force–velocity relationships indicate root canopies reconfigure by streamlining in higher flow velocities while leaf canopies do not. Root canopy streamlining is further explained through biomechanical testing: we found the major vegetative structures of E. crassipes (roots, stolons, and petioles) have similar moduli of elasticity but second moments of area are three orders of magnitude smaller in roots compared to stolons or petioles, leading to significantly lower flexural rigidity in roots than in stolons or petioles. Flow interactions with the root canopy differ for an individual plant compared to a raft assemblage. Laboratory results suggest that water currents are the dominant mechanism for E. crassipes dispersal.     

The Discovery of Intramolecular Stereoelectronic Forces That Drive The Sugar Conformation in Nucleosides and Nucleotides

Abstract

This report summarizes our results⁸ on how the determination of the thermodynamics of the two-state North (N, C2′-exo-C3′-endo) ? South (S,C2′-endo-C3′-exo) pseudorotational equilibrium in aqueous solution (pD 0.6 - 12.0) basing on vicinal ³J_HH extracted from ¹H-NMR spectra measured at 500 MHz from 278K to 358K yields an experimental energy inventory of the unique stereoelectronic forces that dictate the conformation of the sugar moiety in β-D-ribonucleosides (rNs), β-D-nucleotides, in the mirror-image β-D- versus β-L-2′-deoxynucleosides (dNs) as well as in α-D- or L- versus β-D- or L-2′-dNs. Our work shows for the first time that the free-energies of the inherent internal flexibilities of β-D- versus β-L-2′-dNs and α-D- versus α-L-2′-dNs are identical, whereas the aglycone promoted tunability of the constituent sugar conformation is grossly affected in the α-nucleosides compared to the β-counterparts.     

Stomatal sensitivity to vapour pressure difference over a subambient to elevated CO2 gradient in a C3/C4 grassland

In the present study the response of stomatal conductance (g_s) to increasing leaf‐to‐air vapour pressure difference (D) in early season C₃ (Bromus japonicus) and late season C₄ (Bothriochloa ischaemum) grasses grown in the field across a range of CO₂ (200–550 µmol mol^?1) was examined. Stomatal sensitivity to D was calculated as the slope of the response of g_s to the natural log of externally manipulated D (dg_s/dlnD). Increasing D and CO₂ significantly reduced g_s in both species. Increasing CO₂ caused a significant decrease in stomatal sensitivity to D in Br. japonicus, but not in Bo. ischaemum. The decrease in stomatal sensitivity to D at high CO₂ for Br. japonicus fit theoretical expectations of a hydraulic model of stomatal regulation, in which g_s varies to maintain constant transpiration and leaf water potential. The weaker stomatal sensitivity to D in Bo. ischaemum suggested that stomatal regulation of leaf water potential was poor in this species, or that non‐hydraulic signals influenced guard cell behaviour. Photosynthesis (A) declined with increasing D in both species, but analyses of the ratio of intercellular to atmospheric CO₂ (C_i/C_a) suggested that stomatal limitation of A occurred only in Br. japonicus. Rising CO₂ had the greatest effect on g_s and A in Br. japonicus at low D. In contrast, the strength of stomatal and photosynthetic responses to CO₂ were not affected by D in Bo. ischaemum. Carbon and water dynamics in this grassland are dominated by a seasonal transition from C₃ to C₄ photosynthesis. Interspecific variation in the response of g_s to D therefore has implications for predicting seasonal ecosystem responses to CO₂.     

Elevated CO2 did not affect the hydrological balance of a mature native Eucalyptus woodland

Elevated atmospheric CO₂ concentration (eC_a) might reduce forest water‐use, due to decreased transpiration, following partial stomatal closure, thus enhancing water‐use efficiency and productivity at low water availability. If evapotranspiration (E_t) is reduced, it may subsequently increase soil water storage (ΔS) or surface runoff (R) and drainage (D_g), although these could be offset or even reversed by changes in vegetation structure, mainly increased leaf area index (L). To understand the effect of eC_a in a water‐limited ecosystem, we tested whether 2 years of eC_a (~40% increase) affected the hydrological partitioning in a mature water‐limited Eucalyptus woodland exposed to Free‐Air CO₂ Enrichment (FACE). This timeframe allowed us to evaluate whether physiological effects of eC_a reduced stand water‐use irrespective of L, which was unaffected by eC_a in this timeframe. We hypothesized that eC_a would reduce tree‐canopy transpiration (E_tree), but excess water from reduced E_tree would be lost via increased soil evaporation and understory transpiration (E_floor) with no increase in ΔS, R or D_g. We computed E_t, ΔS, R and D_g from measurements of sapflow velocity, L, soil water content (θ), understory micrometeorology, throughfall and stemflow. We found that eC_a did not affect E_tree, E_floor, ΔS or θ at any depth (to 4.5 m) over the experimental period. We closed the water balance for dry seasons with no differences in the partitioning to R and D_g between C_a levels. Soil temperature and θ were the main drivers of E_floor while vapour pressure deficit‐controlled E_tree, though eC_a did not significantly affect any of these relationships. Our results suggest that in the short‐term, eC_a does not significantly affect ecosystem water‐use at this site. We conclude that water‐savings under eC_a mediated by either direct effects on plant transpiration or by indirect effects via changes in L or soil moisture availability are unlikely in water‐limited mature eucalypt woodlands.     

Relationship between allocation of absorbed light energy in PSII and photosynthetic rates of C3 and C4 plants

Two C₃ dicotyledonous crops and five C₄ monocotyledons treated with three levels of nitrogen were used to evaluate quantitatively the relationship between the allocation of absorbed light energy in PSII and photosynthetic rates (P _N) in a warm condition (25–26°C) at four to five levels [200, 400, 800, 1,200 (both C₃ and C₄) and 2,000 (C₄ only) μmol m⁻² s⁻¹] of photosynthetic photon flux density (PPFD). For plants of the same type (C₃ or C₄), there was a linear positive correlation between the fraction of absorbed light energy that was utilized in PSII photochemistry (P) and P _N, regardless of the broad range of their photosynthetic rates due to species-specific effect and/or nitrogen application; meanwhile, the fraction of absorbed light energy that was dissipated through non-photochemical quenching (D) showed a negative linear regression with P _N for each level of PPFD. The intercept of regression lines between P and P _N of C₃ and C₄ plants decreased, and that between D and P _N increased with increasing PPFD. With P and D as the main components of energy dissipation and complementary to each other, the fraction of excess absorbed light energy (E) was unchanged by P _N under the same level of PPFD. At the same level of P _N, C₄ plants had lower P and higher D than C₃ plants, due to the fact that C₄ plants with little or no photorespiration is considered a limited energy sink for electrons. Nevertheless there was a significant negative linear correlation between D and P when data from both C₃ and C₄ plants at varied PPFD levels was merged. The slope of regression lines between P and D was 0.85, indicating that in plants of both types, most of the unnecessary absorbed energy (ca. 85%) could dissipate through non-photochemical quenching, when P was inhibited by low P _N due to species-specific effect and nitrogen limitation at all levels of illumination used in the experiment.     

Dielectric relaxation of collagen in aqueous solutions

The complex dielectric constant of collagen in aqueous solutions (polymer concentration, C_p = 0.02–0.2%) was measured at 10°C in the frequency range from 3 Hz to 30 kHz. The loss peak for C_p = 0.02% is located at 90 Hz and the dielectric relaxation time τ_D is estimated to be 1.8 ± 0.3 msec. The τ_D agrees well with the rotational relaxation time estimated from the reduced viscosity, and the relaxation is ascribed to the end-over-end rotation of the molecule. The C_p dependence of τ_D and the dielectric increment Δε are interpreted in terms of the aggregation of molecules. The dipole moment of a molecule, obtained from Δε at C_p = 0.02% and pH 6.5, is (5.2 ± 0.2) × 10⁴D, which is explained by the asymmetrical distribution of the ionized side chains of the molecule.     

Fast dynamics perturbation analysis for prediction of protein functional sites

Background  

We present a fast version of the dynamics perturbation analysis (DPA) algorithm to predict functional sites in protein structures. The original DPA algorithm finds regions in proteins where interactions cause a large change in the protein conformational distribution, as measured using the relative entropy D _x . Such regions are associated with functional sites.     

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.     

Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs

Background  

Assembling genomic sequences from a set of overlapping reads is one of the most fundamental problems in computational biology. Algorithms addressing the assembly problem fall into two broad categories - based on the data structures which they employ. The first class uses an overlap/string graph and the second type uses a de Bruijn graph. However with the recent advances in short read sequencing technology, de Bruijn graph based algorithms seem to play a vital role in practice. Efficient algorithms for building these massive de Bruijn graphs are very essential in large sequencing projects based on short reads. In an earlier work, an O(n/p) time parallel algorithm has been given for this problem. Here n is the size of the input and p is the number of processors. This algorithm enumerates all possible bi-directed edges which can overlap with a node and ends up generating Θ(nΣ) messages (Σ being the size of the alphabet).     

Optimality of Some Class of Incomplete Block Designs

A class of incomplete block designs called C-design, was considered by Caliński (1971), Saha (1976), Ceranka (1983) and Ceranka , Kozłowska (1983, 1984). In this paper we extend the theory of block designs having the C-property. We consider optimality of C-designs with respect to any criterion of a described form. Das and Kageyama (1991) considered a class of E-optimal proper efficiency balanced designs (strictly speaking, Das and Kageyama considered E_R-optimality of some class of block designs). Hence we consider E_R, A_R, D_R optimality of C-designs.     

Molecular conformation of prostaglandin A1 monoclinic cyrstalline polymorph

The molecular conformation of the monoclinic crystalline polymorph of prostaglandin A₁ has been determined by X-ray diffraction techniques. The space group is P2₁ with a = 13.637 (2), b = 7.567 (1), I c = 10.576 (2) Å, β = 107.37 (3)°; D_c = 1.073 g·cm⁻³ for Z = 2. The molecular conformation is characterized by the nearly parallel arrangement of the C₁–C₇ and C₁₃–C₂₀ side chains, with a general flattening of the overall structure when compared with the orthorhombic polymorph. The cyclopentenone moiety assumes a C₈ envelope conformation with C₈ and O₉ displaced +0.29 Å and −0.18 Å from the C₉–C₁₀=C₁₁–C₁₂ plane respectively. Concerted, small variations of the torsion angles, primarily about the C₈–C₁₂, C₁₄–C₁₅ and C₁₆–C₁₇ bonds, bring the monoclinic and orthorhombic conformations into coincidence.