Sequence finishing and mapping of Drosophila melanogaster heterochromatin

Genome sequences for most metazoans and plants are incomplete because of the presence of repeated DNA in the heterochromatin. The heterochromatic regions of Drosophila melanogaster contain 20 million bases (Mb) of sequence amenable to mapping, sequence assembly, and finishing. We describe the generation of 15 Mb of finished or improved heterochromatic sequence with the use of available clone resources and assembly methods. We also constructed a bacterial artificial chromosome-based physical map that spans 13 Mb of the pericentromeric heterochromatin and a cytogenetic map that positions 11 Mb in specific chromosomal locations. We have approached a complete assembly and mapping of the nonsatellite component of Drosophila heterochromatin. The strategy we describe is also applicable to generating substantially more information about heterochromatin in other species, including humans.     

The influence of hydrology on the recruitment of brown trout in an Alpine river,the Ybbs River,Austria

Abstract – We monitored yearly recruitment (1997–2008) of brown trout (Salmo trutta) in a fourth‐order Austrian Alpine river. The relative proportion of recruits to adult fish varied strongly among years (5.6–66.4%). These proportions were strongly correlated with specific flow patterns. High flows before and during the spawning period were positively correlated with recruitment, whereas high flows during incubation and emergence were negatively correlated with recruitment success. Unsteady flow modelling supported a causal hypothesis for these relationships in demonstrating that discharges > 30 m³·s^?1 resulted in substantial sediment motion (erosion and deposition) in suitable spawning areas within the study stretch.     

Effects of rhizobacteria on parasitism by Meloidogyne ethiopica on grapevines

Meloidogyne ethiopica is one of the most important plant-parasitic nematodes affecting vines in Chile and is very aggressive and difficult to control. This study evaluated 16 strains of rhizobacteria, originally isolated from roots of grapevines, for their effects on parasitism and nematode damage to potted vine plants. The antagonistic effect of rhizobacteria was assessed by treating 2-month-old plants of cv. Chardonnay in 3-l pots with a suspension containing 1?×?10⁶?cfu?ml^?1 of the bacteria and 1,000 nematode eggs. After 6?months of growth, the plants were cut and root and canopy weights, nematode populations and root damage determined. The effect of rhizobacterial culture filtrate on hatching of nematode eggs was also assessed in vitro. Seven strains of rhizobacteria proved effective in inhibiting damage or reproduction of the nematode. These were strains of Serratia marcescens, Comamonas acidovorans, Pantoea agglomerans, Sphingobacterium spiritivorum, Bacillus mycoides, Alcaligenes piechaudii and Serratia plymuthica. A further three strains, of Bacillus megaterium, P. agglomerans and Pseudomonas savastanoi, significantly increased root weight, but did not decrease nematode damage or population density. The supernatant of all strains significantly decreased hatching of juvenile nematodes after 24?h of immersion, with isolates of P. putida and B. megaterium being the most effective.     

Molecular identification of detritivorous soil invertebrates from their faecal pellets

Faecal pellets of macro-decomposers form an important component of upper soil layers. It is, however, not yet specifically known which species’ faecal pellets are important in the process of humus and soil formation. Here we present a novel approach, based on the detection of short DNA fragments, to species-specifically assign faecal pellets to their detritivorous producers. Using diagnostic polymerase chain reaction (PCR), DNA of the two millipede species Cylindroiulus fulviceps and C. meinerti, abundant macro-decomposers on European alpine pastureland, could be detected in their faecal pellets. Although in both species detection was possible up to 5 days post-defecation (no longer intervals were tested), detection rates were significantly higher in C. fulviceps (81.3%) than in Cylindroiulus meinerti (60.9%) in repetitive PCRs. Employing a binomial mixture model, the probability that the producer’s DNA was present in a faecal sample which tested negative in five subsequent PCRs was estimated as 22.0% for C. fulviceps and 41.9% for C. meinerti, suggesting to adopt a flexible stopping rule for assaying this type of samples. This proof-of-concept study demonstrates that the molecular assignment of faecal pellets to their macro-invertebrate producers is possible, offering a new approach to examine the role of decomposer faecal pellets in soil formation and functioning as well as to complement molecular profiling of faunal communities.     

Degradation of scrapie associated prion protein (PrPSc) by the gastrointestinal microbiota of cattle

A food-borne origin of the transmission of bovine spongiform encephalopathy (BSE) to cattle is commonly assumed. However, the fate of infectious prion protein during polygastric digestion remains unclear. It is unknown at present, whether infectious prion proteins, considered to be very stable, are degraded or inactivated by microbial processes in the gastrointestinal tract of cattle. In this study, rumen and colon contents from healthy cattle, taken immediately after slaughter, were used to assess the ability of these microbial consortia to degrade PrP(Sc). Therefore, the consortia were incubated with brain homogenates of scrapie (strain 263K) infected hamsters under physiological anaerobic conditions at 37 degrees C. Within 20 h, PrP(Sc) was digested both with ruminal and colonic microbiota up to immunochemically undetectable levels. Especially polymyxin resistant (mainly gram-positive) bacteria expressed PrP(Sc) degrading activity. These data demonstrate the ability of bovine gastrointestinal microbiota to degrade PrP(Sc) during digestion.     

Determination of optimum N-supply in sugar beet by different mathematical methods

Various mathematical models used to predict optimum N-supply (fertilizer-N + N_min) for maximum root yield, sugar yield and white sugar yield were compared by fitting data from 39 field trials in Northwest Germany (1980–1992). Quadratic, modified exponential and square root models resulted in higher estimates of optimum N-supply than did 2-regressions and plateau type spline models with differences as high as 130 kg N/ha between models. Residual variance was lower with the latter two models. Data were grouped at 40 kg/ha intervals of N-supply for analysis of variance and resulted in the lowest estimates for optimum N-supply. Based on the overall average, the optimum fertilizer-N dressings were 80 kg N/ha for root and sugar yield and 70 kg N/ha for white sugar yield while mineral soil-N in spring was 70 kg N/ha.     

Phaeozem in einigen trockenen Alpentälern der Schweiz

Phaeozem Soils in some dry valleys of the Swiss Alps The term Phaeozem has been adopted as a soil unit in the legend of the FAO-Unesco Soil map of the world. This soil requires a diagnostic mollic A-horizon or a mollic epipedon, with definite properties with respect to structure, color, base saturation, organic-carbon content and thickness. Phaeozems take place in some low rainfall valleys of the Swiss Alps, between 600 m and 1700 m a.s.l. Within these limits of altitude its occurence is conform to the local climatic, geological, and geomorphological conditions. In Switzerland Phaeozem are developed in a continental like climate with warm and rather dry summers and cold winters, on mixed parent materials of glacial deposits, alluvium and colluvium. Since the ice age, the erosion on the steeps slopes in the Alpine valleys delayed the soil formation, therefore clearly developed profiles of Phaeozems are not very common.     

Acidification in the Rhizosphere of Rape Seedlings and in Bulk Soil by Nitrification and Ammonium Uptake

Ammonium salts used as fertilizers may cause soil acidification by two different processes: nitrification in soil and net release of protons from roots. Their influence on soil pH may vary depending on the distance from root surface. The aim of this study was to distinguish between these two processes. For this purpose rape seedlings were grown 10 d in a system which separated roots from soil by a fine-meshed screen. As a function of distance from the plane root layer formed on the screen, pH, titratable and exchangeable acidity and NO₃- and NH₄-nitrogen were determined. The soil, a luvisol from loess, was supplied with no N or (NH₄)₂SO₄ either with or without a nitrification inhibitor (DCD). The bulk soil pH remained unaffected when no N or 400 mg NH₄? N kg^?1 soil plus DCD was applied but it decreased from 6.6 to 5.8 without DCD. In contrast, rhizosphere pH decreased in all cases, mainly within a distance of 1 mm from the root plane only, but with gradients extending to between 2 and 4 mm into the soil. The strongest pH decrease, from 6.6 to 4.9, occurred at the root surface of plants treated with both NH₄-N and DCD where most of the mineral N remained as ammonium. In this case Al was solubilized in the rhizosphere as indicated by exchangeable acidity. Total soil acidity produced in the NH₄ treatment without DCD was mainly derived from nitrification compared to root released protons. However, acidification of the rhizosphere was diminished by nitrification because nitrate ions taken up by the roots counteracted net proton release. It is concluded that nitrification inhibitors may reduce proton input from ammonium fertilizers but enhance acidification at the soil-root interface which may cause Al toxicity to plants.