Implementation of an artificial reaction control in a TaqMan method for PCR detection of <Emphasis Type="Italic">Ralstonia solanacearum</Emphasis> race 3 biovar 2

A previously published TaqMan PCR test for R. solanacearum race 3 biovar 2 was modified to enable both the validation of negative results and the confirmation of positive results in a closed-tube system. Negative results were validated through the use of a reaction control plasmid, designated pRB2C2, which was designed to generate a 94bp product using the same amplimers targeting the primary diagnostic 68bp sequence in R. solanacearum race 3 biovar 2 DNA. SYBR Green was included in the reaction mix to facilitate the identification of post-reaction products using melt peak analysis. The 94bp reaction control had a melt peak temperature of about 90°C, while the diagnostic target amplicon had a melt peak temperature of about 83°C; thus positive results could be easily confirmed and distinguished from the reaction control product. Addition of pRB2C2 at 100 copies per reaction had no effect on the sensitivity of the TaqMan assay for R. solanacearum race 3 biovar 2, and the modified assay successfully detected R. solanacearum race 3 biovar 2 in infected, asymptomatic tomato stems and leaves as well as in potato tubers and stems.     

Ameliorative effects of nurse shrubs on soil chemical characteristics are driven by plant size in the Monte desert

In deserts, shrubs determine landscape structure and influence plant productivity by creating nutrient-enriched environments. Attributes vary among shrub species, thus their contribution to soil characteristics is expected to vary as well, and nutrient input under shrub cover will depend on species attributes. We propose that plant size determines the contribution to soil chemical characteristics. Therefore, the contribution of larger species will be higher than smaller ones. Also, each species will contribute differentially for each chemical parameter. To corroborate these premises, we measured six soil chemical characteristics in areas covered by shrubs and in bare soil, as well as among five nurse species, in four sites of the Monte desert (La Rioja, Argentina). A multivariate analysis of variance (MANOVA) indicated significant variation between cover conditions and locations. Supporting previous studies, the presence of shrubs improved soil properties. Chemical concentration between soils under shrubs and bare soils, respectively, showed as mean and (SD) were: carbon(%): 0.82 (0,47), 0.52 (0.22); nitrates (ppm): 33,33 (67,36), 2.63 (0.56); phosphorous(ppm): 16.76 (25.02), 6.56 (1.92); electrical conductivity (dS m^?1): 0.24 (0,43), 0.03 (0,02); pH: 6.93 (0.56), 7.62 (0.53); and water content (%): 3,17 (8.94), 2.47 (9.15). Chemical characteristics also varied according to the nurse species. Larger nurse species affected the ensemble of chemical characteristics, after controlling for cover condition and site. Larger plant species (Bulnesia retama, Prosopis torquata, and Zuccagnia punctata) were significantly associated with higher carbon and higher nitrates concentration. These results suggest that soil properties are enhanced by the size of nurse plant species.     

Sensitivity,specificity, and predictive values of reagent test strip estimations of blood urea nitrogen

Azostix-reagent-tests(R) strips (Ames, Miles, Inc., Diagnostic Division, Elkhart, IN) were used to measure blood urea nitrogen values in blood samples from 125 dogs and cats at the North Carolina State University, College of Veterinary Medicine. Results of the tests were compared with standard serum urea nitrogen results. Sensitivity, specificity, and negative predictive values were high (86.4, 90.3, and 96.5%, respectively). Positive predictive value was low, 65.5% of the dogs and cats with elevated blood urea nitrogen values were correctly classified as abnormal The test performs well when the prevalence of abnormal values is near 50%.     

GENETICS. The Human Variome Project

An ambitious plan to collect, curate, and make accessible information on genetic variations affecting human health is beginning to be realized.     

Habitat associations of invertebrates in reedbeds,with implications for management

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Soluble and Insoluble Dietary Fiber Content and Composition in Oat

Six oat genotypes were grown in nursery yield trials during 1989-1992 at Lisbon, ND. Groats were analyzed for soluble and insoluble dietary fiber content and composition. Genotype-by-growing year interaction was not significant for soluble or insoluble dietary fiber. Soluble and insoluble dietary fiber differed with genotype (6.0–7.1% and 4.1– 4.9%, respectively) and with growing year (6.0–6.9% and 3.9–5.2%, respectively). The genotype-by-growing year interaction was significant for soluble β-glucan content but not for total neutral sugar or uronic acid content of the soluble dietary fiber. Genotypes did vary in total neutral sugar content but not in uronic acid content. The genotype-by-growing year interaction was not significant for total neutral sugar, β-glucan, uronic acid, or Klason lignin content of insoluble dietary fiber. Genotypes did vary in total neutral sugar, β-glucan, and Klason lignin content but not in uronic acid content of insoluble dietary fiber. The neutral sugar content of soluble dietary fiber was composed of glucose, arabinose, xylose, and galactose. The neutral sugar content of insoluble fiber was composed of glucose, arabinose, and xylose. The content and composition of soluble and insoluble dietary fiber varied with oat genotype. Therefore, oat genotypes could be bred for specific dietary fiber content and composition.     

Modeling production of antifungal compounds and their role in biocontrol product inhibitory activity

Partial least squares (PLS) regression modeling was used to relate the antifungal activity of Bacillus subtilis solid-state fermentation extracts to the individual high-performance liquid chromatography (HPLC) peaks from those extracts. A model was developed that predicted bioassay inhibition based on the extract HPLC profile (R(2) = 0.99). Concentrations of the members of the antifungal lipopeptide families iturin A and fengycin were found to correlate positively with extract inhibition, but a peak with unidentified chemical composition (designated as peak 48) showed the strongest correlation with extract inhibition. HPLC data were used to construct models for the production of iturin A, fengycin, and peak 48 as a function of the substrate moisture content, incubator temperature, and aeration rate in the solid-state bioreactors. Maximum production of all compounds occurred at the highest moisture content (1.7 g/g dry basis) and lowest incubator temperature (19 degrees C) tested. Optimal aeration rates for the production of the two known lipopeptides and peak 48 were 0.1 and 1.5 L/min, respectively.     

Bathymetric modeling of sediments and organic carbon of polluted rivers in southeastern China

Purpose

Rivers in low plains in the subtropical regions of China, where the population is dense and economies are active and well-developed, might be a large terrestrial carbon pool. This present study of the Sanyang wetlands in Wenzhou, southeastern China, aims to quantitatively estimate the volume of sediments in this region’s polluted river systems and their carbon storage.

Materials and methods

The bathymetry of river sections were surveyed using an echo sounder equipped with a differential GPS. An underwater digital elevation model (DEM) was then developed using the anisotropic ordinary Kriging method. Sediment samples were collected and analyzed for carbon content and sediment properties. Carbon storage in sediments was calculated using bathymetric and sediment analysis data.

Results and discussion

The studied rivers have been receiving organic pollutants from local residences and industries for decades. Results from a river network of 1.2 km² revealed a total carbon storage of 46.7 million kg in the sediments which had a volume of 1.4 million m³, with the upper 20 cm depth of sediments contributing about one third of this carbon storage.

Conclusions

The present work demonstrated that GIS technologies can be used to create digital river sediment surfaces and assess sediment amounts as well as determine the spatial distribution of sediments and their components. This could provide further insight into river restoration planning and other options from a carbon-balance perspective.