Changes in the Metabolome of Picea balfouriana Embryogenic Tissues That Were Linked to Different Levels of 6-BAP by Gas Chromatography-Mass Spectrometry Approach

Embryogenic cultures of Picea balfouriana, which is an important commercial species for reforestation in Southern China, easily lose their embryogenic ability during long-term culture. Embryogenic tissue that proliferated at lower concentrations (3.6 μM and 2.5 μM) of 6-benzylaminopurine (6-BAP) were more productive, and generated 113 ± 6 and 89 ± 3 mature embryos per 100 mg embryogenic tissue, respectively. A metabolomic approach was used to study the changes in metabolites linked to embryogenic competence related to three different 6-BAP concentrations (2.5 μM, 3.6 μM, and 5 μM). A total of 309 compounds were obtained, among which 123 metabolites mapped to Kyoto Encyclopedia of Genes and genomes (KEGG) pathways. The levels of 35 metabolites were significantly differentially regulated among the three 6-BAP treatments, and 32 metabolites differed between the 2.5 μM and 5 μM treatments. A total of 17 metabolites appeared only once among the three comparisons. The combination of a score plot and a loading plot showed that in the samples with higher embryogenic ability (3.6 μM and 2.5 μM), up-regulated metabolites were mostly amino acids and down-regulated metabolites were mostly primary carbohydrates (especially sugars). These results suggested that 6-BAP may influence embryogenic competence by nitrogen metabolism, which could cause an increase in amino acid levels and higher amounts of aspartate, isoleucine, and leucine in tissues with higher embryogenic ability. Furthermore, we speculated that 6-BAP may affect the amount of tryptophan in tissues, which would change the indole-3-acetic acid levels and influence the embryogenic ability.     

Interactions during in vitro germination of Scots pine pollen

Pre-zygotic pollen competition is believed to play an important role in nonrandom mating, i.e., the unequal success of different pollen donors. We studied pollen–pollen interactions of Scots pine in vitro using multiwell plates with freely permeable inserts. Six genotypes were included in our experiments: three from northern Finland and three from southern Finland. We conducted control experiments by placing pollen of each genotype in both the well and its insert. In competition experiments each southern genotype was incubated in insert with each northern genotype in well, and vice-versa. Samples for the germinability observations were taken from inserts. The mean germination percentage of northern genotypes was lower when incubating with southern genotypes in competition experiments than in control experiments. In one case, a northern genotype showed lower mean germination percentage in competition experiment than in control experiment and in another case a southern genotype showed a higher value. Our results suggest a chemically mediated interaction between pollen from different genotypes and one which can vary among genotypes.     

An efficient variance component approach implementing an average information REML suitable for combined LD and linkage mapping with a general complex pedigree

Variance component (VC) approaches based on restricted maximum likelihood (REML) have been used as an attractive method for positioning of quantitative trait loci (QTL). Linkage disequilibrium (LD) information can be easily implemented in the covariance structure among QTL effects (e.g. genotype relationship matrix) and mapping resolution appears to be high. Because of the use of LD information, the covariance structure becomes much richer and denser compared to the use of linkage information alone. This makes an average information (AI) REML algorithm based on mixed model equations and sparse matrix techniques less useful. In addition, (near-) singularity problems often occur with high marker densities, which is common in fine-mapping, causing numerical problems in AIREML based on mixed model equations. The present study investigates the direct use of the variance covariance matrix of all observations in AIREML for LD mapping with a general complex pedigree. The method presented is more efficient than the usual approach based on mixed model equations and robust to numerical problems caused by near-singularity due to closely linked markers. It is also feasible to fit multiple QTL simultaneously in the proposed method whereas this would drastically increase computing time when using mixed model equation-based methods.     

The effect of Echinorhynchus borealis (Acanthocephala) infection on the anti-predator behavior of a benthic amphipod

In benthic habitats, predators can generally not be detected visually, so olfaction may be particularly important for inducing anti-predation behaviors in prey organisms. Manipulative parasites infecting benthic hosts could suppress these responses so as to increase the probability of predation and thus trophic transmission. We studied how infection with the acanthocephalan Echinorhynchus borealis affects the response of the benthic amphipod Pallasea quadrispinosa to water conditioned by burbot (Lota lota), the parasite's definitive host. In normal lake water, refuge use by infected and uninfected amphipods was similar, but when exposed to burbot-conditioned water, uninfected amphipods spent much more time hiding than infected amphipods. Thus, rather than affecting ambient hiding behavior, E. borealis infection seems to alter host response to a predator. A group of amphipods sampled from a postglacial spring that is devoid of fish predators exhibited only a weak response to burbot-conditioned water, perhaps suggesting these anti-predator behaviors are costly to maintain. The hiding behavior of spring and infected amphipods was very similar. If the reduced refuge use by the spring amphipods reflects adaptation to a predator-free environment, this indicates that E. borealis severely weakens its host's anti-predator behavior. Presumably this increases the likelihood of parasite transmission.     

The efficiency of designs for fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage

In a simulation study, different designs were compared for efficiency of fine-mapping of QTL. The variance component method for fine-mapping of QTL was used to estimate QTL position and variance components. The design of many families with small size gave a higher mapping resolution than a design with few families of large size. However, the difference is small in half sib designs. The proportion of replicates with the QTL positioned within 3 cM of the true position is 0.71 in the best design, and 0.68 in the worst design applied to 128 animals with a phenotypic record and a QTL explaining 25% of the phenotypic variance. The design of two half sib families each of size 64 was further investigated for a hypothetical population with effective size of 1000 simulated for 6000 generations with a marker density of 0.25 cM and with marker mutation rate 4 × 10^-4 per generation. In mapping using bi-allelic markers, 42~55% of replicated simulations could position QTL within 0.75 cM of the true position whereas this was higher for multi allelic markers (48~76%). The accuracy was lowest (48%) when mutation age was 100 generations and increased to 68% and 76% for mutation ages of 200 and 500 generations, respectively, after which it was about 70% for mutation ages of 1000 generations and older. When effective size was linearly decreasing in the last 50 generations, the accuracy was decreased (56 to 70%). We show that half sib designs that have often been used for linkage mapping can have sufficient information for fine-mapping of QTL. It is suggested that the same design with the same animals for linkage mapping should be used for fine-mapping so gene mapping can be cost effective in livestock populations.     

The timber and energy biomass potential of intensively managed cloned Norway spruce stands

We used ecosystem model simulations to study the timber and energy biomass potential offered by intensively managed cloned Norway spruce stands. More specifically, we analysed how the use of cloned trees compared with non‐cloned trees, together with thinning, nitrogen (N) fertilisation and rotation length (from 60 to 100 years), affects the annual mean production of timber (i.e., saw logs, pulpwood) and energy biomass (i.e., stumps and harvesting residuals in the final felling) and its economic profitability [annual mean of net present value (NPV) with a 2% interest rate]. Furthermore, we employed a life cycle analysis/emission calculation tool to assess the total net CO₂ emissions per unit of energy (kg CO₂ MW h^?1) produced based on energy biomass. We found that both the annual mean production of timber and the NPV increased substantially, regardless of the management regime, if cloned trees with an annual growth increase of up to 30% compared with non‐cloned trees were used in regeneration. In general, the use of a short rotation with N fertilisation clearly increased the annual mean of the NPV. Consequently, the use of cloned trees also clearly increased the annual mean production of energy biomass and decreased the total net CO₂ emissions per unit of energy produced based on energy biomass. However, the total annual net CO₂ emissions were the lowest if a long rotation was used with N fertilisation. To conclude, the use of cloned trees together with intensive management could potentially be highly beneficial for the cost‐efficient and sustainable production of timber and energy biomass in an integrated way.     

Rule-Based Models of the Interplay between Genetic and Environmental Factors in Childhood Allergy

Both genetic and environmental factors are important for the development of allergic diseases. However, a detailed understanding of how such factors act together is lacking. To elucidate the interplay between genetic and environmental factors in allergic diseases, we used a novel bioinformatics approach that combines feature selection and machine learning. In two materials, PARSIFAL (a European cross-sectional study of 3113 children) and BAMSE (a Swedish birth-cohort including 2033 children), genetic variants as well as environmental and lifestyle factors were evaluated for their contribution to allergic phenotypes. Monte Carlo feature selection and rule based models were used to identify and rank rules describing how combinations of genetic and environmental factors affect the risk of allergic diseases. Novel interactions between genes were suggested and replicated, such as between ORMDL3 and RORA, where certain genotype combinations gave odds ratios for current asthma of 2.1 (95% CI 1.2-3.6) and 3.2 (95% CI 2.0-5.0) in the BAMSE and PARSIFAL children, respectively. Several combinations of environmental factors appeared to be important for the development of allergic disease in children. For example, use of baby formula and antibiotics early in life was associated with an odds ratio of 7.4 (95% CI 4.5-12.0) of developing asthma. Furthermore, genetic variants together with environmental factors seemed to play a role for allergic diseases, such as the use of antibiotics early in life and COL29A1 variants for asthma, and farm living and NPSR1 variants for allergic eczema. Overall, combinations of environmental and life style factors appeared more frequently in the models than combinations solely involving genes. In conclusion, a new bioinformatics approach is described for analyzing complex data, including extensive genetic and environmental information. Interactions identified with this approach could provide useful hints for further in-depth studies of etiological mechanisms and may also strengthen the basis for risk assessment and prevention.     

A novel tetravalent bispecific TandAb (CD30/CD16A) efficiently recruits NK cells for the lysis of CD30+ tumor cells

To improve recruitment and activation of natural killer (NK) cells to lyse tumor cells, we isolated a human anti-CD16A antibody with similar affinity for the CD16A 158F/V allotypes, but no binding to the CD16B isoform. Using CD16A-targeting Fv domains, we constructed a tetravalent bispecific CD30/CD16A tandem diabody (TandAb®) consisting solely of Fv domains. This TandAb has two binding sites for CD16A and two for CD30, the antigen identifying Hodgkin lymphoma cells. The binding and cytotoxicity of the TandAb were compared with antibodies with identical anti-CD30 domains: (1) a native IgG, (2) an IgG optimized for binding to Fc receptors, and (3) a bivalent bispecific CD30/CD16A diabody. Due to its CD16A-bivalency and reduced k_off, the TandAb was retained longer on the surface of NK cells than the IgGs or the diabody. This contributed to the higher potency and efficacy of the TandAb relative to those of the other anti-CD30 antibodies. TandAb cytotoxicity was independent of the CD16A allotype, whereas the anti-CD30 IgGs were substantially less cytotoxic when NK cells with low affinity CD16A allotype were employed. TandAb activation of NK cells was strictly dependent on the presence of CD30⁺ target cells. Therefore, the CD30/CD16A TandAb may represent a promising therapeutic for the treatment of Hodgkin’s lymphoma; further, anti-CD16A TandAbs may function as potent immunotherapeutics that specifically recruit NK cells to destroy cancer cells.     

The size and germinability of Scots pine pollen in different temperatures in vitro

The effect of genotype, the origin of genotype, and germination temperature on Scots pine pollen grain size, hydration rate, germinability, and tube growth was studied in vitro. The mean sizes of dry and germinated pollen grains varied among pollen genotypes in different ways, thus the hydration rate varied among genotypes. Pollen from Scots pine that originates in northern Finland hydrated more than pollen from a population in southern Finland. Germination temperature had no effect on the hydration rate. Germinability and tube growth rate of northern genotypes were higher at 20 °C than at 15 °C. Differences among southern genotypes were not significant. At 15 °C, the germinability and pollen tube growth rate of northern genotypes were lower than southern genotypes. At 20 °C, the differences were not significant. It appears that germination and growth of pollen from northern populations are enhanced at higher temperatures whereas pollen from southern populations is unaffected.