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Publikationen - Molekulare Signalverarbeitung

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Bücher und Buchkapitel

Carbonell, A.; Flores, R.; Gago, S. Hammerhead Ribozymes Against Virus and Viroid RNAs (Erdmann, V. A. & Barciszewski, J., eds.). RNA Technologies 411-427, (2012) ISBN: 978-3-642-27426-8 DOI: 10.1007/978-3-642-27426-8_16

The hammerhead ribozyme, a small catalytic motif that promotes self-cleavage of the RNAs in which it is found naturally embedded, can be manipulated to recognize and cleave specifically in trans other RNAs in the presence of Mg2+. To be really effective, hammerheads need to operate at the low concentration of Mg2+ existing in vivo. Evidence has been gathered along the last years showing that tertiary stabilizing motifs (TSMs), particularly interactions between peripheral loops, are critical for the catalytic activity of hammerheads at physiological levels of Mg2+. These TSMs, in two alternative formats, have been incorporated into a new generation of more efficient trans-cleaving hammerheads, some of which are active in vitro and in planta when targeted against the highly structured RNA of a viroid (a small plant pathogen). This strategy has potential to confer protection against other RNA replicons, like RNA viruses infecting plants and animals.
Bücher und Buchkapitel

Möller, B.; Bürstenbinder, K. Semi-Automatic Cell Segmentation from Noisy Image Data for Quantification of Microtubule Organization on Single Cell Level 199-203, (2019) ISBN: 978-1-5386-3640-4 DOI: 10.1109/ISBI.2019.8759145

The structure of the microtubule cytoskeleton provides valuable information related to morphogenesis of cells. The cytoskeleton organizes into diverse patterns that vary in cells of different types and tissues, but also within a single tissue. To assess differences in cytoskeleton organization methods are needed that quantify cytoskeleton patterns within a complete cell and which are suitable for large data sets. A major bottleneck in most approaches, however, is a lack of techniques for automatic extraction of cell contours. Here, we present a semi-automatic pipeline for cell segmentation and quantification of microtubule organization. Automatic methods are applied to extract major parts of the contours and a handy image editor is provided to manually add missing information efficiently. Experimental results prove that our approach yields high-quality contour data with minimal user intervention and serves a suitable basis for subsequent quantitative studies.
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

Vaira, A. M.; Gago-Zachert, S.; Garcia, M. L.; Guerri, J.; Hammond, J.; Milne, R. G.; Moreno, P.; Morikawa, T.; Natsuaki, T.; Navarro, J. A.; Pallas, V.; Torok, V.; Verbeek, M.; Vetten, H. J. Family - Ophioviridae (King, A. M. Q., et al., eds.). 743-748, (2012) ISBN: 978-0-12-384684-6 DOI: 10.1016/B978-0-12-384684-6.00060-4

This chapter focuses on Ophioviridae family whose sole member genus is Ophiovirus. The member species of the genus include Citrus psorosis virus (CPsV), Freesia sneak virus(FreSV), Lettuce ring necrosis virus (LRNV), and Mirafiori lettuce big-vein virus (MiLBVV).The single stranded negative/possibly ambisense RNA genome is divided into 3–4 segments, each of which is encapsidated in a single coat protein (43–50 kDa) forming filamentous virions of about 3 nm in diameter, in shape of kinked or probably internally coiled circles of at least two different contour lengths. Ophioviruses can be mechanically transmitted to a limited range of test plants, inducing local lesions and systemic mottle. The natural hosts of CPsV, ranunculus white mottle virus (RWMV), MiLBVV, and LRNV are dicotyledonous plants of widely differing taxonomy. CPsV has a wide geographical distribution in citrus in the Americas, in the Mediterranean and in New Zealand. FreSV has been reported in two species of the family Ranunculacae from Northern Italy, and in lettuce in France and Germany. Tulip mild mottle mosaic virus (TMMMV) has been reported in tulips in Japan. LRNV is closely associated with lettuce ring necrosis disease in The Netherlands, Belgium, and France, and FreSV has been reported in Europe, Africa, North America and New Zealand.
Bücher und Buchkapitel

Yamaguchi, I.; Cohen, J. D.; Culler, A. H.; Quint, M.; Slovin, J. P.; Nakajima, M.; Yamaguchi, S.; Sakakibara, H.; Kuroha, T.; Hirai, N.; Yokota, T.; Ohta, H.; Kobayashi, Y.; Mori, H.; Sakagami, Y. Plant Hormones (Liu, H.-W. & Mander, L., eds.). Comprehensive Natural Products II 4, 9-125, (2010) ISBN: 978-0-08-045382-8 DOI: 10.1016/B978-008045382-8.00092-7

The definition of a plant hormone has not been clearly established, so the compounds classified as plant hormones often vary depending on which definition is considered. In this chapter, auxins, gibberellins (GAs), cytokinins, abscisic acid, brassinosteroids, jasmonic acid-related compounds, and ethylene are described as established plant hormones, while polyamines and phenolic compounds are not included. On the other hand, several peptides that have been proven to play a clear physiological role(s) in plant growth and development, similar to the established plant hormones, are referred. This chapter will focus primarily on the more recent discoveries of plant hormones and their impact on our current understanding of their biological role. In some cases, however, it is critical to place recent work in a proper historical context.
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

Flores, R.; Carbonell, A.; de la Peña, M.; Gago, S. RNAs autocatalíticos: ribozimas de cabeza de martillo (Fenoll, C., Marcos, J., Pallás, V., Rodriguez Palenzuela, P.). Spanish Society of Phytopathology 407-420, (2007) ISBN: 84-6476-319-6

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Bücher und Buchkapitel

Flores, R.; Carbonell, A.; Gago, S.; Martínez de Alba, A.E.; Delgado, S.; Rodio, M.E.; di Serio, F. Viroid-host interactions: A molecular dialogue between two uneven partners (Lorito, M., Woo, S. L., Scala, F.). 6 (chap. 58), 1-9, (2008)

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Bücher und Buchkapitel

Wasternack, C.; Hause, B. Jasmonates and octadecanoids: Signals in plant stress responses and development (Moldave, K.). 72, 165-221, (2002) DOI: 10.1016/S0079-6603(02)72070-9

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