Improving validation practices in "omics" research

"Omics" research poses acute challenges regarding how to enhance validation practices and eventually the utility of this rich information. Several strategies may be useful, including routine replication, public data and protocol availability, funding incentives, reproducibility rewards or penalties, and targeted repeatability checks.     

The Determination of Contaminant Release from the PBO-Fe2O3-SiO2-Na2O Vitrification System, Using Industrial Solid Waste or Artificial Mixtures

In the current study, the leachability of lead from the PbO-Fe₂O₃-SiO₂-Na₂O vitrification system was examined by the application of DIN 38414 S4 and TCLP (Toxicity Characteristic Leaching Procedure) standard leaching tests. Various compositions, containing industrial or artificially created solid waste, were examined. Among the main conclusions from the results obtained was that the initial lead content, expressed as PbO and varied between 4–24% w/w, does not influence directly the release of lead from the vitrified samples. The other oxides, as well as other factors e.g. crystal formation on the glass surface, proved to be more important. Similar data were obtained regarding the content of iron oxide (the initial content of Fe₂O₃ varied from 30–54% w/w), although in this case the sodium concentrations measured in the leachates were generally found to increase with increasing initial iron oxide content and with the respective formation of crystals. The stoichiometry of lead and sodium, as measured in the leachates, was not constant for all the examined cases, showing that the mechanism of release depends upon the initial compositions and the presence of crystals on the glass surface. Improved results, regarding leachability and homogeneity without the presence of crystallites on the glass surface, were obtained when the initial ratio SiO₂/Na₂O (% w/w) was 2.33. By maintaining this ratio and when the examined waste was gradually added in the initial composition, the results obtained, concerning sodium concentration and pH values, can be described mathematically, by introducing an appropriate constant factor.     

Influence of fungicide spray schedules on the sensitivity of Cercospora beticola to the sterol demethylation-inhibiting fungicide flutriafol

A field experiment was conducted over a three-year period (1997–1999) to study the efficacy of several fungicide spray-schedules and their effects on the sensitivity of Cercospora beticola populations to the DMI fungicide flutriafol. Spray applications of flutriafol, either alone at the recommended dose, or at a reduced dose in mixtures with maneb, or in alternation with tank mixed fentin-acetate and maneb, were included in the spray programs. Applications of flutriafol at the recommended dose showed a significantly greater control efficacy in comparison with the other treatments, while applications of flutriafol alternated with tank mixed fentin-acetate and maneb showed lower efficacy in comparison with the remaining flutriafol treatments. Fungal populations from plots continuously treated with flutriafol, either alone at the full dose or at reduced dose with maneb, had lower sensitivity to flutriafol in comparison with populations from plots treated alternatively with flutriafol and tank mixed fentin-acetate and maneb. Repeated applications of flutriafol, at full or reduced doses, favoured the selection of highly resistant strains. Since applications of flutriafol in alternation with tank mixed fentin-acetate and maneb do not maintain a high level of disease control, the only available anti-resistance strategy would be the restriction of the number of flutriafol treatments, by applying them only when environmental conditions are favourable for disease development and by using alternative fungicides during the rest of the growing season.     

Lack of influence of host plant disease resistance on the evolution of resistance to sterol demethylation-inhibiting (DMI) fungicides in<Emphasis Type="Italic">Cercospora beticola</Emphasis>

Field experiments were conducted during 1997 and 1998 to determine the effects of sugar beet cultivar susceptibility to Cercospora leaf-spot on the sensitivity ofCercospora beticola isolates to the triazole fungicide flutriafol. Four cultivars with different levels of disease resistance were treated in experimental plots with six spray applications of flutriafol. Disease assessments were carried out at 15-day intervals. Sensitivity to flutriafol was measured on isolates collected from the plots ∼15 days after the last flutriafol application. Measurements of disease severity and calculations of AUDPC (area under disease progress curve) values showed a distinct differentiation among cultivars, reflecting their level of disease resistance. Disease severity was significantly lower in cvs. ‘Bianca’ and ‘Areth’ than in ‘Univers’ and ‘Rizor’ both in the untreated and in the flutriafol-treated plots. Fungal isolates from flutriafol-treated plots were less sensitive to the fungicide than were isolates from untreated plots. However, no differences in isolate sensitivity were observed among the cultivars, as regards their level of disease resistance. Despite the fact that the use of resistant cultivars cannot eliminate selectively the resistant strains, it can eliminate both resistant and sensitive isolates. Reducing the number of treatments with DMIs, by applying them only when environmental conditions are favorable for disease development, is a prerequisite for successful resistance management; therefore, the use of disease-resistant varieties could aid toward management of DMIs resistance inC. beticola. http://www.phytoparasitica.org posting May 6, 2003.     

Detection of resistance to sterol demethylation-inhibiting (DMI) fungicides in<Emphasis Type="Italic">Cercospora beticola</Emphasis> and efficacy of control of resistant and sensitive strains with flutriafol

Single-lesion isolates ofCercospora beticola (n=150) were collected in 1998 from sugar beet fields in the area of Serres, N. Greece. In this area, sterol demethylation-inhibiting (DMI) fungicides have been used for almost 20 years to control sugar beet leaf spot. The sensitivity of these isolates to the DMI fungicides flutriafol and difenoconazole (EC₅₀ values) was determined on the basis of inhibition of mycelial growth at several fungicide concentrations. The relative growth (RG) of isolates was correlated at all tested concentrations with the respective EC₅₀ values, indicating that RG provides a reliable estimate for the sensitivity of the isolates. The highest correlation coefficients were obtained for concentrations of 1 μg ml⁻¹ flutriafol and of 0.05 μg ml⁻¹ difenoconazole, respectively. Consequently, they are proposed for monitoring of DMI sensitivity inC. beticola populations, as single discriminatory concentrations in a simplified test method. Based on the RG values at the discriminatory concentration of 1 μg ml⁻¹ flutriafol,C. beticola isolates were classified as either resistant or sensitive. The efficacy of flutriafol, applied at the commercially recommended dose, in controlling Cercospora leaf spot was examined in field experiments conducted during 1999 and 2000. Disease incidence in plots artificially inoculated with resistant isolates and treated with flutriafol was significantly higher than in similar plots inoculated with sensitive strains. These results suggest that poor disease control after application of flutriafol may be based on the presence of resistant strains within the pathogen population in northern Greece. This emphasizes the risk of the development of practical resistance if there is increased frequency of such strains within the population. http://www.phytoparasitica.org posting July 13, 2003.     

Fitness of Cercospora Beticola Field Isolates – Resistant And – Sensitive to Demethylation Inhibitor Fungicides

Isolates of Cercospora beticola resistant to fungicides that inhibit sterol demethylation (DMIs) were collected from sugar beet fields in Northern Greece. Fitness of these isolates was compared to that of DMI-sensitive isolates. The parameters measured were competitive ability both under growth chamber and field conditions, mycelial growth, spore germination, germ tube length, incubation period, virulence and spore production. The competitive ability under growth chamber conditions was measured for 4 pairs of one resistant and one sensitive isolate. Results showed that after 4 disease cycles, in 2 out of 4 pairs tested, the resistant isolates competed well with the sensitive isolates, but in the remaining two pairs the frequency of the resistant isolate decreased significantly. The competition experiment in the field was carried out by inoculating field plots with a conidial suspension consisting of a spore mixture from all the resistant and all the sensitive isolates used in this study. Results showed that at the end of the growing period the frequency of the resistant isolates had slightly decreased (P < 0.05). The measurements of fitness components of individual isolates showed that the resistant isolates had significantly lower (P < 0.05) virulence and spore production than the sensitive isolates, while no significant differences (P > 0.05) to the remaining 4 fitness components, were detected. With correlation analysis it was determined whether there is a relationship between values of each fitness component and the level of sensitivity to flutriafol of individual isolates. The correlation coefficients for virulence (r = 0.45) and spore production (r = 0.41) were significantly different from 0 (P > 0.05), indicating that resistance to DMIs affected, to some degree, the fitness of the resistant isolates.     

Reduced sensitivity of Cercospora beticola isolates to sterol-demethylation-inhibiting fungicides

In a survey conducted during October 1995, single-lesion isolates of the sugar beet leaf-spot fungus, Cercospora beticola , were tested for sensitivity to the sterol demethylation inhibiting fungicides (DMIs) flutriafol and bitertanol. The isolates were collected from fields in three different areas of northern Greece. Fields at Serres and Imathia had been sprayed with DMIs for about 15 years to control sugar beet leaf-spot. At the third site, Amyndeon, DMI fungicides had not been used. From each area 150 isolates were tested. ED₅₀ values were calculated for individual isolates by regressing the relative inhibition of colony growth against the natural logarithm of the fungicide concentration. The mean ED₅₀ values for flutriafol for the Serres, Imathia and Amyndeon populations were 1·07, 0·73 and 0·5 µg mL⁻¹, respectively (significantly different at P  = 0·05). For bitertanol the mean ED₅₀ values for the Serres and Imathia populations were 0·72 and 0·81 µg mL⁻¹, respectively, which were not significantly different at P  = 0·05. The mean ED₅₀ value of the Amyndeon population was 0·48 µg mL⁻¹, which was significantly lower than those of the other two populations ( P  < 0·05). A cross-resistance relationship was found to exist between the two triazole fungicides tested when log transformed ED₅₀ values of 60 isolates were subjected to a linear regression analysis ( r  = 0·81).     

Dual-porosity modelling of the pore structure and transport properties of a contaminated soil

We have developed a new method to characterize the pore structure of mineral soils. We combined data from the analysis of back-scattered scanning electron microscope (BSEM) images of resin-impregnated pore-casts, and mercury intrusion porosimetry (MIP) data, with analytical percolation models and inverse modeling algorithms. The pore space is regarded as a dual-pore network consisting of a primary Euclidean pore-and-throat network and a secondary, fractal, pore system that is accessed through primary pores. The digitized 2-D BSEM images of resin-impregnated soil samples are employed to determine the autocorrelation function. The Fourier transform of this function provides the small-angle neutron scattering (SANS) intensity function, which is extended by using the surface fractal dimension obtained from high-pressure MIP data. Inversion of the extended scattering intensity function produces the volume-based radius distribution function of spherical pore bodies (PBRD). The complete volume-based PBRD is fitted with a composite number-based PBRD composed of a lognormal primary PBRD and a power (fractal) secondary PBRD with upper and lower cut-offs. Based on the concepts of invasion percolation, an analytic mathematical model that describes Hg intrusion into dual pore networks is developed. The complete PBRD and pore-throat radius distribution (PTRD) functions of the primary network along with the drainage accessibility functions (DAFs) of the primary and secondary pore networks are estimated with inverse modelling of the Hg intrusion curve. Based on critical path analysis of percolation theory, approximate analytical relationships are developed to calculate explicitly the absolute permeability and electrical formation factor from the geometrical and topological parameters of the primary pore network. The method is demonstrated with application to four soil samples.