Inheritance of foliar stable carbon isotope discrimination and third-year height in Pinus taeda clones on contrasting sites in Florida and Georgia

Quantifying foliar stable carbon isotope discrimination (Δ) is a powerful approach for understanding genetic variation in gas exchange traits in large populations. The genetic architecture of Δ and third-year height is described for more than 1,000 clones of Pinus taeda tested on two contrasting sites. for Δ was 0.14 (±0.03), 0.20 (±0.07), and 0.09 (±0.04) at Florida, Georgia, and across sites, respectively. for stable carbon isotope discrimination ranged from 0.25 (±0.03) at the Florida site to 0.33 (±0.03) at the Georgia site, while the across-site estimate of was 0.19 (±0.02). For third-year height, ranged from 0.13 (±0.05) at the Georgia site to 0.20 (±0.06) at the Florida site with an across-site estimate of 0.09 (±0.05). Broad-sense heritability estimates for third-year height were 0.23 (±0.03), 0.28 (±0.03), and 0.13 (±0.02) at the Florida site, Georgia site, and across sites, respectively. Type B total genetic correlation for Δ was 0.70 ± 0.06, indicating that clonal rankings were relatively stable across sites, while for third-year height, rankings of clones were more unstable across the two trials . Third-year height and Δ were negatively correlated at the parental , full-sib family , and clonal levels, suggesting that genetic variation for Δ in P. taeda may be a result of differences in photosynthetic capacity. We conclude that Δ may be a useful selection trait to improve water-use efficiency and for guiding deployment decisions in P. taeda.     

Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy

We adapt here a surprising technique, the boustrophedon method, to speed up the sampling of RNA secondary structures from the Boltzmann low-energy ensemble. This technique is simple and its implementation straight-forward, as it only requires a permutation in the order of some operations already performed in the stochastic traceback stage of these algorithms. It nevertheless greatly improves their worst-case complexity from to , for n the size of the original sequence. Moreover the average-case complexity of the generation is shown to be improved from to in an Boltzmann-weighted homopolymer model based on the Nussinov–Jacobson free-energy model. These results are extended to the more realistic Turner free-energy model through experiments performed on both structured (Drosophilia melanogaster mRNA 5S) and hybrid (Staphylococcus aureus RNAIII) RNA sequences, using a boustrophedon modified version of the popular software UnaFold. This improvement allows for the sampling of greater and more significant sets of structures in a given time.      

Survival Chances of Mutants Starting With One Individual

A simple theoretical model of a Darwinian system (a periodic system with a multiplication phase and a selection phase) of entities (initial form of polymer strand, primary mutant and satellite mutants) is given. First case: one mutant is considered. One individual of the mutant appears in the multiplication phase of the first generation. The probabilities to find N individuals of the mutant after the multiplication phase M of the n-th generation (with probability δ of an error in the replication, where all possible errors are fatal errors) and after the following selection phase S (with probability β that one individual survives) are given iteratively. The evolutionary tree is evaluated. Averages from the distributions and the probability of extinction are obtained. Second case: two mutants are considered (primary mutant and new form). One individual of the primary mutant appears in the multiplication phase of the first generation. The probabilities to find N _p individuals of the primary mutant and N _m individuals of the new form after the multiplication phase M of the n-th generation (probability ɛ of an error in the replication of the primary mutant giving the new form) and after the following selection phase S (probabilities β _p and β _m that one individual each of the primary mutant and of the new form survives) are given iteratively. Again the evolutionary tree is evaluated. Averages from the distributions are obtained. The online version of the original article can be found at .     

Sources of variability in spotted owl population growth rate: testing predictions using long-term mark–recapture data

For long-lived iteroparous vertebrates that annually produce few young, life history theory predicts that reproductive output (R) and juvenile survival should influence temporal variation in population growth rate (λ) more than adult survival does. We examined this general prediction using 15 years of mark–recapture data from a population of California spotted owls (Strix occidentalis occidentalis). We found that survival of individuals ≥1 year old (ϕ) exhibited much less temporal variability , where CV is coefficient of variation, than R and that R was strongly influenced by environmental stochasticity. Although λ was most sensitive ( ; log-transformed sensitivity) to ϕ and much less sensitive to either R or juvenile survival (survival rate of owls from fledging to 1 year old; ), we estimated that R contributed as much as ϕ to the observed annual variability in λ. The contribution of juvenile survival to variability in λ was proportional to its These results are consistent with the hypothesis that natural selection may have favored the evolution of longevity in spotted owls as a strategy to increase the probability of experiencing favorable years for reproduction. Our finding that annual weather patterns that most affected R (temperature and precipitation during incubation) and ϕ (conditions during winter related to the Southern Oscillation Index) were equally good at explaining temporal variability in λ supports the conclusion that R and ϕ were equally responsible for variability in λ. Although currently accepted conservation measures for spotted owl populations attempt to enhance survival, our results indicated that conservation measures that target R may be as successful, as long as actions do not reduce ϕ.     

Cell-to-cell pathway dominates xylem-epidermis hydraulic connection in<Emphasis Type="Italic"> Tradescantia fluminensis</Emphasis> (Vell. Conc.) leaves

A steady supply of water is indispensable for leaves to fulfil their photosynthetic function. Understanding water movement in leaves, especially factors that regulate the movement of water flux from xylem to epidermis, requires that the nature of the transport pathway be elucidated. To determine the hydraulic linkage between xylem and epidermis, epidermal cell turgor pressure (P _t) in leaves of Tradescantia fluminensis was monitored using a cell pressure probe in response to a 0.2 MPa step change in xylem pressure applied at the leaf petiole. Halftime of P _t changes were 10–30 times greater than that of water exchange across an individual cell membrane suggesting that cell-to-cell water transport constitutes a significant part of the leaf hydraulic path from xylem to epidermis. Furthermore, perfusion of H₂O₂ resulted in increases of both and by a factor of 2.5, indicating that aquaporins may play a role in the xylem to epidermis hydraulic link. The halftime for water exchange did not differ significantly between cells located at the leaf base (2.5 s), middle (2.6 s) and tip (2.5 s), indicating that epidermal cell hydraulic properties are similar along the length of the leaf. Following the pressure application to the xylem (0.2 MPa), P _t changed by 0.12, 0.06 and 0.04 MPa for epidermal cells at the base, middle and the tip of the leaf, respectively. This suggests that pressure dissipation between xylem and epidermis is significant, and that the pressure drop along the vein may be due to its structural similarities to a porous pipe, an idea which was further supported by measurements of xylem hydraulic resistance using a perfusion technique.     

A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci*

Analysis of linkage disequilibrium (=mean squared correlation of allele frequencies at different gene loci) provides a means of estimating effective population size (N _e) from a single sample, but this method has seen much less use than the temporal method (which requires at least two samples). It is shown that for realistic numbers of loci and alleles, the linkage disequilibrium method can provide precision comparable to that of the temporal method. However, computer simulations show that estimates of N _e based on for unlinked, diallelic gene loci are sharply biased downwards ( in some cases) if sample size (S) is less than true N _e. The bias is shown to arise from inaccuracies in published formula for when S and/or N _e are small. Empirically derived modifications to for two mating systems (random mating and lifetime monogamy) effectively eliminate the bias (residual bias in % in most cases). The modified method also performs well in estimating N _e in non-ideal populations with skewed sex ratio or non-random variance in reproductive success. Recent population declines are not likely to seriously affect , but if N has recently increased from a bottleneck can be biased downwards for a few generations. These results should facilitate application of the disequilibrium method for estimating contemporary N _e in natural populations. However, a comprehensive assessment of performance of with highly polymorphic markers such as microsatellites is needed.The US Governmentȁ9s right to retain a non-exclusive, royalty-free license in and to any copyright is acknowledged.     

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.     

Redox properties of the Fe3+/Fe2+ couple in Arthromyces ramosus class II peroxidase and its cyanide adduct

The thermodynamics of the one-electron reduction of the ferric heme in free and cyanide-bound Arthromyces ramosus peroxidase (ARP), a class II plant peroxidase, were determined through spectro-electrochemical experiments. The data were compared with those for class III horseradish peroxidase C (HRP) and its cyanide adduct, and were interpreted in terms of ligand binding features, electrostatic effects and solvent accessible surface area of the heme group and of catalytically relevant residues in the heme distal site. The values for free and cyanide-bound ARP (−0.183 and −0.390 V, respectively, at 25 °C and pH 7) are higher than those for HRP and HRP-CN. ARP features an enthalpic stabilization of the ferrous state and a remarkably negative reduction entropy, which are both unprecedented for heme peroxidases. Once the compensatory contributions of solvent reorganization are partitioned from the measured reduction enthalpy, the resulting protein-based value for ARP turns out to be less positive than that for HRP by +10 kJ mol⁻¹. The smaller stabilization of the oxidized heme in ARP most probably results from the less pronounced anionic character of the proximal histidine, and the decreased polarity in the heme distal site as compared with HRP, as indicated by the X-ray structures. The surprisingly negative value for ARP is the result of peculiar reduction-induced solvent reorganization effects.     

Species persistence decreases with habitat fragmentation: an analysis in periodic stochastic environments

This paper presents a study of a nonlinear reaction–diffusion population model in fragmented environments. The model is set on , with periodic heterogeneous coefficients obtained using stochastic processes. Using a criterion of species persistence based on the notion of principal eigenvalue of an elliptic operator, we provided a precise numerical analysis of the interactions between habitat fragmentation and species persistence. The obtained results clearly indicated that species persistence strongly tends to decrease with habitat fragmentation. Moreover, comparing two stochastic models of landscape pattern generation, we observed that in addition to local fragmentation, a more global effect of the position of the habitat patches also influenced species persistence.      

Genetic differentiation of Rosa canina (L.) at regional and continental scales

We investigated the genetic differentiation of Rosa canina at regional and continental scales to delineate provenance regions for seed collection. Using RAPD technique, we examined eight populations in Brandenburg (Germany) and 13 samples from Bavaria and Hungary. AMOVA and $\upphiWe investigated the genetic differentiation of Rosa canina at regional and continental scales to delineate provenance regions for seed collection. Using RAPD technique, we examined eight populations in Brandenburg (Germany) and 13 samples from Bavaria and Hungary. AMOVA and -statistics revealed a significant differentiation ( = 0.23, P < 0.0001) between accessions from Brandenburg and the two other regions. The interpopulation differentiation in Brandenburg was low ( = 0.13). We found the greatest interpopulation distance between Hungary and Brandenburg (Hoher Fl?ming, = 0.47) and the lowest between Dahmeland and Hoher Fl?ming (both Brandenburg, = 0.01). UPGMA dendrogram and PCA showed a clear disjunction between Brandenburg and other regions. Due to the outcrossing mating and seed dispersal system, the genetic variation within R. canina populations is moderately high (87% for Brandenburg, 76% for Bavaria and Hungary). The significant genetic differentiation at the continental scale suggests lower gene flow with increasing geographical distance and underlines the usefulness of regional provenances for planting.     

A Combined Patch-Clamp and Electrorotation Study of the Voltage- and Frequency-Dependent Membrane Capacitance Caused by Structurally Dissimilar Lipophilic Anions

Interactions of structurally dissimilar anionic compounds with the plasma membrane of HEK293 cells were analyzed by patch clamp and electrorotation. The combined approach provides complementary information on the lipophilicity, preferential affinity of the anions to the inner/outer membrane leaflet, adsorption depth and transmembrane mobility. The anionic species studied here included the well-known lipophilic anions dipicrylamine (DPA⁻), tetraphenylborate (TPB⁻) and [W₂(CO)₁₀(S₂CH)]⁻, the putative lipophilic anion and three new heterocyclic W(CO)₅ derivatives. All tested anions partitioned strongly into the cell membrane, as indicated by the capacitance increase in patch-clamped cells. The capacitance increment exhibited a bell-shaped dependence on membrane voltage. The midpoint potentials of the maximum capacitance increment were negative, indicating the exclusion of lipophilic anions from the outer membrane leaflet. The adsorption depth of the large organic anions DPA⁻, TPB⁻ and increased and that of W(CO)₅ derivatives decreased with increasing concentration of mobile charges. In agreement with the patch-clamp data, electrorotation of cells treated with DPA⁻ and W(CO)₅ derivatives revealed a large dispersion of membrane capacitance in the kilohertz to megahertz range due to the translocation of mobile charges. In contrast, in the presence of TPB⁻ and no mobile charges could be detected by electrorotation, despite their strong membrane adsorption. Our data suggest that the presence of oxygen atoms in the outer molecular shell is an important factor for the fast translocation ability of lipophilic anions.     

Topological research on diamagnetic susceptibilities of organic compounds

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

Genetic gain from selection for rooting ability and early growth in vegetatively propagated clones of loblolly pine

A successful clonal forestry program for loblolly pine based on rooted cutting technology needs to consider selection for both rooting ability and subsequent field growth. Rooting ability and second-year height were assessed in more than 2,000 clones from 70 full-sib families of loblolly pine. The bivariate analysis of rooting ability from five rooting trials and field growth from six field trials allowed for estimation of the genetic covariance between rooting ability and second-year height for parental effects, full-sib family effects, and the total genetic value of clones within full-sib family. There was a positive genetic relationship between rooting ability and second-year height at all three genetic levels. The genetic correlation at the parental level between rooting ability and second-year height was 0.32. At the full-sib family level, the genetic correlation between traits was 0.39. The correlation of total genetic values of clones for rooting ability and second-year height was 0.29. The genetic gain in rooting ability and second-year height was estimated for a number of deployment options based on various selection scenarios using the best linear unbiased prediction (BLUP) values from the bivariate analysis. The deployment strategies compared were (1) half-sib family deployment, (2) full-sib family deployment, and (3) clonal deployment. Moderate to high family and clonal mean heritabilities, moderate to high type B genetic correlations, and substantial among-family and among-clone genetic variation indicate the potential for increasing rooting efficiency and improving growth.     

Modification of the data-processing method for the turbidimetric bioassay of nisin

The data processing method of the turbidimetric bioassay of nisin was modified to facilitate its industrial application. The influence of the initial indicator concentration was minimized by a redefined specific dose of the bacteriocin as the quotient between the titer of the added bacteriocin and the initial population density of the indicator in the suspension. It was found that d _c = 0.125 μg ml⁻¹ was the critical dose of nisin that can cause a complete inhibition of the indicator, Pediococcus acidilactici UL5, with an initial OD of 0.135. To eliminate the interference of the cell debris, an equation, , exploiting d _c, was formulated to obtain the intrinsic survival proportion. The use of the specific dose of the bacteriocin and the intrinsic survival proportion as parameters of the dose/response curve greatly enhanced its repeatability and feasibility. A dual-dosage approach was developed to further simplify the conventional standard dose/response curve method.     

Phase Behavior, Stability, and Mesomorphism of Monostearin–oil–water Gels

This paper is the characterization of a new material comprised of oil, water, monostearin and stearic acid, which can be used as a heart-friendly, low-saturate, trans fatty acid-free spreadable fat and shortening. Oil–water–monstearin mixtures formed a gel above 2% monostearin and 30% water and were stable over a month’s time. An increase in the storage modulus (G′), and peak melting temperature (T _m) was observed over time, which suggests a slow change in structure to a more solid form. Powder x-ray diffraction measurements at temperatures above the Krafft temperature of the monglyceride (57°C) indicated the existence of a lamellar liquid crystalline phase $ {\left( {L_{\alpha } } \right)} This paper is the characterization of a new material comprised of oil, water, monostearin and stearic acid, which can be used as a heart-friendly, low-saturate, trans fatty acid-free spreadable fat and shortening. Oil–water–monstearin mixtures formed a gel above 2% monostearin and 30% water and were stable over a month’s time. An increase in the storage modulus (G′), and peak melting temperature (T _m) was observed over time, which suggests a slow change in structure to a more solid form. Powder x-ray diffraction measurements at temperatures above the Krafft temperature of the monglyceride (57°C) indicated the existence of a lamellar liquid crystalline phase with a (001) reflection occurring at 50 ?. In addition to the 50 ? reflection at small angles, a wide angle reflection at 4.2 ? was observed upon cooling below 60°C, indicating a transition from the to the phase, which upon storage at 22°C for one day converted to the coagel, or β-gel phase.     

RBE of quasi-monoenergetic 60 MeV neutron radiation for induction of dicentric chromosomes in human lymphocytes

The production of dicentric chromosomes in human lymphocytes by high-energy neutron radiation was studied using a quasi-monoenergetic 60 MeV neutron beam. The average yield coefficient of the linear dose–response relationship for dicentric chromosomes was measured to be (0.146±0.016) Gy⁻¹. This confirms our earlier observations that above 400 keV, the yield of dicentric chromosomes decreases with increasing neutron energy. Using the linear-quadratic dose–response relationship for dicentric chromosomes established in blood of the same donor for ⁶⁰Co γ-rays as a reference radiation, an average maximum low-dose RBE (RBE_M) of 14±4 for 60 MeV quasi-monoenergetic neutrons with a dose-weighted average energy of 41.0 MeV is obtained. A correction procedure was applied, to account for the low-energy continuum of the quasi-monoenergetic spectral neutron distribution, and the yield coefficient α for 60 MeV neutrons was determined from the measured average yield coefficient . For α, a value of (0.115±0.026) Gy⁻¹ was obtained corresponding to an RBE_M of 11±4. The present experiments extend earlier investigations with monoenergetic neutrons to higher energies.     

Biological functions of antioxidants in plant transformation

Browning and necrosis of transformed cells/tissues, and difficulty to regenerate transgenic plants from the transformed cells/tissues (recalcitrance) are common in Agrobacterium-mediated transformation process in many plant species. In addition, most crop transformation methods that use NPTII selection produce a significant number of nontransgenic shoots, called “shoot escapes” even under stringent selection conditions. These common problems of plant transformation, (browning and necrosis of transformed cells/tissues, recalcitrance, and the occurrence of shoot escapes) severely reduces transformation efficiency. Recent research indicates that reactive oxygen species (ROS) such as superoxide radical , the hydrogen peroxide (H₂O₂), the hydroxyl radical (OH′), and the peroxyl radical () may be playing an important role in tissue browning and necrosis during transformation. This review examines the role of ROS in in vitro recalcitrance and genetic transformation and the opportunities to improve transformation efficiency using antioxidants.     

A graph-theoretic method for the basic reproduction number in continuous time epidemiological models

In epidemiological models of infectious diseases the basic reproduction number is used as a threshold parameter to determine the threshold between disease extinction and outbreak. A graph-theoretic form of Gaussian elimination using digraph reduction is derived and an algorithm given for calculating the basic reproduction number in continuous time epidemiological models. Examples illustrate how this method can be applied to compartmental models of infectious diseases modelled by a system of ordinary differential equations. We also show with these examples how lower bounds for can be obtained from the digraphs in the reduction process.     

Theoretical study of AlH(2+)n (n=1-7) dications

The structures and stability of 1–7 dications were calculated at the ab initio MP2/aug-cc-pVTZ level of theory. The dications AlH²⁺ 1 and 2 were characterized to be unstable thermodynamically. However, these and the stable dications, 3–7 have considerable kinetic barriers for deprotonation. Each of the structures 3–7 contains one or more two-electron three-center (2e–3c) bonds. Aluminum atoms of these dications carry most of the positive charges, as indicated by NBO charge calculations.Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday     

Genetic transformation of <Emphasis Type="Italic">Gentiana macrophylla</Emphasis> with <Emphasis Type="Italic">Agrobacterium rhizogenes</Emphasis>: growth and production of secoiridoid glucoside gentiopicroside in transformed hairy root cultures

Hairy root cultures of Gentiana macrophylla were established by infecting the different explants four Agrobacterium rhizogenes strains namely A₄GUS, R1000, LBA 9402 and ATCC11325, and hairy root lines were established with A. rhizogenes strain R1000 in 1/2 MS + B₅ medium. Initially, 42 independent hairy root clones were maintained and seven clones belongs to different category were evaluated for growth, morphology, integration and expression of Ri T-DNA genes, and alkaloid contents in dry root samples. On the basis of total root elongation, lateral root density and biomass accumulation on solid media, hairy root clones were separated into three categories. PCR and Southern hybridization analysis revealed both left and right T-DNA integration in the root clones and RT-PCR analysis confirmed the expression of hairy root inducible gene. GUS assay was also performed to confirm the integration of left T-DNA. The accumulation of considerable amounts of the root-specific secoiridoid glucosides gentiopicroside was observed in GM1 ( and ) and the GM2 ( and DNA) type clones in considerably higher amount whether as two but callus-type clones (GM3) accumulated much less or only very negligible amounts of gentiopicroside. Out of four media composition the 1/2 MS + B₅ vitamin media was found most suitable. We found that initial establishment of root cultures largely depends on root:media ratio. Maximum growth rate was recorded in 1:50 root:media ratio. The maximum biomass in terms of fresh weight (33-fold) was achieved in 1/2 MS + B₅ media composition after 35 days in comparison to sixfold increase in control. The biomass increase was most abundant maximum from 15 to 30 days. Influence of A. rhizogenes strains and Ri plasmid of hairy root induction, the possible role of the T_L-DNA and T_R-DNA genes on growth pattern of hairy root, initial root inoculum:media ratio and effect of media composition is discussed.