A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors

Background

The diploid, Solanum caripense, a wild relative of potato and tomato, possesses valuable resistance to potato late blight and we are interested in the genetic base of this resistance. Due to extremely low levels of genetic variation within the S. caripense genome it proved impossible to generate a dense genetic map and to assign individual Solanum chromosomes through the use of conventional chromosome-specific SSR, RFLP, AFLP, as well as gene- or locus-specific markers. The ease of detection of DNA polymorphisms depends on both frequency and form of sequence variation. The narrow genetic background of close relatives and inbreds complicates the detection of persisting, reduced polymorphism and is a challenge to the development of reliable molecular markers. Nonetheless, monomorphic DNA fragments representing not directly usable conventional markers can contain considerable variation at the level of single nucleotide polymorphisms (SNPs). This can be used for the design of allele-specific molecular markers. The reproducible detection of allele-specific markers based on SNPs has been a technical challenge.

Results

We present a fast and cost-effective protocol for the detection of allele-specific SNPs by applying Sequence Polymorphism-Derived (SPD) markers. These markers proved highly efficient for fingerprinting of individuals possessing a homogeneous genetic background. SPD markers are obtained from within non-informative, conventional molecular marker fragments that are screened for SNPs to design allele-specific PCR primers. The method makes use of primers containing a single, 3'-terminal Locked Nucleic Acid (LNA) base. We demonstrate the applicability of the technique by successful genetic mapping of allele-specific SNP markers derived from monomorphic Conserved Ortholog Set II (COSII) markers mapped to Solanum chromosomes, in S. caripense. By using SPD markers it was possible for the first time to map the S. caripense alleles of 16 chromosome-specific COSII markers and to assign eight of the twelve linkage groups to consensus Solanum chromosomes.

Conclusion

The method based on individual allelic variants allows for a level-of-magnitude higher resolution of genetic variation than conventional marker techniques. We show that the majority of monomorphic molecular marker fragments from organisms with reduced heterozygosity levels still contain SNPs that are sufficient to trace individual alleles.     

Segmentation of Somatic Cells in Goat Milk Using Color Space CIELAB

Somatic cell counts （SCCs） levels indicate the occurrence of infections in goat udders and are related to the productivity of goat milk, cheese and yoghurt. This work presents a segmentation method for counting somatic cells in goat milk images, intending to detect an infection known as mastiffs, which is the major cause of loss in dairy farming. The image segmentation procedure is devised by using the lab color space and the watershed transform. A large number of samples under variable preparation conditions are treated with the proposed method. A comparison between manual and the proposed technique is presented. Promising results indicates that video-microscopy systems may be employed to develop automated SCC for goat milk.     

Quinone and Hydroquinone Metabolites from the Ascidians of the Genus Aplidium

Ascidians of the genus Aplidium are recognized as an important source of chemical diversity and bioactive natural products. Among the compounds produced by this genus are non-nitrogenous metabolites, mainly prenylated quinones and hydroquinones. This review discusses the isolation, structural elucidation, and biological activities of quinones, hydroquinones, rossinones, longithorones, longithorols, floresolides, scabellones, conicaquinones, aplidinones, thiaplidiaquinones, and conithiaquinones. A compilation of the ¹³C-NMR spectral data of these compounds is also presented.     

Antagonistic activity of <Emphasis Type="Italic">Trichoderma</Emphasis> spp. against <Emphasis Type="Italic">Scytalidium lignicola</Emphasis> CMM 1098 and antioxidant enzymatic activity in cassava

Trichoderma spp. are used as antagonists against different pathogens. Despite many possibilities of using Trichoderma as an antagonist, there are gaps in the knowledge of the interaction between Trichoderma, cassava and Scytalidium lignicola. This fungus causes cassava black root rot and is an inhabitant of the soil, so it is difficult to control. Antagonists may contribute to the possible induction of resistance of plants because, when exposed to such pathosystems, plants respond by producing antioxidative enzymes. The test for potential inhibition of growth of S. lignicola CMM 1098 in vitro was performed in potato-dextrose-agar with two Trichoderma strains T. harzianum URM3086 and T. aureoviride URM 5158. We evaluated the effect of the two selected Trichoderma to reduce the severity of cassava black root rot and shoots. Subsequently, the production of enzymes (ascorbate peroxidase, catalase, peroxidase and polyphenol oxidase) was evaluated in cassava plants. All two Trichoderma strains show an inhibition of the growth of S. lignicola CMM 1098. The most efficient was T. harzianum URM 3086, with 80.78% of mycelial growth inhibition. T. aureoviride URM 5158 was considered the best chitinase producer. All treatments were effective in reducing severity, especially treatments using Trichoderma. Cassava plants treated with T. aureoviride URM 5158 had the highest enzyme activity, especially peroxidase and ascorbate peroxidase. Trichoderma harzianum URM3086 and Trichoderma aureoviride URM 5158 were effective in reducing the severity of cassava black root rot caused by S. lignicola CMM 1098.     

Genotoxicity in the Offspring of Rats Exposed to Contaminated and Acidified Experimentally Soils

The aim of this study was to evaluate the genotoxic and mutagenic potential of contaminated soil diluted in acidic solutions and not acidic, in the offspring of rats exposed during pregnancy and neonatal periods. To this end, a comet assay and micronucleus test were performed. Soil samples were solubilized in the following three solvents: distilled water (control group), acid solvent at pH 5.2, and acid solvent at pH 3.6. Soil and solvent were mixed in a rate of 1:2 in g/mL, and hydrofluoric acid was used in the acid solvents. In the comet assay, the tail length, percentage of DNA within the tail and tail moment was analyzed in the whole blood of the pups that were studied. The number of micronuclei found in the bone marrow cells was counted in the micronucleus test. In all parameters evaluated in the comet assay, the group exposed to the lowest pH value when associated with contaminated soil (p < 0.05) had the most damage. However, the micronucleus test showed differences between all exposed groups and the control group (p < 0.05). These results reaffirm the health risks related to the exposure to soil contaminants.     

Do water dynamics and land use in riparian areas change the spatial pattern of physical–mechanical properties of a Cambisol?

Precision Agriculture - Changes in land use in riverside ecosystems added to the flood and ebb regimes of rivers modify the spatial variability of the physical–mechanical attributes of soil,...