Virome identification in wheat in the Czech Republic using small RNA deep sequencing

High-throughput deep-sequencing technology and bioinformatics analysis of the small RNA(sRNA) population isolated from plants allows universal virus detection and complete virome reconstruction for a given sample. In the present sRNA deep-sequencing analysis of virus-infected wheat samples in the Czech Republic, samples were firstly tested for barley yellow dwarf viruses(BYDVs), wheat streak mosaic virus(WSMV) and wheat dwarf virus(WDV) using ELISA, RT-PCR and PCR. Subsequent sRNA sequencing of these samples yielded more than ～60 million single-end 50-bp reads with high confidence for nine field samples of wheat. Overall, 16.5% of reads were virus-specific and 83.5% were mapped to the host. More 21-nt reads(～7.7 E+06 reads) were found than 24-nt(～6.20 E+06 reads) or 22-nt(～4.30 E+06 reads) reads. De novo assembly of the high-quality contigs revealed the presence of three earlier reported viruses in the Czech Republic: BYDVs(31.48%), WSMV(24.23%) and WDV(26.66%). We also showed the presence of cereal yellow dwarf virus(14.33%; two species CYDV-RPS and CYDV-RPV(family Luteoviridae/Polerovirus) and wheat yellow dwarf virus(WYDV, 3.30%; Luteoviridae). Phylogenetic analysis showed CYDV and WYDV grouped separately from BYDVs. Furthermore, several recombination breakpoints were found among the groups of yellow dwarf viruses(BYDVs, CYDV, and WYDV). Using RNA deep sequencing, we confirmed the presence of the three known viruses(BYDVs, WSMV, and WDV) and the first record of two species of CYDV and WYDV in wheat in the Czech Republic.     

Mobility of copper and zinc fractions in fungicide-amended vineyard sandy soils

The purpose of this study was to evaluate the mobility of copper (Cu) and zinc (Zn) in the profile and distribution of sandy soil fractions from vineyards. Soil samples were collected from two vineyards of different ages (14 and 30 years) and a natural field area in the south of Brazil. The chemical characteristics, Cu levels and Zn levels, were analyzed in the soils by extraction with ethylenediamine tetraacetic acid (EDTA) using the 3050B method of USEPA and by chemical fractionation. Cu and Zn were accumulated in the vineyard soils, especially in the uppermost soil layers and in the soil from the oldest vineyard. Approximately, 75% of the total Cu was extracted by EDTA, but only 30% of the total Zn was extracted by EDTA. Most of the Cu, especially in the oldest vineyard, was distributed in the mineral-associated fraction, which is characterized by low geochemical mobility, but another important part of the Cu was distributed in the soil organic matter. Most of the Zn in the soil was distributed in the residual and mineral-associated fractions, which are characterized by low mobility and have potential for causing toxicity to plants.     

Cortical constriction during abscission involves helices of ESCRT-III-dependent filaments

After partitioning of cytoplasmic contents by cleavage furrow ingression, animal cells remain connected by an intercellular bridge, which subsequently splits by abscission. Here, we examined intermediate stages of abscission in human cells by using live imaging, three-dimensional structured illumination microscopy, and electron tomography. We identified helices of 17-nanometer-diameter filaments, which narrowed the cortex of the intercellular bridge to a single stalk. The endosomal sorting complex required for transport (ESCRT)-III co-localized with constriction zones and was required for assembly of 17-nanometer-diameter filaments. Simultaneous spastin-mediated removal of underlying microtubules enabled full constriction at the abscission site. The identification of contractile filament helices at the intercellular bridge has broad implications for the understanding of cell division and of ESCRT-III-mediated fission of large membrane structures.     

Synthesis and characterization of polyurethane-based side-chain cholesteric liquid crystal polymers

Polyurethane-based side-chain cholesteric liquid crystalline polymers (ChLCPs) with variable clearing temperatures were synthesized in a two-step reaction. The chemical structures of ChLCPs were confirmed by FT-IR and ¹H-NMR spectroscopy. The mesogenic properties and phase transition behavior were investigated by means of differential scanning calorimetry (DSC), polarizing optical microscopy (POM), and X-ray diffraction measurements. The DSC studies show that the melting temperature and isotropic transition temperature of the ChLCPs increased with the weight percentage of cholesterol in the polymer. POM shows that the ChLCPs had a distinct spherulite structure that melted at about 140 °C, and these results are consistent with those of the DSC studies. The thermogravimetric studies show that the ChLCPs were stable up to 200 °C, though there was a reduction in the thermal stability as the weight proportion of cholesterol and glycerol in the polymer increased.     

Dynamics of Macro- and Micronutrients in Cuphea

Temporal dynamics of nutrient densities, their interrelationships, and remobilization from leaves to seeds of cuphea were quantified in growth chamber and field studies. Temporal nutrient densities in leaf samples exhibited large levels of variation, whether remobilized and largely accumulated in the seed [copper, (Cu), potassium (K), phosphorus (P), sulfur (S) and zinc (Zn)], remobilized and accumulated in the seed coat [boron (B), calcium (Ca), iron (Fe), magnesium (Mg), manganese (Mn), and sodium (Na)] or almost excluded from the seed [barium (Ba), selenium (Se) and strontium (Sr)]. The temporal seed-to-leaf nutrient density “[S]/[L]” ratios and the proportion of variance unique to each nutrient separated the nutrients into a group (Cu, Fe, S, and Zn) with large [S]/[L] ratios and large unique variances, and another group (B, Ca, Mg, Mn and Sr) with small [S]/[L] ratios and small unique variances; the first group was selectively stored in the developing embryo. Nutrients with large densities in leaves at harvest may constitute a resource potentially available for subsequent crops.     

Plasticity of animal genome architecture unmasked by rapid evolution of a pelagic tunicate

Genomes of animals as different as sponges and humans show conservation of global architecture. Here we show that multiple genomic features including transposon diversity, developmental gene repertoire, physical gene order, and intron-exon organization are shattered in the tunicate Oikopleura, belonging to the sister group of vertebrates and retaining chordate morphology. Ancestral architecture of animal genomes can be deeply modified and may therefore be largely nonadaptive. This rapidly evolving animal lineage thus offers unique perspectives on the level of genome plasticity. It also illuminates issues as fundamental as the mechanisms of intron gain.     

A rapid real-time PCR assay for detecting columnar growth in apples (Malus × domestica)

Columnar growth in apples can have considerable positive consequences for orchard maintenance, but the lack of columnar cultivars producing fruits with desired market quality prevents their broader utilization in orchards. New crossings focused on their breeding are therefore conducted throughout the world every year. Unfortunately, the reliable discrimination between columnar growth and normal phenotype is difficult until seedlings are 2–3 years of age. However, molecular marker–assisted selection (MAS) can be used in seedlings several weeks old providing immense help in breeding programmes focused on columnar apple production. Here, we describe a rapid and reliable method for the detection of both wild-type (WT) and columnar (Co) alleles originating from ‘McIntosh Wijcik’ in a single reaction using a real-time PCR allelic discrimination approach. Our assay was tested in 130 genotypes (80 normal and 50 columnar habit) from various crossings and their parents, and in all cases, genotype corresponded to phenotype. The assay is thus suitable for laboratories interested in high-throughput MAS for columnar tree habit breeding.     

Identification of barriers to interspecific crosses in the genus Trifolium

Summary A study of pre- and post-fertilisation barriers after interspecific crosses of diploid and tetraploid Trifolium pratense L. and wild species T. alpestre L., T. medium L. and T. sarosiense Hazsl. was aimed at finding of a promising cross combination for obtaining hybrids. The growth of pollen tubes was arrested in interspecific crosses mainly when T. pratense was at a diploid level. To investigate the post-fertilisation barriers in detail, the hybrid embryo viability was traced by two clearing treatments of immature seeds: (1) using chloral hydrate (which proved to be most appropriate); and (2) a mixture of benzyl benzoate and dibutly phthalate. In interspecific combinations T. pratense (4×) × either T. alpestre or T. sarosiense, enlargement of immature seeds occurred, but no hybrid embryo was traced. Of the wild species used as a male parent for crosses, T. medium was the only exception from the point of view of fertilisation. Globular, heart and the early torpedo stages of hybrid embryos were observed 7 days after pollination (DAP) but only when T. pratense was at a tetraploid level. When T. pratense (2×, 4×) was used as a male parent for interspecific crosses with T. alpestre, T. medium and T. sarosiense, strong defects in various stages of embryogenesis were observed, particularly wrinkled and narrowing embryo sacs caused by an expansion of endothelial cells. We conclude with the following finding: (1) to make crosses only in one direction with T. pratense as a female parent and T. medium as a male; (2) to use tetraploid plants of T. pratense; (3) and to excise hybrid embryos at an early torpedo stage, about 7 DAP.