Kulturschutz – Arbeitszeitbedarf beim Einsatz von Netzen

The product quality requirements of modern outdoor vegetable cultivation are becoming more stringent and increasing importance is also attached to a defined guarantee of yield. These demands may be satisfied by using protective netting. The working methods employed in practice and the process technology hardly differ. The differences between individual variants - 1 to 7% per net – are therefore relatively low, as is the size degression. An average of 1.3 manpower-minutes per m are required for the complete process. The time requirement per net is about 26.7 min., 13 min. of which are needed for placement and 11.1 min. for removal. The difference is made up by transportation to and from the field and loading the nets. Covering the crop takes up 48 % or almost half the total working time requirement. Removing the nets accounts for 42 %. 10 % is used in driving to and from the field for placement and in loading the rolls or bales of netting before placement and after removal. There is no additional transportation time, as the nets are carried as part of the relevant transport to and from the field. Removal involves no extra journey times if the netting is removed from the crop immediately prior to harvesting, the journey to and from the field then being calculated as part of the working time requirement for harvesting

MetaCrop 2.0: managing and exploring information about crop plant metabolism

MetaCrop is a manually curated repository of high-quality data about plant metabolism, providing different levels of detail from overview maps of primary metabolism to kinetic data of enzymes. It contains information about seven major crop plants with high agronomical importance and two model plants. MetaCrop is intended to support research aimed at the improvement of crops for both nutrition and industrial use. It can be accessed via web, web services and an add-on to the Vanted software. Here, we present several novel developments of the MetaCrop system and the extended database content. MetaCrop is now available in version 2.0 at http://metacrop.ipk-gatersleben.de

Beam Test of Silicon Strip Sensors for the ZEUS Micro Vertex Detector

For the HERA upgrade, the ZEUS experiment has designed and installed a high precision Micro Vertex Detector (MVD) using single sided micro-strip sensors with capacitive charge division. The sensors have a readout pitch of 120 microns, with five intermediate strips (20 micron strip pitch). An extensive test program has been carried out at the DESY-II testbeam facility. In this paper we describe the setup developed to test the ZEUS MVD sensors and the results obtained on both irradiated and non-irradiated single sided micro-strip detectors with rectangular and trapezoidal geometries. The performances of the sensors coupled to the readout electronics (HELIX chip, version 2.2) have been studied in detail, achieving a good description by a Monte Carlo simulation. Measurements of the position resolution as a function of the angle of incidence are presented, focusing in particular on the comparison between standard and newly developed reconstruction algorithms.Comment: 41 pages, 21 figures, 2 tables, accepted for publication in NIM

A generic algorithm for layout of biological networks

BackgroundBiological networks are widely used to represent processes in biological systems and to capture interactions and dependencies between biological entities. Their size and complexity is steadily increasing due to the ongoing growth of knowledge in the life sciences. To aid understanding of biological networks several algorithms for laying out and graphically representing networks and network analysis results have been developed. However, current algorithms are specialized to particular layout styles and therefore different algorithms are required for each kind of network and/or style of layout. This increases implementation effort and means that new algorithms must be developed for new layout styles. Furthermore, additional effort is necessary to compose different layout conventions in the same diagram. Also the user cannot usually customize the placement of nodes to tailor the layout to their particular need or task and there is little support for interactive network exploration.ResultsWe present a novel algorithm to visualize different biological networks and network analysis results in meaningful ways depending on network types and analysis outcome. Our method is based on constrained graph layout and we demonstrate how it can handle the drawing conventions used in biological networks.ConclusionThe presented algorithm offers the ability to produce many of the fundamental popular drawing styles while allowing the exibility of constraints to further tailor these layouts.publishe

Modularization of biochemical networks based on classification of Petri net t-invariants

<p>Abstract</p> <p>Background</p> <p>Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior.</p> <p>With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system.</p> <p>Methods</p> <p>Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find the optimal number of t-clusters to consider for interpretation, the cluster validity measure, Silhouette Width, is applied.</p> <p>Results</p> <p>We considered two different case studies as examples: a small signal transduction pathway (pheromone response pathway in <it>Saccharomyces cerevisiae</it>) and a medium-sized gene regulatory network (gene regulation of Duchenne muscular dystrophy). We automatically classified the t-invariants into functionally distinct t-clusters, which could be interpreted biologically as functional modules in the network. We found differences in the suitability of the various distance measures as well as the clustering methods. In terms of a biologically meaningful classification of t-invariants, the best results are obtained using the Tanimoto distance measure. Considering clustering methods, the obtained results suggest that UPGMA and Complete Linkage are suitable for clustering t-invariants with respect to the biological interpretability.</p> <p>Conclusion</p> <p>We propose a new approach for the biological classification of Petri net t-invariants based on cluster analysis. Due to the biologically meaningful data reduction and structuring of network processes, large sets of t-invariants can be evaluated, allowing for model validation of qualitative biochemical Petri nets. This approach can also be applied to elementary mode analysis.</p

Comparative evaluation of the treatment efficacy of suberoylanilide hydroxamic acid (SAHA) and paclitaxel in ovarian cancer cell lines and primary ovarian cancer cells from patients

BACKGROUND: In most patients with ovarian cancer, diagnosis occurs after the tumour has disseminated beyond the ovaries. In these cases, post-surgical taxane/platinum combination chemotherapy is the "gold standard". However, most of the patients experience disease relapse and eventually die due to the emergence of chemotherapy resistance. Histone deacetylase inhibitors are novel anticancer agents that hold promise to improve patient outcome. METHODS: We compared a prototypic histone deacetylase inhibitor, suberoylanilide hydroxamic acid (SAHA), and paclitaxel for their treatment efficacy in ovarian cancer cell lines and in primary patient-derived ovarian cancer cells. The primary cancer cells were isolated from malignant ascites collected from five patients with stage III ovarian carcinomas. Cytotoxic activities were evaluated by Alamar Blue assay and by caspase-3 activation. The ability of SAHA to kill drug-resistant 2780AD cells was also assessed. RESULTS: By employing the cell lines OVCAR-3, SK-OV-3, and A2780, we established SAHA at concentrations of 1 to 20 μM to be as efficient in inducing cell death as paclitaxel at concentrations of 3 to 300 nM. Consequently, we treated the patient-derived cancer cells with these doses of the drugs. All five isolates were sensitive to SAHA, with cell killing ranging from 21% to 63% after a 72-h exposure to 20 μM SAHA, while four of them were resistant to paclitaxel (i.e., <10% cell death at 300 nM paclitaxel for 72 hours). Likewise, treatment with SAHA led to an increase in caspase-3 activity in all five isolates, whereas treatment with paclitaxel had no effect on caspase-3 activity in three of them. 2780AD cells were responsive to SAHA but resistant to paclitaxel. CONCLUSION: These ex vivo findings raise the possibility that SAHA may prove effective in the treatment of paclitaxel-resistant ovarian cancer in vivo

Zea mays iRS1563: A Comprehensive Genome-Scale Metabolic Reconstruction of Maize Metabolism

The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species

Vacuum-Ultraviolet Photoionization and Mass Spectrometric Characterization of Lignin Monomers Coniferyl and Sinapyl Alcohols

The fragmentation mechanisms of monolignols under various energetic processes are studied with jet-cooled thermal desorption molecular beam (TDMB) mass spectrometry (MS), 25 keV Bi3+ secondary ion MS (SIMS), synchrotron vacuum-ultraviolet secondary neutral MS (VUV-SNMS) and theoretical methods. Experimental and calculated appearance energies of fragments observed in TDMB MS indicate that the coniferyl alcohol photoionization mass spectra contain the molecular parent and several dissociative photoionization products. Similar results obtained for sinapyl alcohol are also discussed briefly. Ionization energies of 7.60 eV ? 0.05 eV for coniferyl alcohol and<7.4 eV for both sinapyl and dihydrosinapyl alcohols are determined. The positive ion SIMS spectrum of coniferyl alcohol shares few characteristic peaks (m/z = 137 and 151) with the TDMB mass spectra, shows extensive fragmentation, and does not exhibit clear molecular parent signals. VUV-SNMS spectra, on the other hand, are dominated by the parent ion and main fragments also present in the TDMB spectra. Molecular fragmentation in VUV-SNMS spectra can be reduced by increasing the extraction delay time. Some features resembling the SIMS spectra are also observed in the desorbed neutral products. The monolignol VUV-SNMS peaks shared with the TDMB mass spectra suggest that dissociative photoionization of ion-sputtered neutral molecules predominate in the VUV-SNMS mass spectra, despite the extra internal energy imparted in the initial ion impact. The potential applications of these results to imaging mass spectrometry of bio-molecules are discussed