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.     

Regional Assessment of N Saturation using Foliar and Root \varvec {\delta}^{\bf 15}{\bf N}

N saturation induced by atmospheric N deposition can have serious consequences for forest health in many regions. In order to evaluate whether foliar may be a robust, regional-scale measure of the onset of N saturation in forest ecosystems, we assembled a large dataset on atmospheric N deposition, foliar and root and N concentration, soil C:N, mineralization and nitrification. The dataset included sites in northeastern North America, Colorado, Alaska, southern Chile and Europe. Local drivers of N cycling (net nitrification and mineralization, and forest floor and soil C:N) were more closely coupled with foliar than the regional driver of N deposition. Foliar increased non-linearly with nitrification:mineralization ratio and decreased with forest floor C:N. Foliar was more strongly related to nitrification rates than was foliar N concentration, but concentration was more strongly correlated with N deposition. Root was more tightly coupled to forest floor properties than was foliar . We observed a pattern of decreasing foliar values across the following species: American beech>yellow birch>sugar maple. Other factors that affected foliar included species composition and climate. Relationships between foliar and soil variables were stronger when analyzed on a species by species basis than when many species were lumped. European sites showed distinct patterns of lower foliar , due to the importance of ammonium deposition in this region. Our results suggest that examining values of foliage may improve understanding of how forests respond to the cascading effects of N deposition.     

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.     

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.     

Use of isotopic signatures to assess the food web in a tropical shallow marine ecosystem of Southeastern Brazil

A dual isotope approach was used to assess the relative importance of terrestrial vegetation detritus and other primary producers in the trophic web of Flamengo Sound (Ubatuba, SP), SE Brazil, surrounded by the Atlantic Rain Forest. Primary producers showed distinct C signatures and the observed values suggest that little terrestrial or bulk sediment organic matter enter the food web of the sound. Suspended particulate organic matter (POM, supports the bulk of the consumers, with some contribution by macroalgae . Consumers C values ranged from −17.4 to . At least three trophic levels were detectable in the food web. The N value of POM was , while that of sediment and detritus was . The N values of suspension feeding benthic invertebrates were 8.2–, deposit feeders 8.3–, and carnivores 10.7–. Values for fishes were for detritivore, 11.4– for benthic feeders, 12.4– for zooplanktivores, and for piscivores/benthic invertebrate feeders. Squid mean value was . There is a reasonable agreement between feeding habits information from the literature and N values from this study. In the sound, the first and second trophic steps seem to be about 1– higher than those of similar organisms studied in temperate waters and this may reflect an input of allochtonous anthropogenic nitrogen enriched in ¹⁵N from human activities.     

Comparisons of genetic parameters and clonal value predictions from clonal trials and seedling base population trials of radiata pine

Different methods for predicting clonal values were explored for diameter growth (diameter at breast height (DBH)) in a radiata pine clonal forestry program: (1) clones were analyzed with a full model in which the total genetic variation was partitioned into additive, dominance, and epistasis (Clone Only—Full Model); (2) clones were analyzed together with seedling base population data (Clone Plus Seedling (CPS)), and (3) clones were analyzed with a reduced model in which the only genetic term was the total genetic variance (Clone Only—Reduced Model). DBH was assessed at age 5 for clones and between ages 4 to 13 at the seedling trials. Significant additive, dominance, and epistatic genetic effects were estimated for DBH using the CPS model. Nonadditive genetic effects for DBH were 87% as large as additive genetic effects. Narrow-sense () and broad-sense () heritability estimates for DBH using the CPS model were 0.14 ± 0.01 and 0.26 ± 0.01, respectively. Accuracy of predicted clonal values increased 4% by combining the clone and seedling data over using clonal data alone, resulting in greater confidence in the predicted genetic performance of clones. Our results indicate that exploiting nonadditive genetic effects in clonal varieties will generate greater gains than that typically obtainable from conventional family-based forestry of radiata pine. The predicted genetic gain for DBH from deployment of the top 5% of clones was 24.0%—an improvement of more than 100% over family forestry at the same selection intensity. We conclude that it is best practice to predict clonal values by incorporating seedling base population data in the clonal analysis.     

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.     

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.     

Regional Assessment of N Saturation using Foliar and Root $\varvec {\delta}^{\bf 15}{\bf N}$\varvec {\delta}^{\bf 15}{\bf N}

N saturation induced by atmospheric N deposition can have serious consequences for forest health in many regions. In order to evaluate whether foliar may be a robust, regional-scale measure of the onset of N saturation in forest ecosystems, we assembled a large dataset on atmospheric N deposition, foliar and root and N concentration, soil C:N, mineralization and nitrification. The dataset included sites in northeastern North America, Colorado, Alaska, southern Chile and Europe. Local drivers of N cycling (net nitrification and mineralization, and forest floor and soil C:N) were more closely coupled with foliar than the regional driver of N deposition. Foliar increased non-linearly with nitrification:mineralization ratio and decreased with forest floor C:N. Foliar was more strongly related to nitrification rates than was foliar N concentration, but concentration was more strongly correlated with N deposition. Root was more tightly coupled to forest floor properties than was foliar . We observed a pattern of decreasing foliar values across the following species: American beech>yellow birch>sugar maple. Other factors that affected foliar included species composition and climate. Relationships between foliar and soil variables were stronger when analyzed on a species by species basis than when many species were lumped. European sites showed distinct patterns of lower foliar , due to the importance of ammonium deposition in this region. Our results suggest that examining values of foliage may improve understanding of how forests respond to the cascading effects of N deposition.     

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.     

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.     

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.     

Genetic variation in nine Shorea species (Dipterocarpaceae) in Indonesia revealed by AFLPs

Shorea is the largest and most important genus of the Dipterocarpaceae. The genetic diversity and structure of nine Shorea species from two different locations, namely Nanjak Makmur in Sumatra and Sumalindo in Borneo, were evaluated using amplified fragment length polymorphism (AFLP) markers. A total of 274 trees were investigated at 85 polymorphic AFLP loci. Levels of genetic diversity of these species ranged from  = 0.100 for S. acuminata to  = 0.165 for S. blumutensis. The population of rare species S. blumutensis possessed the highest genetic diversity suggesting that geographically restricted species can have levels of genetic variation comparable to closely related widespread common congeners. Analyses of molecular variance revealed that the genetic variation was mainly found among species in both locations (57.7% in Sumatra; 56.3% in Borneo). The unweighted pairgroup method using arithmetic averages dendrogram of all samples revealed an almost complete separation of species. Thus, AFLP markers proved appropriate for phylogenetic studies of Shorea species. Specific markers have been detected showing high-frequency differences among species and between regions within species. Sequence information of these markers can be used to develop specific polymerase chain reaction markers for wood identification. The possibility of interspecific hybridization was discussed.     

Probing the interactions of the solvated electron with DNA by molecular dynamics simulations: bromodeoxyuridine substituted DNA

Solvated electrons () are produced during water radiolysis and can interact with biological substrates, including DNA. To augment DNA damage, radiosensitizers such as bromo-deoxyuridine (BUdR), often referred to as an “electron affinic radiosensitizer”, are incorporated in place of isosteric thymidine. However, little is known about the primary interactions of with DNA. In the present study we addressed this problem by applying molecular modeling and molecular dynamics (MD) simulations to a system of normal (BUdR·A)-DNA and a hydrated electron, where the excess electron was modeled as a localized (H₂O)₆ anionic cluster. Our goals were to evaluate the suitability of the MD simulations for this application; to characterize the motion of around DNA (e.g., diffusion coefficients); to identify and describe configurational states of close localization to DNA; and to evaluate the structural dynamics of DNA in the presence of . The results indicate that has distinct space-preferences for forming close contacts with DNA and is more likely to interact directly with nucleotides other than BUdR. Several classes of DNA - contact sites, all within the major groove, were distinguished depending on the structure of the intermediate water layer H-bonding pattern (or its absence, i.e., a direct H-bonding of with DNA bases). Large-scale structural perturbations were identified during and after the approached the DNA from the major groove side, coupled with deeper penetration of sodium counterions in the minor groove. Figure A rare configuration showing direct interaction between the solvated electron and DNA, where (yellow) and N7(A16) are H-bonded. The close approach from the major groove side invokes deep Na⁺ (magenta) penetration into the minor DNA groove (Fig. 7a).     

An Analytical Model of Gene Evolution with 9 Mutation Parameters: An Application to the Amino Acids Coded by the Common Circular Code

We develop here an analytical evolutionary model based on a trinucleotide mutation matrix 64× 64 with nine substitution parameters associated with the three types of substitutions in the three trinucleotide sites. It generalizes the previous models based on the nucleotide mutation matrices 4× 4 and the trinucleotide mutation matrix 64× 64 with three and six parameters. It determines at some time t the exact occurrence probabilities of trinucleotides mutating randomly according to these nine substitution parameters. An application of this model allows an evolutionary study of the common circular code of eukaryotes and prokaryotes and its 12 coded amino acids. The main property of this code is the retrieval of the reading frames in genes, both locally, i.e. anywhere in genes and in particular without a start codon, and automatically with a window of a few nucleotides. However, since its identification in 1996, amino acid information coded by has never been studied. Very unexpectedly, this evolutionary model demonstrates that random substitutions in this code and with particular values for the nine substitutions parameters retrieve after a certain time of evolution a frequency distribution of these 12 amino acids very close to the one coded by the actual genes.     

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.     

Radiosterilization of Fluoroquinolones and Cephalosporins: Assessment of Radiation Damage on Antibiotics by Changes in Optical Property and Colorimetric Parameters

A most common problem encountered in radiosterilization of solid drugs is discoloration or yellowing. By pharmacopoeia method, discoloration can be assessed by measuring absorbance of solutions of irradiated solid samples at 450 nm. We propose to evaluate discoloration of solid samples directly by recording their diffuse reflectance spectra. Further, the reflectance spectrum is used to compute various color parameters: CIE XYZ tristimulus value, CIE Lab, (color difference), yellowness index (YI), dominant wavelength, and excitation purity by CIE method. The investigation of difference reflectance spectra and color parameters revealed that for fluoroquinolones, e-beam was more damaging than gamma radiation, whereas for cephalosporins, trend was reversed. The quantum of discoloration with gamma radiation and e-beam is found to be nearly equal when assessed by pharmacopeia method, and it is therefore inadequate to assess small color differences. The color parameters and ΔYI are found to be reliable indicators of discoloration. The tolerance limits proposed in terms of and ΔYI are ±2 and ±10 U, respectively. The dominant wavelength for all compounds has shifted to higher values indicating change in hue but defining color tolerance limit with this parameter requires adjunct excitation purity value.     

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.