Phytophthora genome sequences uncover evolutionary origins and mechanisms of pathogenesis

Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. O?mycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known o?mycete avirulence genes.     

Nitrogen mineralization from mature bio‐waste compost in vineyard soils II. Test of N‐mineralization parameters in a long‐term in situ incubation experiment

A field incubation experiment was carried out to test the applicability of N‐mineralization parameters for mature bio‐waste compost for use in a simulation model. The parameters were previously obtained from a laboratory experiment. Micro‐lysimeters were used for incubation, containing four different vineyard soils that were treated with three different compost‐application rates (0, 30, and 50 Mg compost ha^–1). Between 2.0% and 45.2% of total bio‐waste compost N was mineralized and leached from the micro‐lysimeters during the two‐year investigation period. The application of a simulation model for soil N dynamics revealed two major drawbacks of the model: (1) in most of the soils, extraordinary high mineralization rates were observed within a few weeks after compost amendment, which could not be explained by the model, and (2) the average compost‐N‐mineralization rates were estimated as being close to the observed rates (–6%), but distinct deviations in some cases (–46% to +29%) led to considerable miscalculations in long‐term simulations. Excluding the effect of these two processes from the data set, the remaining variance could be well explained by the model for all soils treated with compost (modeling efficiency ≥0.98). Based on the average performance, the mineralization parameters for mature bio‐waste compost are considered to be applicable for use in any simulation model based on the double‐exponential approach for calculating fertilizer recommendations, whereas the functions calculating the impact of environmental factors on N mineralization in the model need to be revised. The initial mineralization flush observed in most of the compost treatments was attributed to a priming effect. The experiment showed that such a priming effect can cause exceptionally high rates of N mineralization from mature bio‐waste compost in a viticultural environment, which exceed the potential mineralization rates known for bio‐waste compost applied to arable soils in Germany.     

Laboratory and field testing of a dose calculation model for neutralization of Adirondack acidic lakes

A deterministic lake dose calculation model has been applied to estimate the quantity of Ca carbonate-based material needed to achieve a desired initial water chemistry in a whole lake treatment of two Adirondack acid lakes. The study lakes were treated with calcite during May 30–31, 1985. The model accurately simulated laboratory column water chemistry profiles (spatially and temporally) and dissolution efficiencies; however, the model predicted conservative efficiencies for the study lakes. Time-series water chemistry profiles of the lakes suggest that epilimnetic mixing extended suspension time of fine calcite particles, and that atmospheric carbon dioxide intrusion rate was greater than expected. The combination of these factors enhanced dissolution efficiency.     

Benz(a)pyrene input and occurrence in a marine area affected by refinery effluent

The load of benz(a)pyrene in a marine coastal area in the vicinity of a town and an oil refinery has been estimated. The levels of benz(a)pyrene in refinery effluent, municipal waste water, urban run-off, rivers, and atmospheric fall-out have been determined. In the study area the major source was atmospheric fall-out. The levels of benz(a)pyrene in sediments and in mussels,Mytilus edilus have been determined. The possible removal of benz(a)pyrene from the study area has been evaluated. This includes sedimentation, degradation, and advective water transport.     

Optimizing the indirect extraction of prokaryotic DNA from soils

The objective of this work was to develop protocols to selectively extract prokaryotic DNA from soils, representative of the whole community, amenable to high-throughput whole genome shotgun sequencing. Prokaryotic cells were extracted from soils by blending, followed by gradient centrifugation. Detergent (sodium deoxycholate) was required for complete dispersion of soil aggregates and detachment of prokaryotic cells from a broad range of soil types. Repeated extractions of a given soil sample were critical to maximize cell yield. Furthermore, cells obtained through repeated extractions captured unique prokaryotic assemblages that would otherwise have been missed in single-pass extractions. DNA was isolated from extracted cells using one of the following treatments: i) lysozyme-SDS-proteinase K (enzymatic) digestion; ii) potassium ethyl xanthogenate digestion; or iii) enzymatic digestion of cells embedded in agarose plugs. In addition, these methods were compared to a commercial bead-beating extraction kit (MoBio UltraClean). Of the indirect DNA extraction methods, plug digestion generated the largest yields (up to 70% of yields obtained by direct DNA extraction) of high-molecular weight DNA (>400 kb). Thus, plug digestion is amenable to large-insert metagenomic library construction and analysis. Comparisons of banding patterns generated by RAPD-PCR and DGGE indicated that sequence composition and inferred community composition of a given extract varied greatly with DNA isolation method. While overall diversity did not change significantly with the cell lysis method, analysis of 16S rRNA gene clone libraries revealed that each extraction procedure produced unique distributions of prokaryotic phyla within the sample population.     

Relationship between the contents of bioactive components in grain and the release dates of wheat lines in the HEALTHGRAIN diversity screen

The EU FP6 HEALTHGRAIN has generated an extensive database on the contents of phytochemicals (alkylresorcinols, tocols, sterols, phenolic acids, folates) and dietary fiber components in the grain of wheat, including analyses of 150 lines grown on a single site in Hungary in 2005 and a smaller set of lines grown under five (three lines) or six (23 lines) different environments (in Hungary in 2005, 2006, and 2007 and in France, Poland, and the United Kingdom in 2007). The lines analyzed included land races and varieties bred between the mid-19th and early 21st centuries. These results have been analyzed to determine whether the contents of these groups of bioactive components in the grain have decreased with the development of intensive plant breeding in the second part of the 20th century. No decreases in the contents of any groups of bioactive components were observed in relation to release date, showing that selection for increased yield and protein quality has been effectively neutral for other grain components.     

球毛壳ND35菌株在宿主植物上的侵染定殖

为了解球毛壳Chaetomium globosum ND35菌株在宿主植物上的侵染定殖方式和途径,以毛白杨组培苗为宿主植物,借助光学显微镜、扫描电镜、透射电镜,结合免疫荧光标记技术,研究了球毛壳ND35菌株子囊孢子萌发后在毛白杨上的侵染行为及其菌丝在组培苗根部的定殖。结果显示,子囊孢子萌发后形成的菌丝,能从杨树苗根、茎部表面细胞间的缝隙侵入或在根表面形成附着胞,进而形成侵染钉直接从表皮细胞侵入,在叶部主要从气孔侵入叶片内部。侵入根部的菌丝主要定殖于表皮细胞、外皮层细胞和细胞间隙,未进入内皮层和维管束组织。     

Bombus terrestris as pollinator‐and‐vector to suppress Botrytis cinerea in greenhouse strawberry

BACKGROUND: Bombus terrestris L. bumblebees are widely used as commercial pollinators, but they might also be of help in the battle against economically important crop diseases. This alternative control strategy is referred to as pollinator‐and‐vector technology. The present study was designed to investigate the capacity of B. terrestris to fulfil this role in greenhouse strawberry flowers, which were manually inoculated with a major plant pathogen, the grey mould Botrytis cinerea Pers.: Fr. A model microbiological control agent (MCA) product Prestop‐Mix was loaded in a newly developed two‐way bumblebee dispenser, and, in addition, the use of the diluent Maizena‐Plus (corn starch) was tested. RESULTS: Importantly, loading of the MCA caused no adverse effects on bumblebee workers, with no loss of survival or impairment of flight activity of the workers during the 4 week flowering period. Secondly, vectoring of Prestop‐Mix by bumblebees resulted in a higher crop production, as 71% of the flowers developed into healthy red strawberries at picking (preharvest yield) as compared with 54% in the controls. In addition, these strawberries were better protected, as 79% of the picked berries remained free of B. cinerea after a 2 day incubation (post‐harvest yield), while this percentage was only 43% in the control. Overall, the total yield (preharvest × post‐harvest) was 2–2.5 times higher than the total yield in the controls (24%) in plants exposed to bumblebees vectoring Prestop‐Mix. Thirdly, the addition of the diluent Maizena‐Plus to Prestop‐Mix at 1:1 (w/w) resulted in a similar yield to that of Prestop‐Mix used alone, and in no negative effects on the bumblebees, flowers and berries. CONCLUSIONS: This greenhouse study provides strong evidence that B. terrestris bumblebees can vector a MCA to reduce B. cinerea incidence in greenhouse strawberries, resulting in higher yields. Similar yields obtained in the treatments with Prestop‐Mix and Prestop‐Mix + Maizena‐Plus suggest an equally efficient dissemination of the biocontrol agent into the flowers with only half the initial concentration of Prestop‐Mix, which illustrates the importance of the diluent. Copyright © 2011 Society of Chemical Industry     

Antagonists induce a conformational change in cIAP1 that promotes autoubiquitination

Inhibitor of apoptosis (IAP) proteins are negative regulators of cell death. IAP family members contain RING domains that impart E3 ubiquitin ligase activity. Binding of endogenous or small-molecule antagonists to select baculovirus IAP repeat (BIR) domains within cellular IAP (cIAP) proteins promotes autoubiquitination and proteasomal degradation and so releases inhibition of apoptosis mediated by cIAP. Although the molecular details of antagonist-BIR domain interactions are well understood, it is not clear how this binding event influences the activity of the RING domain. Here biochemical and structural studies reveal that the unliganded, multidomain cIAP1 sequesters the RING domain within a compact, monomeric structure that prevents RING dimerization. Antagonist binding induces conformational rearrangements that enable RING dimerization and formation of the active E3 ligase.