: a software to evaluate model performance

The software (Integrated Resources for Evaluating Numerical Estimates) is a data analysis tool designed to provide easy access to statistical techniques for use in model evaluation. Mostly, non-replicated model estimates (E_i) are compared against non-replicated measurements (M_i). The software also allows comparing individual estimates against replicated measurements (or vice versa) and replicated estimates against replicated measurements. The evaluation of model performance is essentially based on the difference E_i−M_i, or on the correlation–regression of E_i vs. M_i (or vice versa). In addition, model evaluation by probability distributions, pattern analysis, or fuzzy-based aggregation statistics is allowed. Graphics are included in most analytical tasks. The results are displayed in separate spreadsheets and can be exported into MS Excel workbooks.     

Multi metric evaluation of leaf wetness models for large-area application of plant disease models

Leaf wetness (LW) is one of the most important input variables of disease simulation models because of its fundamental role in the development of the infection process of many fungal pathogens. The low reliability of LW sensors and/or their rare use in standard weather stations has led to an increasing demand for reliable models that are able to estimate LW from other meteorological variables. When working on large databases in which data are interpolated in grids starting from weather stations, LW estimation is often penalized by the lack of hourly inputs (e.g., air relative humidity and air temperature), leading researchers to generate such variables from the daily values of the available weather data.Although it is possible to find several papers about models for the estimation of LW, the behavior and reliability of these models were never assessed by running them with inputs at different time resolutions aiming at large-area applications. Furthermore, only a limited number of papers have assessed the suitability of different LW models when used to provide inputs to simulate the development of the infection process of fungal pathogens. In this paper, six LW models were compared using data collected at 12 sites across the U.S. and Italy between 2002 and 2008 using an integrated, multi metric and fuzzy-based expert system developed ad hoc. The models were evaluated for their capability to estimate LW and for their impact on the simulation of the infection process for three pathogens through the use of a potential infection model. This study indicated that some empirical LW models performed better than physically based LW models. The classification and regression tree (CART) model performed better than the other models in most of the conditions tested. Finally, the estimate of LW using hourly inputs from daily data led to a decline of the LW models performances, which should still be considered acceptable. However, this estimate may require further work in data collection and model evaluation for applications at finer spatial resolutions aimed at decision support systems.     

Persistence of a biocontrol Pseudomonas inoculant as high populations of culturable and non-culturable cells in 200-cm-deep soil profiles

Little is known about the ecology of soil inoculants used for pathogen biocontrol, biofertilization and bioremediation under field conditions. We investigated the persistence and the physiological states of soil-inoculated Pseudomonas protegens (previously Pseudomonas fluorescens) CHA0 (10⁸ CFU g^?1 surface soil) in different soil microbial habitats in a planted ley (Medicago sativa L.) and an uncovered field plot. At 72 days, colony counts of the inoculant were low in surface soil (uncovered plot) and earthworm guts (ley plot), whereas soil above the plow pan (uncovered plot), and the rhizosphere and worm burrows present until 1.2 m depth (ley plot) were survival hot spots (10⁵–10⁶ CFU g^?1 soil). Interestingly, strain CHA0 was also detected in the subsoil of both plots, at 10²–10⁵ CFU g^?1 soil between 1.8 and 2 m depth. However, non-cultured CHA0 cells were also evidenced based on immunofluorescence microscopy. Kogure's direct viable counts of nutrient-responsive cells showed that many more CHA0 cells were in a viable but non-culturable (VBNC) or a non-responsive (dormant) state than in a culturable state, and the proportion of cells in those non-cultured states depended on soil microbial habitat. At the most, cells in a VBNC state amounted to 34% (above the plow pan) and those in a dormant state to 89% (in bulk soil between 0.6 and 2 m) of all CHA0 cells. The results indicate that field-released Pseudomonas inoculants may persist at high cell numbers, even in deeper soil layers, and display a combination of different physiological states whose prevalence fluctuates according to soil microbial habitats.     

One- and two-dimensional electrophoretic identification of IgE-binding polypeptides of Lupinus albus and other legume seeds

The prevalence of food allergies in the world population requires integrated approaches to identify new potential allergens, especially those of plant origin. The aim of this work was the allergen in vitro analysis of Lupinus albus seed proteome, a promising food protein source, and the assessment of IgE cross-reactivities with other more diffused legume species. A combination of one- and two-dimensional gel electrophoresis and immunoblotting analyses with specific IgGs for band identification and lupin-sensitized patients' circulating IgEs for allergenicity studies has been used. Two lupin proteins, namely, conglutin gamma and 11S globulin basic subunits, strongly reacted with all patients' sera. Also, cross-reactivities with the homologous polypeptides of other legume species were observed. Otherwise, no reaction at all was detected with a 2S-type lupin protein. This global electrophoretic approach has allowed the identification of a new potential lupin allergen and confirmed the cross-reactivity among the legume 11S globulin basic subunits.     

Simultaneous determination of Cd(II), Cu(II), Pb(II), and Zn(II) in citrus essential oils by derivative potentiometric stripping analysis

Citrus essential oils are widely used in the food, cosmetics, and pharmaceutical industries, so the determination of heavy metals content is of great importance to guarantee their quality. The present work deals with the quantification of Cd(II), Cu(II), Pb(II), and Zn(II) in different varieties of citrus essential oils, using derivative potentiometric stripping analysis. Two different metals extraction procedures, involving concentrated hydrochloric acid treatment and acid-alcoholic dissolution, are tested on lemon, mandarin, sweet orange, and bergamot essential oils, and they give very similar results. Cd(II), Cu(II), Pb(II), and Zn(II) recovery tests spanned from 95 to 100.50%, providing evidence that metals quantification remained unaffected by the cleanup steps of the two procedures. The repeatability of the hydrochloric acid extraction method, applied on different varieties of essential oils, is >95.00% for Cd(II), Cu(II), Pb(II), and Zn(II), whereas the repeatability of the acid-alcoholic dissolution method is >93.00% for Cu and Cd only in lemon oil. Detection limits obtained for the four analytes, using both procedures, ranged from 0.10 to 0.98 ng g(-)(1) in lemon, mandarin, sweet orange, and bergamot essential oils.     

Two-dimensional electrophoresis and western-blotting analyses with anti Ara h 3 basic subunit IgG evidence the cross-reacting polypeptides of Arachis hypogaea, Glycine max, and Lupinus albus seed proteomes

The allergenicity of seed storage proteins, the major components of edible legume seeds, may cause serious reactions in both children and adult population. Updated methodologies for evaluation of the activity of these proteins are needed. In this paper we used two-dimensional (2D) electrophoretic techniques to investigate the immuno-cross-reactivities of anti Ara h 3 basic subunit IgG to the seed proteomes of three legume species, namely, peanut, soybean, and lupin. The seed proteins, extracted with two different procedures, were separated by 2D electrophoresis, and the electrophoretic maps were analyzed by Western blot. In peanut proteome the antibodies strongly reacted with the 23 kDa polypeptides, corresponding to Ara h 3 basic isoforms, the antigen they were raised to, and three unidentified acidic polypeptides near 45 kDa. Remarkable cross-reactivities with lupin and soybean Ara h 3 homologous polypeptides and nonrelated proteins, namely, lupin conglutin gamma and soybean Bg7S, were detected. Therefore, these proteins may be regarded as new putative allergens. The present findings show the potentiality of 2D electrophoresis in the identification of food allergens and open the way to the traceability of the new cross-reacting proteins in the food chain.     

IgE-Mediated Cross-Reactivity among Leguminous Seed Proteins in Peanut Allergic Children

The immunological cross-reactivity among major protein- and oil-crops, including lupin, lentil, pea, peanut, kidney bean and soybean, has been studied by a combination of in vitro and in vivo experimental approaches: SDS-PAGE separations of legume protein extracts and immuno-blot revelations with 12 peanut-sensitive subjects’ sera, Immuno-CAP and Skin Prick tests on the same subjects. The immuno-blotting data showed a wide range of IgE-binding responses both displayed by one subject towards different plant extracts and among subjects. Differences were both quantitative and qualitative. The prevalent responses of most subjects’ sera were seen with peanut polypeptides, as expected, as well as with various polypeptides of the other legumes, the most recurrent of which were the basic subunits of the 11S globulins. The distribution of in vivo responses generally paralleled those obtained by in vitro approaches with strong responses elicited by peanut, lentil and pea protein extracts, especially by most sensitive subjects, thus providing a consistent overall set of results. In this work, the comparison of various approaches has allowed us to get an overall broad picture of the immunological cross-reactivities among proteins of widely used different seed species and to hypothesize the role of most conserved specific polypeptides.     

Properties of lupine proteins relevant to their nutritional performance

Composition, solubility, bound sugar content and quality, subunit composition and structure of the storage proteins of seeds ofLupinus albus are discussed. Aminoacid composition is also given for each protein, the various protein classes and the whole flour. These data allow for the characterization of the molecules of the various storage proteins and their contributions to the nutritional properties of the seed.In vitro digestibility (by mammalian endopeptidases) is reported and is less than for animal proteins. Possible causes, at the molecular level, for this behaviour and possible means to overcome these effects are examined. The relationships between the above data are considered in view of the nutritional performance of the proteins and of the genetical, agronomic and technological approaches most suited to improve the nutritional quality of lupine seeds as a protein source.     

Detection of Allelic Variation in Chinese Wheat (Triticum aestivum L.) Germplasm with Drought Tolerance Using SSR Markers

Allelic variation in two domestic wheat landraces, Pingyaobaimai and Mazhamai, two cornerstone breeding materials and their derived cultivars with drought tolerance was detected by SSR (simple sequence repeat) markers. The clustering of 25 accessions showed that the similarity between Pingyaobaimai and Yanda1817, the latter was developed from the former, was 0.71, the highest one of all accessions, but the similarities were very low between these two accessions and other accessions including their derived cultivars. A similar situation was revealed between Mazhamai and its derived cultivars. Pingyaobaimai and its three derived cultivars shared three alleles at loci Xgwm526, Xgwm538 and Xgwm126 on chromosome arms 2BL, 4BL and 5AL, respectively. There were six shared alleles in Mazhamai and its derived cultivars, in order of Xgwm157,Xgwm126, Xgwm212, Xgwm626, Xgwm471 and Xgwm44 on chromosome arms 2DL, 5AL, 5DL, 6BL, 7AS and 7DC, respectively. Only one shared allele was detected between the pedigrees of Pingyaobaimai and Mazhamai. The difference of shared alleles in two cornerstone breeding materials and their derived cultivars revealed the diversity in Chinese wheat germplasm with drought tolerance and the complication in genetic basis of drought tolerance in wheat.