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.     

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.     

Genotype by environment interaction for growth of Eucalyptus globulus in Australia

This study assessed the genotype by environment (G × E) interaction for diameter growth in 15 Eucalyptus globulus progeny trials in Australia. Single-site analyses revealed significant subrace and family-within-subrace variance in all trials. Across-site subrace () and family () correlations were estimated by linear mixed model analyses of pairs of trials. Using a factor analytic structure for subrace and family random terms in a multi-environment mixed model analysis, best linear unbiased predictions of subrace effects were obtained for each trial. These were then averaged for each of four states (Victoria, Tasmania, South Australia and Western Australia) and across all sites. Statistically significant G × E interaction was detected, and weighted means across states for and were 0.73 and 0.76, respectively. Nevertheless, the three subraces from the Otway Ranges were both fast growing and relatively stable in their ranks over all sites. We evaluated the sensitivity of subraces to changing environmental conditions, on the basis of random coefficient models regressing subrace performance on selected trial climatic variables. The results suggested differential susceptibility of subraces to water, light and (to a less extent) temperature stresses during summer. Moreover, using multivariate techniques to visualize and interpret the across-site correlation structure for subrace effects, we could identify site clusters of reduced G × E interaction related to soil water availability and evaporative demand during summer. A revised site-type classification using these factors should allow a better capture of genetic gains from breeding and deployment.     

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.     

Genetic structure of an insect-pollinated and bird-dispersed tropical tree in vegetation fragments and corridors: implications for conservation

In the vegetation corridors that connect small remnants of undisturbed primary forest in the Lavras landscape (Brazil), Protium spruceanum is a representative of a mass-flowering insect-pollinated and bird-dispersed tree. Allozyme variation was quantified from five forest remnants (N = 150) from secondary vegetation corridors linking them (N = 80) to generate information for genetic conservation. The species adhered to H-W equilibrium in all fragments in most of the loci. The results indicated high gene diversity in the fragments and corridors positively correlated with the plant density (r = 0.742, R ² = 0.551, d.f. = 4). We did not find evidence of inbreeding within fragments nor overall The genetic differentiation among remnants was low Evidence of recent bottlenecks by anthropogenic disturbance was detected in fragments (P < 0.05, Wilcoxon sign-rank test). The minimal viable population was estimated for conservation in situ, indicating fragments with possibilities of maintaining genetic equilibrium diversity in the short term (except F3) and in the long term (only F5). The ratios was also calculated to contribute to vegetation enrichment, area recovery or creation of new vegetation corridors. We found high levels of gene diversity in the vegetation corridors, genetic identity with the fragments and absence of inbreeding. Thus, our results suggest that landscape management strategies should therefore consider both the creation of new vegetation corridors and the protection of extant ones.     

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.     

Bifurcation Analysis of Genetically Engineered Pacemaking in Mammalian Heart

Genetically engineered pacemaking in ventricular cells has been achieved by down-regulation of the time independent inward rectifying current (I _K1), or insertion of the hyperpolarisation-activated funny current (I _f). We analyse the membrane system (i.e. ionic concentrations clamped) of an epicardial Luo-Rudy dynamic cell model using continuation algorithms with the maximum conductance () of I _K1 and I _f as bifurcation parameters. Pacemaker activity can be induced either via Hopf or homoclinic bifurcations. As _K1 is decreased by ≈74%, autorhythmicity emerged via a homoclinic bifurcation, i.e., the periodicity first appear with infinitely large periods. In contrast, the insertion of _f induced periodicity via a subcritical Hopf bifurcation at _f≈ 0.25 mSμF⁻¹. Stable autorhythmic action potentials occurred at _f > 0.329 mSμF⁻¹.     

Threshold Conditions for a Non-Autonomous Epidemic System Describing the Population Dynamics of Dengue

A non-autonomous dynamical system, in which the seasonal variation of a mosquito vector population is modeled, is proposed to investigate dengue overwintering. A time-dependent threshold, R(t), is deduced such that when its yearly average, denoted by , is less than 1, the disease does not invade the populations and when is greater than 1 it does. By not invading the population we mean that the number of infected individuals always decrease in subsequent seasons of transmission. Using the same threshold, all the qualitative features of the resulting epidemic can be understood. Our model suggests that trans-ovarial infection in the mosquitoes facilitates dengue overwintering. We also explain the delay between the peak in the mosquitoes population and the peak in dengue cases. An erratum to this article can be found at     

Soil algal communities inhabiting zinc and lead mine spoils

Algal communities inhabiting four calamine mine spoils differing in time since cessation of exploitation and loaded with high concentrations of zinc (20,284–61,599 μg g⁻¹ soil DW), lead (2,620–3,885 μg g⁻¹ DW) and cadmium (104–232 μg g⁻¹ DW) were studied. In dump soils of slightly alkaline pH (7.28–7.52) and low nutrient (, , ) concentrations, chlorophyll a content ranged from 0.41 to 2.27 μg g⁻¹ soil DW. In total, 23 algal species were recorded. Chlorophyta were the dominant taxonomic group (42–55% of all identified species) followed by Cyanobacteria (28–36%) and Heterokontophyta (13–21%). The highest species richness (18) was observed in the oldest dump (120 years old) with natural succession, while in younger dumps it was lower (11–15). Total algal abundance ranged between 5.5 and 19.1 × 10² ind. g⁻¹ soil DW, and values of Margalef’s diversity indices (1.59–2.25) were low. These results may suggest that both high concentrations of heavy metals and low nutrient content influenced the algal communities in all the dumps studied. The differences in algal microflora observed between tailing dumps may indicate that habitat quality improved with time and that algae isolated from Zn/Pb-loaded soils may be Zn/Pb-resistant ecotypes of ubiquitous species.     

Genetic relatedness and genetic diversity of ornamental mei (Prunus mume Sieb. et Zucc.) as analysed by AFLP markers

The genetic diversity and genetic relatedness of mei (Prunus mume; 2n = 16) were studied using amplified fragment length polymorphism (AFLP) markers. Eight EcoRI–PstI AFLP primer combinations were applied to 121 distinct genotypes of mei cultivars and related species. A total of 508 AFLP product bands were produced, of which 382 were polymorphic. The unweighted pair group method with arithmetic averages analysis was carried out based on these AFLP markers. From this analysis, “Qugeng Mei,” “Yan Mei,” “Chaodou Mei,” and mei cultivars were seen to share the same P. mume genetic stem. The AFLP data were able to clearly discriminate P. mume from other species in the genus Prunus, with P. armeniaca aligning as its closest related species. Two major groups and nine subgroups of mei flower were identified, and there was a strong coincidence of these AFLP-based groupings with the respective morphological characters of the accessions. The genetic diversity of mei accessions was greatest in the Yunnan Province and decreased toward Eastern China and Japan, so supporting the hypothesis that the southwest of China represents the genetic diversity center of the species.     

Deletion of a 236 kb region around S 4-RNase in a stylar-part mutant S 4 sm -haplotype of Japanese pear

Japanese pear (Pyrus pyrifolia Nakai) has a gametophytic self-incompatibility (GSI) mechanism controlled by a single S-locus with multiple S-haplotypes, each of which contains separate genes that determine the allelic identity of pistil and pollen. The pistil S gene is the S-ribonuclease (S-RNase) gene, whereas good candidates for the pollen S gene are the F-box protein genes. A self-compatible (SC) cultivar, ‘Osa-Nijisseiki’, which is a bud mutant of ‘Nijisseiki’ (S ₂ S ₄), has a stylar-part mutant -haplotype, which lacks the S ₄-RNase gene but retains the pollen S gene. To delineate the deletion breakpoint in the -haplotype, we constructed a bacterial artificial chromosome (BAC) library from an S ₄-homozygote, and assembled a BAC contig of 570 kb around the S ₄-RNase. Genomic PCR of DNA from S ₄- and -homozygotes and the DNA sequence of the BAC contig allowed the identification of a deletion of 236 kb spanning from 48 kb upstream to 188 kb downstream of S ₄-RNase. The -haplotype lacks 34 predicted open reading frames (ORFs) including the S ₄-RNase and a pollen-specific F-box protein gene (termed as S ₄ F-box0). Genomic PCR with a primer pair designed from the deletion junctions yielded a product specific for the -haplotype. The product could be useful as a maker for early selection of SC cultivars harboring the -haplotype. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

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.     

Hydrochemical fluctuations and crustacean community composition in an ephemeral saline lake (Sua Pan,Makgadikgadi Botswana)

Fluctuating hydrochemistry, as a result of extreme hydrological regimes, imposes major physiological constraints on the biota of ephemeral saline lakes. While the inverse relationship between salinity and zooplankton species richness is well-known across salinity gradients, few studies have documented closely the response of zooplankton to seasonal changes in salinity. Weekly sampling during two flood seasons at Sua Pan, an intermittent saline lake in central Botswana demonstrated the importance of spatial and temporal salinity gradients for crustacean community composition, associated with a decline in species richness, from 11 to three species. Conductivity ranged between 320 and 125,800 μS cm⁻¹ during seasonal flooding; changing from dominance by and , Ca²⁺ and Mg²⁺, at the beginning of the floods, to NaCl dominated waters as the lake dried out and salinities increased. pH estimates generally ranged between 8.6 and 10, with maximum values recorded during initial flooding. Crustaceans comprised mainly Branchinella spinosa, Moina belli, Lovenula africana and Limnocythere tudoranceai, all of which occurred across a wide range of salinities, while halotolerant freshwater species (Metadiaptomus transvaalensis, Leptestheria striatochonca and the ostracods Plesiocypridopsis aldabrae, Cypridopsis newtoni and a newly identified Potamocypris species) disappeared above conductivities of 1,500 μS cm⁻¹. A unique crustacean composition in southern Africa was attributed to Sua Pans’ rare chemical composition among southern African saline lakes; flood waters on Sua Pan contained a higher proportion of Na⁺ and , and less K⁺, Mg²⁺ and than over 80% of records from salt pans elsewhere in southern African. The freshwater species of crustaceans in Sua Pan were similar to those found in other southern Africa lakes, and these similarities decreased in lakes with higher pH and proportions of Na, and less SO₄ and Mg in their chemical composition. The predominant saline tolerant species on Sua Pan, however, showed a greater similarity to those in saline lakes in southern and East Africa with higher proportions of and, particularly, Mg²⁺ in their chemical composition. Handling editor: J. M. Melack     

Can biological nitrification inhibition (BNI) genes from perennial Leymus racemosus (Triticeae) combat nitrification in wheat farming?

Using a recombinant luminescent Nitrosomonas europaea assay to quantify biological nitrification inhibition (BNI), we found that a wild relative of wheat (Leymus racemosus (Lam.) Tzvelev) had a high BNI capacity and releases about 20 times more BNI compounds (about 30 ATU g⁻¹ root dry weight 24 h⁻¹) than Triticum aestivum L. (cultivated wheat). The root exudate from cultivated wheat has no inhibitory effect on nitrification when applied to soil; however, the root exudate from L. racemous suppressed formation and kept more than 90% of the soil’s inorganic-N in the -form for 60 days. The high-BNI capacity of L. racemosus is mostly associated with chromosome Lr#n. Two other chromosomes Lr#J, and Lr#I also have an influence on BNI production. Tolerance of L. racemosus to is controlled by chromosome 7Lr#1-1. Sustained release of BNI compounds occurred only in the presence of in the root environment. Given the level of BNI production expressed in DALr#n and assuming normal plant growth, we estimated that nearly 87,500,000 ATU of BNI activity ha⁻¹ day⁻¹ could be released in a field of vigorously growing wheat; this amounts to the equivalent of the inhibitory effect from the application of 52.5 g of the synthetic nitrification inhibitor nitrapyrin (one AT unit of BNI activity is equivalent to 0.6 μg of nitrapyrin). At this rate of BNI production it would take only 19 days for a BNI-enabled wheat crop to produce the inhibitory power of a standard commercial application of nitrapyrin, 1 kg ha⁻¹. The synthetic nitrification inhibitor, dicyandiamide, blocked specifically the AMO (ammonia monooxygenase) pathway, while the BNI from L. racemosus blocked the HAO (hydroxylamine oxidoreductase) pathway in Nitrosomonas. Here we report the first finding of high production of BNI in a wild relative of any cereal and its successful introduction and expression in cultivated wheat. These results demonstrate the potential for empowering the new generation of wheat cultivars with high-BNI capacity to control nitrification in wheat-production systems. Responsible Editor: Hans Lambers.     

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.     

Leaching losses of inorganic N and DOC following repeated drying and wetting of a spruce forest soil

Forest soils are frequently subjected to dry–wet cycles, but little is known about the effects of repeated drying and wetting and wetting intensity on fluxes of , and DOC. Here, undisturbed soil columns consisting of organic horizons (O columns) and organic horizons plus mineral soil (O + M columns) from a mature Norway spruce stand at the Fichtelgebirge; Germany, were repeatedly desiccated and subsequently wetted by applying different amounts of water (8, 20 and 50 mm day⁻¹) during the initial wetting phase. The constantly moist controls were not desiccated and received 4 mm day⁻¹ during the entire wetting periods. Cumulative inorganic N fluxes of the control were 12.4 g N m⁻² (O columns) and 11.4 g N m⁻² (O + M columns) over 225 days. Repeated drying and wetting reduced cumulative and fluxes of the O columns by 47–60 and 76–85%, respectively. Increasing (0.6–1.1 g N m⁻²) and decreasing fluxes (7.6–9.6 g N m⁻²) indicate a reduction in net nitrification in the O + M columns. The negative effect of dry–wet cycles was attributed to reduced net N mineralisation during both the desiccation and wetting periods. The soils subjected to dry–wet cycles were considerably drier at the final wetting period, suggesting that hydrophobicity of soil organic matter may persist for weeks or even months. Based on results from this study and from the literature we hypothesise that N mineralisation is mostly constrained by hydrophobicity in spruce forests during the growing season. Wetting intensity did mostly not alter N and DOC concentrations and fluxes. Mean DOC concentrations increased by the treatment from 45 mg l⁻¹ to 61–77 mg l⁻¹ in the O tlsbba columns and from 12 mg l⁻¹ to 21–25 mg l⁻¹ in the O + M columns. Spectroscopic properties of DOC from the O columns markedly differed within each wetting period, pointing to enhanced release of rather easily decomposable substrates in the initial wetting phases and the release of more hardly decomposable substrates in the final wetting phases. Our results suggest a small additional DOC input from organic horizons to the mineral soil owing to drying and wetting.     

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.     

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.