Non-iterative variance component estimation in QTL analysis

In variance component quantitative trait loci (QTL) analysis, a mixed model is used to detect the most likely chromosome position of a QTL. The putative QTL is included as a random effect and a method is needed to estimate the QTL variance. The standard estimation method used is an iterative method based on the restricted maximum likelihood (REML). In this paper, we present a novel non-iterative variance component estimation method. This method is based on Henderson's method 3, but relaxes the condition of unbiasedness. Two similar estimators were compared, which were developed from two different partitions of the sum of squares in Henderson's method 3. The approach was compared with REML on data from a European wild boar × domestic pig intercross. A meat quality trait was studied on chromosome 6 where a functional gene was known to be located. Both partitions resulted in estimated QTL variances close to the REML estimates. From the non-iterative estimates, we could also compute good approximations of the likelihood ratio curve on the studied chromosome.     

Soot in urban atmospheres: determination by an optical absorption technique

We have used the high optical absorptivity of urban and source particulates to trace their "graphitic" component. The optical absorptivity and the particulate carbon loading show a strong correlation. Analyses of the data indicate that primary soot emissions compose a major fraction of the carbonaceous aerosol and put a low limit on secondary organic material produced in correlation with the ozone concentration.     

The influence of compost addition on heavy metal distribution between operationally defined geochemical fractions and on metal accumulation in plant

Purpose

Metal distribution patterns among geochemical fractions are informative for metal phytoavailability. Compost added to polluted soils may adsorb metals on the less phytoavailable fractions. A bioassay experiment was conducted to establish possible correlations between metal concentrations in different soil fractions and metal contents in edible plant parts and to investigate the influence of different compost loads on heavy metal availability to plants.

Materials and methods

Chinese cabbage plants were grown in pots with sandy and clayey soils and soils mixed with different doses of biosolid compost spiked with soluble heavy metal salts (Cd, Cu, and Pb). The metals’ distribution pattern in the soil and mixed samples was determined by sequential extraction procedure (modified BCR protocol). The studied fractions, from most to least bioavailable, were water-extractable (WE), exchangeable-adsorbed (EXC), associated with carbonates and acetic acid-soluble forms (CARB), occluded by reducible (hydro)oxides of Fe and Mn (RO), and associated with organic matter (OM) and a residual fraction (RES). Metal concentrations in soil extracts and in the digested plant tissue were measured by ICP-AES.

Results and discussion

The highest compost doses (72 and 115 Mg ha^?1) enhanced cabbage yield significantly. No excessive phytoaccumulation of metals was observed in plants grown in the clayey soil or its mixtures with compost. The compost dose of 72 Mg ha^?1 was optimal in decreasing Cu accumulation by plants grown in sandy soil, and 28.8 Mg ha^?1 was found to be effective in reducing Cd and Pb uptake. Metals were accumulated in plants primarily from the WE, EXC, and CARB fractions, whereas other fractions decreased phytoaccumulation. Compost addition suppressed heavy metal mobility, but different fractions were active in pollutant sorption, depending on soil type and metal.

Conclusions

Compost addition increased metal proportions in the RO and OM fractions, reducing metal phytoavailability. This is especially important for sandy soils with low adsorption ability and higher vulnerability to metal pollution than clayey soils. A compost dose of 20% v/v (or 28.8 Mg ha^?1) effectively reduced plant accumulation of Cd and Pb. We propose using the first three steps of the modified BCR protocol as a three-step sequential-extraction procedure for the most phytoavailable fractions of heavy metal: WE, EXC, and CARB.     

Partial sequence of the DNA-dependent DNA polymerase gene of fowl adenoviruses: a reference panel for a general diagnostic PCR in poultry

Adenoviruses are frequent infectious agents in different poultry species. The traditional, serological typing of new isolates by virus neutralisation tests is now in transition to be replaced by PCR and sequencing. The first PCRs, recommended for the detection of adenoviruses, had been designed to target the gene of the major capsid protein, the hexon. In birds, members of three different genera of the family Adenoviridae may occur. Accordingly, three specific hexon PCRs had to be elaborated for the detection of adenoviruses in poultry. A significantly more sensitive PCR, targeting the viral DNA-dependent DNA polymerase gene, has been described recently. This method proved to be an efficient alternative for the general detection of adenoviruses irrespective of their genus affiliation. Fowl adenoviruses (FAdVs), isolated from chicken to date, comprise twelve serotypes classified into five virus species (FAdV-A to E). The polymerase gene sequence has been determined yet only from three FAdV types representing three species. In the present work, the panel of polymerase gene sequences was completed with those of the rest of FAdVs. The newly determined sequences will facilitate the identification of new FAdV isolates as an existing species or as a putative new FAdV. Once the polymerase sequence is known, more specific PCRs for the amplification of the hexon and other genes can be designed and performed according to the preliminary species classification.     

Potassium uptake characteristics of prunus rootstocks: Influence of solution Ca/Mg ratios and solution nickel

Abstract

Nutrient solution experiments were conducted in the growth chamber to study the influence of rootstock, solution Ca/Mg ratios and solution nickel on K uptake. The experimental plants were one‐year‐old prune trees: ‘French’ prune (Prunus domestica L.) scions grafted on Myrobalan 29C (P. cerasifera Ehrh.), Marianna 2624 (P. cerasifera x P. munsoniana?) or Nemaguard (P. persica x P. davidiana) rootstocks. Ion uptake parameters Imax, Km, and Cmin were calculated from ion depletion measurements over a 6 to 10‐hr period.

With K solution concentrations initially adjusted to 100 μM, K uptake rates of Prunus rootstocks were constant down to approximately 20–30 μM, then declined. Rootstocks were able to deplete solution K to concentrations less than 1 μM. There were no significant differences in K uptake parameters among the rootstocks tested.

Varying solution Ca/Mg ratio from 2.75/1 to 1/4 (Ca + Mg = 3.75 mM) had no effect on K uptake. Potassium uptake rates of Myrobalan 29C rootstocks in the presence of 100 μM nickel were not significantly different from those in the absence of nickel. Rates of nickel uptake were significantly lower than those of K. After eight days of pretreatment in solutions adjusted daily to 100 μM Ni(NO₃)₂, prune leaves began to show signs of interveinal chlorosis. Potassium uptake by nickel pretreated trees was not significantly different from that by control trees. Results are discussed in relation to field observations of K deficiency in prune orchards.     

The Effect of Calcium Sprays and Fruit Thinning on Bitter Pit Incidence and Calcium Content in ‘Honeycrisp’ Apple

‘Honeycrisp’ is a recently released cultivar of apple (Malus x domestica) developed by the University of Minnesota, now in high demand by growers and consumers. This cultivar is susceptible to bitter pit, especially when the trees are young and the fruit load is low. The effects of calcium (Ca) sprays, fruit thinning, vegetative growth, fruit and leaf nutrient concentration on bitter pit incidence, and two sampling methods for nutrient analysis were studied. Bitter pit incidence was associated with several variables, including Ca and phosphorus (P) concentrations in leaves and fruits, magnesium (Mg) concentration in leaves, and yield parameters. Fruit Ca concentration and content for the growing season were modeled, which allowed the determinations of Ca levels associated with bitter pit incidence. Our data suggest that plug analysis was less sensitive than fruit-segment analysis for finding differences in Ca concentrations.     

PCR-sequence characterization of new adenoviruses found in reptiles and the first successful isolation of a lizard adenovirus

A consensus nested PCR was used to screen diagnostic samples from approximately 70 reptiles for the presence of adenoviruses (AdV) in the years 2006-2007. Classical virus isolation methods were also used with all samples. After adenoviruses were detected in a group of helodermatid lizards in a Danish zoo, a follow-up study was also carried out on lizards from this group (10 Mexican beaded lizards and 24 Gila monsters) over the period of a year. Adenoviruses were detected in a total of 26 lizards and snakes by PCR. The PCR amplicons from all positive animals were sequenced and the resulting polymerase gene sequences were used for phylogenetic analysis. Altogether six Agamid AdVs were amplified, with a minimal sequence variation between one another and between these and GenBank Agamid AdVs. The sequence obtained from one of the Gila monsters is identical with the GenBank Helodermatid AdV, while the sequences from the Mexican beaded lizards differ from this. In a snake collection we have detected a new AdV from an Asp viper. All of the above mentioned adenoviruses cluster in the Atadenovirus genus. However, the sequence from a new Varanid AdV detected in this study clusters outside this genus. On cell culture, viruses were isolated from three of the AdV positive helodermatid lizards (one Mexican beaded lizard and two Gila monsters) and identified as AdVs based on electron microscopy and PCR and sequencing using cell culture supernatant. This is the first report of the successful isolation of a lizard AdV.