Using Scipion for stream image processing at Cryo-EM facilities.

Three dimensional electron microscopy is becoming a very data-intensive field in which vast amounts of experimental images are acquired at high speed. To manage such large-scale projects, we had previously developed a modular workflow system called Scipion (de la Rosa-Trevín et al., 2016). We present here a major extension of Scipion that allows processing of EM images while the data is being acquired. This approach helps to detect problems at early stages, saves computing time and provides users with a detailed evaluation of the data quality before the acquisition is finished. At present, Scipion has been deployed and is in production mode in seven Cryo-EM facilities throughout the world.

Insights into the Impact of Impurities and Non-Stoichiometric Effects on the Electrochemical Performance of Li2 MnSiO4.

A series of Li2 MnSiO4 samples with various Li, Mn, and/or Si concentrations are reported to study for the first time the effect of impurities and deviation from ideal stoichiometry on electrochemical behavior. Carbon-coated and nanosized powders are obtained at 600 °C and compared with those synthetized at 900 °C. Samples are investigated using XRD, SEM, high-resolution TEM, attenuated total reflection infrared spectroscopy and Brunauer-Emmett-Teller surface area to characterize crystal structure, particle size, impurity amount, morphology, and surface area. Electrochemical performance depends on impurities such as MnO as well as crystallite size, surface area, and non-stoichiometric phases, which lead to the formation of additional polymorphs such as Pmnb and P21 /n of Li2 MnSiO4 at low calcination temperatures. A systematic analysis of the main parameters affecting the electrochemical behavior is performed and trends in synthesis are identified. The findings can be applied to optimize different synthesis routes for attaining stoichiometric and phase-pure Pmn21 Li2 MnSiO4 as cathode material for Li-ion batteries.

Comparative study of extraction methods for the determination of PAHs from contaminated soils and sediments.

The following four methods were compared on the extraction efficiency of 16 EPA (US Environmental Protection Agency) polycyclic aromatic hydrocarbons (PAHs): German method of the Verband Deutscher Landwirtschaftlicher Untersuchungs und Forschungsanstalten (VDLUFA), two methods of the International Organization for Standardization using shaking (ISO A) and Soxhlet extraction (ISO B) and an ultrasonic method. Recovery rates of 16 PAHs were determined in two soils. Extraction efficiency was evaluated in five soils and three sediments. Effect of drying soils and sediments on extraction efficiency was tested using the VDLUFA and the ultrasonic methods. Our study shows that the number of aromatic rings, rather than extraction procedures, significantly influenced recovery rates of individual PAHs. No significant differences in extraction efficiency of the four methods were observed for less polluted samples. For highly polluted soils, extraction efficiency decreased in the following order: VDLUFA method > ISO A > ultrasonic method > ISO B. Influence of soil moisture on extraction efficiency depended to some extent on both solvent used and content of PAHs in samples. A mixture of dichloromethane/acetone (5:1) is recommended for PAH extraction from moist samples when the ultrasonic method is used.

Evaluation and refinement of a continuous seed germination and early seedling growth test for the use in the ecotoxicological assessment of soils.

Four higher plant species (Avena sativa L., oat; Lepidium sativum L., cress; Brassica rapa Metzg., turnip; and Phaseolus vulgaris L., bush bean) and 15 soils including five mineral oil-contaminated soils were tested to assess a soil-based continuous seed germination and early seedling growth bioassay. Seed germination was recorded and the shoot biomass of 14-day seedlings measured. An automatic self-watering system was compared with the daily hand watering. Results obtained from this study show that the self-watering system had minor effects on both seed germination and early seedling growth, and that soil nutrient status rather than soil texture significantly affected both seedling emergence and shoot biomass. Proportional dilution of suspicious samples from primary tests with an appropriate control soil is recommended for secondary tests. Shoot biomass is a more sensitive measurement endpoint than seed germination. Bush bean should not be recommended for use due to its low sensitivity to mineral oil and poor germination in soil.

Use of a mechanical dissociation device to improve standardization of flow cytometric cytokeratin DNA measurements of colon carcinomas.

In order to standardize dual-fluorescence DNA flow cytometry using cytokeratin (CK) antibodies, normal colonic mucosa and tumor tissue were sampled from 308 colorectal surgical specimens. Fresh colon specimens were processed directly and stored frozen until dissociation. The samples were divided into aliquots for manual dissociation with tweezers and scalpel, and parallel dissociation with an automated disaggregation device (Medimachine, DAKO Diagnostika GmbH, Hamburg, Germany). An indirect immunofluorescence method with anti-cytokeratin antibodies and propidiumiodide was applied and measured on a single-laser flow cytometer (FACScan, Becton Dickinson [BDI], Heidelberg, Germany). Evaluation with CellFit (BDI) or MultiPlus (Phoenix Flow Systems, San Diego, CA) showed that dual-parameter fluorescence propidiumiodide (DNA staining) and fluorescein-isothiocyanate (cytokeratin labeling) provides a reasonable staining method for DNA analysis of epithelial cells. No significant differences in coefficient of variation in CK-gated versus ungated cells could be observed. Normal colon mucosa served as a reliable internal, diploid DNA control. Medimachine dissociation led to a significantly higher gain of cytokeratin-positive cells compared to percentage of cytokeratin-positive cells after manual tissue disaggregation. Cytokeratin gating led to a clear-cut separation of S-phase fractions within the respective ploidy groups, irrespective of manual or automated dissociation. The S-phase fraction increased significantly from normal tissue to diploid and nondiploid tumors. In general, automated tissue preparation with the Medimachine allows simple cell-isolation for dual DNA/CK-flow cytometric measurement, improving the gain of CK-positive cells, and facilitating a standardized DNA analysis.

Soil-based phytotoxicity of 2,4,6-trinitrotoluene (TNT) to terrestrial higher plants

Seed germination and early stage seedling growth tests were conducted to determine the ecotoxicological threshold of 2,4, 6-trinitrotoluene (TNT) in two soils of different properties. Soils were amended up to 1,600 mg TNT kg-1 soil and four representative species of higher plants, two dicotyledons (Lepidium sativum L., common name: cress; and Brassica rapa Metzg., turnip) and two monocotyledons (Acena sativa L., oat; and Triticum aestivum L., wheat), were assessed. Cumulative seed germination and fresh shoot biomass were measured as evaluation endpoints. Phytotoxicity of TNT was observed to be affected by soil properties and varied between plant species. Cress and turnip showed higher sensitivity to TNT than did oat and wheat. The lowest observable adverse effect concentration (LOAEC) of TNT derived from this study was 50 mg kg-1 soil. In contrast to high TNT concentrations, low levels of TNT, i.e. , 5-25 mg kg-1 soil for cress and turnip and 25-50 mg kg-1 for oat and wheat, stimulated seedling growth. Oat was capable of tolerating as much as 1,600 mg TNT kg-1 and demonstrated a potential ability of TNT detoxification in one of the soils tested, suggesting that this plant might be useful in the bioremediation of TNT contaminated soils.