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.     

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.     

Immobilization of the recombinant invertase INVB from <Emphasis Type="Italic">Zymomonas mobilis</Emphasis> on Nylon-6

The recombinant invertase INVB (re-INVB) from Zymomonas mobilis was immobilized on microbeads of Nylon-6, by means of covalent bonding. The enzyme was strongly and successfully bound to the support. The activity of the free and immobilized enzyme was determined, using 10% (w/v) sucrose, at a temperature ranging between 15 and 60 °C and a pH ranging between 3.5 and 7. The optimal pH and temperature for the immobilized enzyme were 5.5 and 25 °C, respectively. Immobilization of re-INVB on Nylon-6 showed no significant change in the optimal pH, but a difference in the optimal temperature was evident, as that for the free enzyme was shown to be 40 °C. The values for kinetic parameters were determined as: 984 and 98 mM for of immobilized and free re-INVB, respectively. values for immobilized and free enzymes were 6.1 × 10² and 1.2 × 10⁴ s⁻¹, respectively, and immobilized re-INVB showed of 158.73 μmol h min⁻¹ mg⁻¹. Immobilization of re-INVB on Nylon-6 enhanced the thermostability of the enzyme by 50% at 30 °C and 70% at 40 °C, when compared to the free enzyme. The immobilization system reported here may have future biotechnological applications, owing to the simplicity of the immobilization technique, the strong binding of re-INVB to the support and the effective thermostability of the enzyme.     

Phase Transitions of Frozen Camu-camu (Myrciaria dubia (H.B.K.) McVaugh) Pulp: Effect of Cryostabilizer Addition

Camu-camu is a tropical fruit with very high vitamin C content and commercialized as frozen pulp. Enthalpies of freezing, temperatures of the onset of ice melting, and glass transition temperatures of the maximally freeze-concentrated phase () of camu-camu pulp and of samples containing maltodextrin (DE20) and sucrose were measured by differential scanning calorimetry. Maltodextrin exhibited the largest freeze stabilization potential, increasing from −58.2 °C (natural pulp) to −39.6 °C when 30% (w/w) maltodextrin DE 20 was added. Sucrose showed negligible effect on but enhanced considerably the freezing point depression and less amount of ice was formed.     

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.     

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.     

Factors affecting denitrification in agricultural headwater streams in Northeast Ohio,USA

As a result of increased anthropogenic nitrogen (N) loading in surface waters of agricultural watersheds, there is enhanced interest to understand and quantify N removal mechanisms. Denitrification, an important N removal mechanism in aquatic systems, may contribute to reducing N pollution in agricultural headwater streams. However, the key factors controlling this process in lotic systems remain unclear. The objective of our study was to examine the factors regulating rates of denitrification in the sediments of agricultural headwater streams in the mid-western USA. Denitrification rates were variable among streams and treatments (<0.1–28.0 μg N g AFDM⁻¹ h⁻¹) and on average, were higher than those reported for similar headwater streams. Carbon quantity and quality, and pH had no effect on denitrification, while temperature and nitrate ( ) concentrations had a positive effect on rates of denitrification. Specifically, controlled denitrification following Michaelis-Menten kinetics. We calculated a value of k_m (1.0 mg -N L^-1) that was comparable to other studies in aquatic sediments but was well below the median in-stream concentrations (5.2–17.4 mg -N L⁻¹) observed at the study sites. Despite high rates of denitrification, this removal mechanism is most likely saturated in the agricultural headwater streams we examined, suggesting that these systems are not effective at removing in-stream N. Handling editor: D. Ryder     

Concentration-Dependent Effects on Intracellular and Surface pH of Exposing <Emphasis Type="Italic">Xenopus</Emphasis> oocytes to Solutions Containing NH<Subscript>3</Subscript>/NH<Subscript>4</Subscript><Superscript>+</Superscript>

Others have shown that exposing oocytes to high levels of (10–20 mM) causes a paradoxical fall in intracellular pH (pH_i), whereas low levels (e.g., 0.5 mM) cause little pH_i change. Here we monitored pH_i and extracellular surface pH (pH_S) while exposing oocytes to 5 or 0.5 mM NH₃/NH₄ ⁺. We confirm that 5 mM causes a paradoxical pH_i fall (−ΔpH_i ≅ 0.2), but also observe an abrupt pH_S fall (−ΔpH_S ≅ 0.2)—indicative of NH₃ influx—followed by a slow decay. Reducing [NH₃/NH₄ ⁺] to 0.5 mM minimizes pH_i changes but maintains pH_S changes at a reduced magnitude. Expressing AmtB (bacterial Rh homologue) exaggerates −ΔpH_S at both levels. During removal of 0.5 or 5 mM NH₃/NH₄ ⁺, failure of pH_S to markedly overshoot bulk extracellular pH implies little NH₃ efflux and, thus, little free cytosolic NH₃/NH₄ ⁺. A new analysis of the effects of NH₃ vs. NH₄ ⁺ fluxes on pH_S and pH_i indicates that (a) NH₃ rather than NH₄ ⁺ fluxes dominate pH_i and pH_S changes and (b) oocytes dispose of most incoming NH₃. NMR studies of oocytes exposed to ¹⁵N-labeled show no significant formation of glutamine but substantial accumulation in what is likely an acid intracellular compartment. In conclusion, parallel measurements of pH_i and pH_S demonstrate that NH₃ flows across the plasma membrane and provide new insights into how a protein molecule in the plasma membrane—AmtB—enhances the flux of a gas across a biological membrane.

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 .     

Kinetics and mechanistic studies of the reactions of metleghemoglobin, ferrylleghemoglobin, and nitrosylleghemoglobin with reactive nitrogen species

It is now established that nitrogen monoxide is produced not only in animals but also in plants. However, much less is known about the pathways of generation and the functions of in planta. One of the possible targets of is leghemoglobin (Lb), the hemoprotein found in high concentrations in the root nodules of legumes that establish a symbiosis with nitrogen-fixing bacteria. In analogy to hemoglobin and myoglobin, we have shown that different forms of Lb react not only with , but also with so-called reactive nitrogen species derived from it, among others peroxynitrite and nitrite. Because of the wider active-site pocket, the rate constants measured in this work for and for nitrite binding to metLb are 1 order of magnitude larger than the corresponding values for binding of these species to metmyoglobin and methemoglobin. Moreover, we showed that reactive nitrogen species are able to react with two forms of Lb that are produced in vivo but that cannot bind oxygen: ferrylLb is reduced by and nitrite, and nitrosylLb is oxidized by peroxynitrite. The second-order rate constants of these reactions are on the order of 10², 10⁶, and 10⁵ M⁻¹ s⁻¹, respectively. In all cases, the final reaction product is metLb, a further Lb form that has been detected in vivo. Since a specific reductase is active in nodules, which reduces metLb, reactive nitrogen species could contribute to the recycling of these inactive forms to regenerate deoxyLb, the oxygen-binding form of Lb.     

Probing the interactions of the solvated electron with DNA by molecular dynamics simulations: II. bromodeoxyuridine-thymidine mismatched DNA

The interaction of solvated electrons with DNA results in various types of DNA lesions. The in vitro and in vivo sensitisation of DNA to -induced damage is achieved by incorporation of the electron-affinity radiosensitiser bromodeoxyuridine (BUdR) in place of thymidine. However, in DNA duplexes containing single-stranded regions (bulged BUdR-DNA), the type of lesion is different and the efficiency of damage is enhanced. In particular, DNA interstrand crosslinks (ICL) form at high efficiency in bulged DNA but are not detectable in completely duplex DNA. Knowledge about the processes and interactions leading to these differences is obscure. Previously, we addressed the problem by applying molecular modelling and molecular dynamics (MD) simulations to a system of normal (BUdR·A)-DNA and a hydrated electron, where the excess electron was modelled as a localised eˉ(H₂O)₆ anionic cluster. The goal of the present study was to apply the same MD simulation to a wobble system, containing a pyrimidine–pyrimidine mismatched base pair, BUdR·T. The results show an overall dynamic pattern similar to that of the motion around normal DNA. However, the number of configuration states when was particularly close to DNA is different. Moreover, in the (BUdR·T)-wobble DNA system, the electron frequently approaches the brominated strand, including BUdR, which was not observed with the normal (BUdR·A)-DNA. The structure and exchange of water at the sites of immobilisation near DNA were also characterised. The structural dynamics of the wobble DNA is prone to more extensive perturbations, including frequent formation of cross-strand (cs) interatomic contacts. The structural deviations correlated with approaching DNA from the major groove side, with sodium ions trapped deep in the minor groove. Altogether, the obtained results confirm and/or throw light on dynamic-structure determinants possibly responsible for the enhanced radiation damage of wobble DNA. Figure The structure of the tightly bound single water-layer between the DNA and the electron (Site-8, five H₂O molecules, bold capped sticks); the rest of the “second” shell waters (lines, in atom type colour) surround the ˉ(H₂O)₆ cluster (yellow, space fill). Orange dashed lines H-bonds; only one of the five molecules from the single H₂O layer mediates a single-step H-bond bridge with N7(A8); the other four present a network of two(three)-step H-bond bridges between DNA/ partner atoms     

Determination of the chemical composition of ulvan, a cell wall polysaccharide from Ulva spp. (Ulvales, Chlorophyta) by FT-IR and chemometrics

The water-soluble cell wall polysaccharides from green seaweeds of Ulva spp. (Ulvales, Chlorophyta), referred to as ulvan, demonstrate composition- and structure-related functional properties. Mid-infrared spectroscopy combined with chemometric techniques was investigated as a means to rapidly predict the chemical composition of ulvan extracts. A calibration was realized with 41 ulvan extracts from two Ulva species. The variables studied included the constituent sugars (rhamnose, xylose, glucose, galactose, glucuronic acid, iduronic acid), protein, and sulfate contents. The correlation between Fourier transform infrared and chemical data was developed using partial least squares (PLS) regression with full cross-validation (leave one out). The coefficients of determination in cross-validation () and the standard error in cross-validation were determined for each variable. The PLS model validation resulted in a coefficient of determination () and a standard error in prediction. Good predictions were obtained for rhamnose ( = 0.9244), xylose ( = 0.8758), glucuronic acid ( = 0.9415), and sulfate ( = 0.9218), which are the main ulvan constituents. However, minor components such as proteins, glucose, galactose, and iduronic acid were not correctly predicted. This study showed that mid-infrared spectroscopy combined with PLS regression is a reliable and fast method for the quantification of the main chemical constituents of ulvan extracts.     

Three-dimensional quantitative structure-activity relationship (3D-QSAR) studies of various benzodiazepine analogues of γ-secretase inhibitors

A 3D QSAR analysis has been performed on a series of 67 benzodiazepine analogues reported as γ-secretase inhibitors using molecular field analysis (MFA), with G/PLS to predict steric and electrostatic molecular field interaction for the activity. The MFA study was carried out using a training set of 54 compounds. The predictive ability of model developed was assessed using a test set of 13 compounds ( as high as 0.729). The analyzed MFA model has demonstrated a good fit, having r² value of 0.858 and cross validated coefficient, value as 0.790. The analysis of the best MFA model provided insight into possible modification of the molecules for better activity.   Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

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.     

The effect of temperature on post-feeding ammonia excretion and oxygen consumption in the southern catfish

The post-prandial rates of ammonia excretion (TAN) and oxygen consumption in the southern catfish (Silurus meridionalis) were assessed at 2 h intervals post-feeding until the rates returned to those of the fasting rates, at 17.5, 22.5, 27.5, and 32.5°C, respectively. Both fasting TAN and increased with temperature, and were lower than those previously reported for many fish species. The relationship between fasting TAN (mmol NH₃–N kg⁻¹ h⁻¹) and temperature (T, °C) was described as: fasting TAN = 0.144e ^0.0266T (r = 0.526, n = 27, P < 0.05). The magnitude of ammonia excretion and its ratio to total N intake during the specific dynamic action (SDA) tended to increase initially, and then decrease with increasing temperature. The ammonia quotient (AQ), calculated as mol NH₃–N/mol O₂, following feeding decreased as temperature increased. The relationship between AQ during SDA and temperature was described as: AQ_{during SDA} = 0.303e ^−0.0143T (r = 0.739, n = 21, P < 0.05). Our results suggest that ammonia excretion and oxygen consumption post-feeding are operating independently of each other. Furthermore, it appears that the importance of protein as a metabolic substrate in postprandial fish decreases with temperature.     

Insect cells respiratory activity in bioreactor

Specific respiration rate ( ) is a key parameter to understand cell metabolism and physiological state, providing useful information for process supervision and control. In this work, we cultivated different insect cells in a very controlled environment, being able to measure . Spodoptera frugiperda (Sf9) cells have been used through virus infection as host for foreign protein expression and bioinsecticide production. Transfected Drosophila melanogaster (S2) cells can be used to produce different proteins. The objective of this work is to investigate respiratory activity and oxygen transfer during the growth of different insect cells lines as Spodoptera frugiperda (Sf9), Drosophila melanogaster (S2) wild and transfected for the expression of GPV and EGFP. All experiments were performed in a well-controlled 1-L bioreactor, with SF900II serum free medium. Spodoptera frugiperda (Sf9) cells reached 10.7 × 10⁶ cells/mL and maximum specific respiration rate () of 7.3 × 10⁻¹⁷ molO₂/cell s. Drosophila melanogaster (S2) cells achieved 51.2 × 10⁶ cells/mL and of 3.1 × 10^–18 molO₂/cell s. S2AcGPV (expressing with rabies virus glycoprotein) reached 24.9 × 10⁶ cells/mL and of 1.7 × 10^–17 molO₂/cell s, while S2MtEGFP (expressing green fluorescent protein) achieved 15.5 × 10⁶ cells/mL and  = 1.9 × 10⁻¹⁷ molO₂/cell s. Relating to the Sf9, S2 cells reached higher maximum cell concentrations and lower specific respiration rate, which can be explained by its smaller size. These results presented useful information for scale-up and process control of insect cells.     

Determination of the average shear rate in a stirred and aerated tank bioreactor

A method for evaluating the average shear rate () in a stirred and aerated tank bioreactor has been proposed for non-Newtonian fluids. The volumetric oxygen transfer coefficient (k _L a) was chosen as the appropriate characteristic parameter to evaluate the average shear rate (). The correlations for the average shear rate as a function of N and rheological properties of the fluid (K and n) were obtained for two airflow rate conditions (ϕ_air). The shear rate values estimated by the proposed methodology lay within the range of the values calculated by classical correlations. The proposed correlations were utilized to predict the during the Streptomyces clavuligerus cultivations carried out at 0.5 vvm and four different rotational impeller speeds. The results show that the values of the average shear rate () varied from 437 to 2,693 s⁻¹ by increasing with N and flow index (n) and decreasing with the fluid consistency index (K).     

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.