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Publikationen - Molekulare Signalverarbeitung

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Bücher und Buchkapitel

Mielke, S.; Gasperini, D. Plant–Insect Bioassay for Testing Arabidopsis Resistance to the Generalist Herbivore Spodoptera littoralis (Champion, A. & Laplaze, L., eds.). Methods Mol Biol 2085, 69-78, (2020) ISBN: 978-1-0716-0142-6 DOI: 10.1007/978-1-0716-0142-6_5

Jasmonates are essential engineers of plant defense responses against many pests, including herbivorous insects. Herbivory induces the production of jasmonic acid (JA) and its bioactive conjugate jasmonoyl-l-isoleucine (JA-Ile), which then triggers a large transcriptional reprogramming to promote plant acclimation. The contribution of the JA pathway, including its components and regulators, to defense responses against insect herbivory can be evaluated by conducting bioassays with a wide range of host plants and insect pests. Here, we describe a detailed and reproducible protocol for testing feeding behavior of the generalist herbivore Spodoptera littoralis on the model plant Arabidopsis thaliana and hence infer the contribution of JA-mediated plant defense responses to a chewing insect.
Bücher und Buchkapitel

Möller, B.; Poeschl, Y.; Klemm, S.; Bürstenbinder, K. Morphological Analysis of Leaf Epidermis Pavement Cells with PaCeQuant (Cvrčková, F. & Žárský, V., eds.). Methods Mol Biol 1992, 329-349, (2019) ISBN: 978-1-4939-9469-4 DOI: 10.1007/978-1-4939-9469-4_22

Morphological analysis of cell shapes requires segmentation of cell contours from input images and subsequent extraction of meaningful shape descriptors that provide the basis for qualitative and quantitative assessment of shape characteristics. Here, we describe the publicly available ImageJ plugin PaCeQuant and its associated R package PaCeQuantAna, which provides a pipeline for fully automatic segmentation, feature extraction, statistical analysis, and graphical visualization of cell shape properties. PaCeQuant is specifically well suited for analysis of jigsaw puzzle-like leaf epidermis pavement cells from 2D input images and supports the quantification of global, contour-based, skeleton-based, and pavement cell-specific shape descriptors.
Bücher und Buchkapitel

Möller, B.; Zergiebel, L.; Bürstenbinder, K. Quantitative and Comparative Analysis of Global Patterns of (Microtubule) Cytoskeleton Organization with CytoskeletonAnalyzer2D (Cvrčková, F. & Žárský, V., eds.). Methods Mol Biol 1992, 151-171, (2019) ISBN: 978-1-4939-9469-4 DOI: 10.1007/978-1-4939-9469-4_10

The microtubule cytoskeleton plays important roles in cell morphogenesis. To investigate the mechanisms of cytoskeletal organization, for example, during growth or development, in genetic studies, or in response to environmental stimuli, image analysis tools for quantitative assessment are needed. Here, we present a method for texture measure-based quantification and comparative analysis of global microtubule cytoskeleton patterns and subsequent visualization of output data. In contrast to other approaches that focus on the extraction of individual cytoskeletal fibers and analysis of their orientation relative to the growth axis, CytoskeletonAnalyzer2D quantifies cytoskeletal organization based on the analysis of local binary patterns. CytoskeletonAnalyzer2D thus is particularly well suited to study cytoskeletal organization in cells where individual fibers are difficult to extract or which lack a clearly defined growth axis, such as leaf epidermal pavement cells. The tool is available as ImageJ plugin and can be combined with publicly available software and tools, such as R and Cytoscape, to visualize similarity networks of cytoskeletal patterns.
Bücher und Buchkapitel

Ziegler, J.; Hussain, H.; Neubert, R. H. H.; Abel, S. Sensitive and Selective Amino Acid Profiling of Minute Tissue Amounts by HPLC/Electrospray Negative Tandem Mass Spectrometry Using 9-Fluorenylmethoxycarbonyl (Fmoc-Cl) Derivatization (Alterman, M. A., ed.). Methods Mol Biol 2030, 365-379, (2019) ISBN: 978-1-4939-9639-1 DOI: 10.1007/978-1-4939-9639-1_27

A method for selective and sensitive quantification of amino acids is described. The combination of established derivatization procedures of secondary and primary amino groups with 9-fluorenylmethoxycarbonyl chloride (Fmoc-Cl) and subsequent detection of derivatized amino acids by LC-ESI-MS/MS using multiple reaction monitoring provides high selectivity. The attachment of an apolar moiety enables purification of derivatized amino acids from matrix by a single solid-phase extraction step, which increases sensitivity by reduced ion suppression during LC-ESI-MS/MS detection. Additionally, chromatography of all amino acids can be performed on reversed-phase HPLC columns using eluents without additives, which are known to cause significant decreases in signal to noise ratios. The method has been routinely applied for amino acid profiling of low amounts of liquids and tissues of various origins with a sample throughput of about 50–100 samples a day. In addition to a detailed description of the method, some representative examples are presented.
Bücher und Buchkapitel

Hellmuth, A.; Calderón Villalobos, L. I. A. Radioligand Binding Assays for Determining Dissociation Constants of Phytohormone Receptors (Lois, L. M. & Matthiesen, R., eds.). Methods Mol Biol 1450, 23-34, (2016) ISBN: 978-1-4939-3759-2 DOI: 10.1007/978-1-4939-3759-2_3

In receptor–ligand interactions, dissociation constants provide a key parameter for characterizing binding. Here, we describe filter-based radioligand binding assays at equilibrium, either varying ligand concentrations up to receptor saturation or outcompeting ligand from its receptor with increasing concentrations of ligand analogue. Using the auxin coreceptor system, we illustrate how to use a saturation binding assay to determine the apparent dissociation constant (K D ′ ) for the formation of a ternary TIR1–auxin–AUX/IAA complex. Also, we show how to determine the inhibitory constant (K i) for auxin binding by the coreceptor complex via a competition binding assay. These assays can be applied broadly to characterize a one-site binding reaction of a hormone to its receptor.

De Nardi, B.; Dreos, R.; Del Terra, L.; Martellossi, C.; Asquini, E.; Tornincasa, P.; Gasperini, D.; Pacchioni, B.; Rathinavelu, R.; Pallavicini, A.; Graziosi, G. Differential responses of Coffea arabica L. leaves and roots to chemically induced systemic acquired resistance Genome 49, 1594-1605, (2006) DOI: 10.1139/g06-125

Coffea arabica is susceptible to several pests and diseases, some of which affect the leaves and roots. Systemic acquired resistance (SAR) is the main defence mechanism activated in plants in response to pathogen attack. Here, we report the effects of benzo(1,2,3)thiadiazole-7-carbothioic acid-s-methyl ester (BTH), a SAR chemical inducer, on the expression profile of C. arabica. Two cDNA libraries were constructed from the mRNA isolated from leaves and embryonic roots to create 1587 nonredundant expressed sequence tags (ESTs). We developed a cDNA microarray containing 1506 ESTs from the leaves and embryonic roots, and 48 NBS-LRR (nucleotide-binding site leucine-rich repeat) gene fragments derived from 2 specific genomic libraries. Competitive hybridization between untreated and BTH-treated leaves resulted in 55 genes that were significantly overexpressed and 16 genes that were significantly underexpressed. In the roots, 37 and 42 genes were over and underexpressed, respectively. A general shift in metabolism from housekeeping to defence occurred in the leaves and roots after BTH treatment. We observed a systemic increase in pathogenesis-related protein synthesis, in the oxidative burst, and in the cell wall strengthening processes. Moreover, responses in the roots and leaves varied significantly.
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