Spectral fluorescence variation of pollen and spores from recent peat-forming plants

The fluorescence properties of spores and pollen grains examined under ultraviolet incident light are used to assess the maturity of sedimentary organic matter and may have other applications in relation to recent sediments, in areas such as paleoenvironmental research. In this study pollen grains and spores from 33 species common in peat ecosystems were mounted on a glass slide in accordance with standard palynologycal procedures for recent plants. The main objective of this work was to assess the variability of fluorescence spectra of pollens and spores within a single species or even within a single sample. A minimum of 10 spectra were recorded from each sample and were averaged to obtain a spectrum characteristic of each sample. Both the average scattering and the scattering in different spectral regions were calculated using the standard deviation (SD) and the coefficient of variation (CV). The effect of the preparation techniques was assessed on some samples of Ericaceae taxa. The results indicated similar spectra for alcohol-washed and distilled water-washed samples, whereas the application of an acetolysis solution caused an increase in intensity and a shift to longer wavelengths. The spectra corresponding to the Sphagnum spores had the lowest intensity of all the families studied and displayed their maxima at the lowest registered wavelengths. They often showed a peak in the red region of the spectra, causing a larger scatter in fluorescence in this region. This peak is probably the result of wax or cytoplasmic material attached to the exospore. A significant number of Ericaceae taxa had two fluorescing pollen populations: a blue one of high intensity and smaller size and a yellow-orange one of low intensity and larger size. This difference could be related to different degrees of maturity of the pollen grains. In the case of pollen grains of herbaceous, tree and bush plants the largest scatter was found in the tails of the spectra toward the blue and red regions. The decreasing trend of fluorescence intensity with the shift of the spectra toward red was not observed in the pollen and spores of fresh plants. A good correlation was found between the spectral maxima (λmax) and the red-green quotient (QR/G) regardless of the type of plant.Financial support from MICINN (CGL2009-13990-C02-01/02), MINECO (CGL2013-46458-C2-1-R) and a FPU fellowship from MEC for J. Urbanczyk are gratefully acknowledged.Peer reviewe

Characterizations and first plasma operation of the WEST load-resilient actively cooled ICRF launchers

The paper discusses the characterization of the three high power steady-state and load-resilient ICRF launchers of WEST before their installation in the tokamak. These launchers have been characterized and validated in low-power experiments (milliwatt range) as well as in experiments at the nominal RF voltages and currents in the TITAN vacuum chamber (~30 kV and 915 A peak). The successful commissioning of two of the launchers during the WEST C3 campaign at ~1 MW power level is illustrated. Manual and real-time controlled impedance-matching of the launchers are discussed, as well as the validation of their load-resilience. Furthermore, several redundant and complementary protection systems have been validated and are reviewed in the paper

The LAGUNA design study- towards giant liquid based underground detectors for neutrino physics and astrophysics and proton decay searches

The feasibility of a next generation neutrino observatory in Europe is being considered within the LAGUNA design study. To accommodate giant neutrino detectors and shield them from cosmic rays, a new very large underground infrastructure is required. Seven potential candidate sites in different parts of Europe and at several distances from CERN are being studied: Boulby (UK), Canfranc (Spain), Fr\'ejus (France/Italy), Pyh\"asalmi (Finland), Polkowice-Sieroszowice (Poland), Slanic (Romania) and Umbria (Italy). The design study aims at the comprehensive and coordinated technical assessment of each site, at a coherent cost estimation, and at a prioritization of the sites within the summer 2010.Comment: 5 pages, contribution to the Workshop "European Strategy for Future Neutrino Physics", CERN, Oct. 200

Analysis of subcellular metabolite levels of potato tubers (Solanum tuberosum) displaying alterations in cellular or extracellular sucrose metabolism

The expression of a heterologous invertase in potato tubers (Solanum tuberosum) in either the cytosol or apoplast leads to a decrease in total sucrose content and to an increase in glucose. Depending on the targeting of the enzyme different changes in phenotype and metabolism of the tubers occur: the cytosolic invertase expressing tubers show an increase in the glycolytic flux, accumulation of amino acids and organic acids, and the appearance of novel disaccharides; however, these changes are not observed when the enzyme is expressed in the apoplast [Roessner et al. (2001). Plant Cell, 13, 11-29]. The analysis of these lines raised several questions concerning the regulation of compartmentation of metabolites in potato tubers. In the current study we addressed these questions by performing comparative subcellular metabolite profiling. We demonstrate that: (i) hexoses accumulate in the vacuole independently of their site of production, but that the cytosolic invertase expression led to a strong increase in the cytosolic glucose concentration and decrease in cytosolic sucrose, whereas these effects were more moderate in the apoplastic expressors; (ii) three out of four of the novel compounds found in the cytosolic overexpressors accumulate in the same compartment; (iii) despite changes in absolute cellular content the subcellular distribution of amino acids was invariant in the invertase overexpressing tubers. These results are discussed in the context of current models of the compartmentation of primary metabolism in heterotrophic plant tissues

PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments

BACKGROUND: Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis. RESULTS: Here we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs. PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis. PageMan offers a complete user's guide, a web-based over-representation analysis as well as a tutorial, and is freely available at . CONCLUSION: PageMan allows multiple microarray experiments to be efficiently condensed into a single page graphical display. The flexible interface allows data to be quickly and easily visualized, facilitating comparisons within experiments and to published experiments, thus enabling researchers to gain a rapid overview of the biological responses in the experiments

Metal hydrides for concentrating solar thermal power energy storage

The development of alternative methods for thermal energy storage is important for improving the efficiency and decreasing the cost for Concentrating Solar-thermal Power (CSP). We focus on the underlying technology that allows metal hydrides to function as Thermal Energy Storage (TES) systems and highlight the current state-of-the-art materials that can operate at temperatures as low as room-temperature and as high as 1100 oC. The potential of metal hydrides for thermal storage is explored while current knowledge gaps about hydride properties, such as hydride thermodynamics, intrinsic kinetics and cyclic stability, are identified. The engineering challenges associated with utilising metal hydrides for high-temperature thermal energy storage are also addressed

Genome-Wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus Biotype 3

Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains Of V. vulnificus are classified into three different biotypes. The newly emerged biotype 3 has been found to be clonal and restricted to Israel. In the family Vibrionaceae , horizontal gene transfer is the main mechanism responsible for the emergence of new pathogen groups. To better understand the evolution of the bacterium, and in particular to trace the evolution of biotype 3, we performed genome-wide SNP genotyping of 254 clinical and environmental V. vulnificus isolates with worldwide distribution recovered over a 30-year period, representing all phylogeny groups. A custom single-nucleotide polymorphism (SNP) array implemented on the Illumina GoldenGate platform was developed based on 570 SNPs randomly distributed throughout the genome. In general, the genotyping results divided the V. vulnificus species into three main phylogenetic lineages and an additional subgroup, clade B, consisting of environmental and clinical isolates from Israel. Data analysis suggested that 69% of biotype 3 SNPs are similar to SNPs from clade B, indicating that biotype 3 and clade B have a common ancestor. The rest of the biotype 3 SNPs were scattered along the biotype 3 genome, probably representing multiple chromosomal segments that may have been horizontally inserted into the clade B recipient core genome from other phylogroups or bacterial species sharing the same ecological niche. Results emphasize the continuous evolution of V. vulnificus and support the emergence of new pathogenic groups within this species as a recurrent phenomenon. Our findings contribute to a broader understanding of the evolution of this human pathogen

Oscillations by Minimal Bacterial Suicide Circuits Reveal Hidden Facets of Host-Circuit Physiology

Synthetic biology seeks to enable programmed control of cellular behavior though engineered biological systems. These systems typically consist of synthetic circuits that function inside, and interact with, complex host cells possessing pre-existing metabolic and regulatory networks. Nevertheless, while designing systems, a simple well-defined interface between the synthetic gene circuit and the host is frequently assumed. We describe the generation of robust but unexpected oscillations in the densities of bacterium Escherichia coli populations by simple synthetic suicide circuits containing quorum components and a lysis gene. Contrary to design expectations, oscillations required neither the quorum sensing genes (luxR and luxI) nor known regulatory elements in the PluxI promoter. Instead, oscillations were likely due to density-dependent plasmid amplification that established a population-level negative feedback. A mathematical model based on this mechanism captures the key characteristics of oscillations, and model predictions regarding perturbations to plasmid amplification were experimentally validated. Our results underscore the importance of plasmid copy number and potential impact of “hidden interactions” on the behavior of engineered gene circuits - a major challenge for standardizing biological parts. As synthetic biology grows as a discipline, increasing value may be derived from tools that enable the assessment of parts in their final context

Rapid Etiological Classification of Meningitis by NMR Spectroscopy Based on Metabolite Profiles and Host Response

Bacterial meningitis is an acute disease with high mortality that is reduced by early treatment. Identification of the causative microorganism by culture is sensitive but slow. Large volumes of cerebrospinal fluid (CSF) are required to maximise sensitivity and establish a provisional diagnosis. We have utilised nuclear magnetic resonance (NMR) spectroscopy to rapidly characterise the biochemical profile of CSF from normal rats and animals with pneumococcal or cryptococcal meningitis. Use of a miniaturised capillary NMR system overcame limitations caused by small CSF volumes and low metabolite concentrations. The analysis of the complex NMR spectroscopic data by a supervised statistical classification strategy included major, minor and unidentified metabolites. Reproducible spectral profiles were generated within less than three minutes, and revealed differences in the relative amounts of glucose, lactate, citrate, amino acid residues, acetate and polyols in the three groups. Contributions from microbial metabolism and inflammatory cells were evident. The computerised statistical classification strategy is based on both major metabolites and minor, partially unidentified metabolites. This data analysis proved highly specific for diagnosis (100% specificity in the final validation set), provided those with visible blood contamination were excluded from analysis; 6-8% of samples were classified as indeterminate. This proof of principle study suggests that a rapid etiologic diagnosis of meningitis is possible without prior culture. The method can be fully automated and avoids delays due to processing and selective identification of specific pathogens that are inherent in DNA-based techniques