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Publikationen - Molekulare Signalverarbeitung

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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.
Publikation

Ibañez, C.; Poeschl, Y.; Peterson, T.; Bellstädt, J.; Denk, K.; Gogol-Döring, A.; Quint, M.; Delker, C. Ambient temperature and genotype differentially affect developmental and phenotypic plasticity in Arabidopsis thaliana BioRxiv (2017) DOI: 10.1101/017285

Background: Global increase in ambient temperatures constitute a significant challenge to wild and cultivated plant species. Forward genetic analyses of individual temperature-responsive traits have resulted in the identification of several signaling and response components. However, a comprehensive knowledge about temperature sensitivity of different developmental stages and the contribution of natural variation is still scarce and fragmented at best. Results: Here, we systematically analyze thermomorphogenesis throughout a complete life cycle in ten natural Arabidopsis thaliana accessions grown in four different temperatures ranging from 16 to 28 °C. We used Q 10 , GxE, phenotypic divergence and correlation analyses to assess temperature sensitivity and genotype effects of more than 30 morphometric and developmental traits representing five phenotype classes. We found that genotype and temperature differentially affected plant growth and development with variing strengths. Furthermore, overall correlations among phenotypic temperature responses was relatively low which seems to be caused by differential capacities for temperature adaptations of individual accessions. Conclusion: Genotype-specific temperature responses may be attractive targets for future forward genetic approaches and accession-specific thermomorphogenesis maps may aid the assessment of functional relevance of known and novel regulatory components.
Bücher und Buchkapitel

Flores, R.; Gago-Zachert, S.; De la Peña, M.; Navarro, B. Chrysanthemum Chlorotic Mottle Viroid (Ed. A. Hadidi, et al.). 331-338, (2017) ISBN: eBook ISBN: 9780128017029; Hardcover ISBN: 9780128014981. DOI: 10.1016/B978-0-12-801498-1.00031-0

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Publikationen in Druck

Drost, H.-J.; Gabel, A.; Domazet-Lošo, T.; Quint, M.; Grosse, I. Capturing Evolutionary Signatures in Transcriptomes with myTAI BioRxiv (2016) DOI: 10.1101/051565

Combining transcriptome data of biological processes or response to stimuli with evolutionary information such as the phylogenetic conservation of genes or their sequence divergence rates enables the investigation of evolutionary constraints on these processes or responses. Such phylotranscriptomic analyses recently unraveled that mid-developmental transcriptomes of fly, fish, and cress were dominated by evolutionarily conserved genes and genes under negative selection and thus recapitulated the developmental hourglass on the transcriptomic level. Here, we present a protocol for performing phylotranscriptomic analyses on any biological process of interest. When applying this protocol, users are capable of detecting different evolutionary constraints acting on different stages of the biological process of interest in any species. For each step of the protocol, modular and easy-to-use open-source software tools are provided, which enable a broad range of scientists to apply phylotranscriptomic analyses to a wide spectrum of biological questions.
Publikation

Trenner, J.; Poeschl, Y.; Grau, J.; Gogol-Döring, A.; Quint, M.; Delker, C. Auxin-induced expression divergence between Arabidopsis species likely originates within the TIR1/AFB-AUX/IAA-ARF module BioRxiv (2016) DOI: 10.1101/038422

Auxin is an essential regulator of plant growth and development and auxin signaling components are conserved among land plants. Yet, a remarkable degree of natural variation in physiological and transcriptional auxin responses has been described among Arabidopsis thaliana accessions. As intra-species comparisons offer only limited genetic variation, we here inspect the variation of auxin responses between A. thaliana and A. lyrata. This approach allowed the identification of conserved auxin response genes including novel genes with potential relevance for auxin biology. Furthermore, promoter divergences were analyzed for putative sources of variation. De novo motif discovery identified novel and variants of known elements with potential relevance for auxin responses, emphasizing the complex, and yet elusive, code of element combinations accounting for the diversity in transcriptional auxin responses. Furthermore, network analysis revealed correlations of inter-species differences in the expression of AUX/IAA gene clusters and classic auxin-related genes. We conclude that variation in general transcriptional and physiological auxin responses may originate substantially from functional or transcriptional variations in the TIR1/AFB, AUX/IAA, and ARF signaling network. In that respect, AUX/IAA gene expression divergence potentially reflects differences in the manner in which different species transduce identical auxin signals into gene expression responses.
Bücher und Buchkapitel

Wasternack, C. Jasmonates: Synthesis, Metabolism, Signal Transduction and Action (2016) ISBN: ISBN 978-0-4700-1590-2 DOI: 10.1002/9780470015902.a0020138.pub2

Jasmonic acid and other fatty-acid-derived compounds called oxylipins are signals in stress responses and development of plants. The receptor complex, signal transduction components as well as repressors and activators in jasmonate-induced gene expression have been elucidated. Different regulatory levels and cross-talk with other hormones are responsible for the multiplicity of plant responses to environmental and developmental cues.
Publikation

Raschke, A.; Ibañez, C.; Ullrich, K. K.; Anwer, M. U.; Becker, S.; Glöckner, A.; Trenner, J.; Denk, K.; Saal, B.; Sun, X.; Ni, M.; Davis, S. J.; Delker, C.; Quint, M. Natural Variants of ELF3 Affect Thermomorphogenesis by Transcriptionally Modulating PIF4-Dependent Auxin Response Genes BioRxiv (2015) DOI: 10.1101/015305

Perception and transduction of temperature changes result in altered growth enabling plants to adapt to increased ambient temperature. While PHYTOCHROME-INTERACTING FACTOR4 (PIF4) has been identified as a major ambient temperature signaling hub, its upstream regulation seems complex and is poorly understood. Here, we exploited natural variation for thermo-responsive growth in Arabidopsis thaliana using quantitative trait locus (QTL) analysis. We identified GIRAFFE2.1, a major QTL explaining ~18% of the phenotypic variation for temperature-induced hypocotyl elongation in the Bay-0 x Sha recombinant inbred line population. Transgenic complementation demonstrated that allelic variation in the circadian clock regulator EARLY FLOWERING3 (ELF3) is underlying this QTL. The source of variation could be allocated to a single nucleotide polymorphism in the ELF3 coding region, resulting in differential expression of PIF4 and its target genes, likely causing the observed natural variation in thermo-responsive growth. In combination with other recent studies, this work establishes the role of ELF3 in the ambient temperature signaling network. Natural variation of ELF3-mediated gating of PIF4 expression during nightly growing periods seems to be affected by a coding sequence quantitative trait nucleotide that confers a selective advantage in certain environments. In addition, natural ELF3 alleles seem to differentially integrate temperature and photoperiod cues to induce architectural changes. Thus, ELF3 emerges as an essential coordinator of growth and development in response to diverse environmental cues and implicates ELF3 as an important target of adaptation.
Publikation

Drost, H.-G.; Bellstädt, J.; Ó'Maoiléidigh, D. S.; Silva, A. T.; Gabel, A.; Weinholdt, C.; Ryan, P. T.; Dekkers, B. J. W.; Bentsink, L.; Hilhorst, H. W. M.; Ligterink, W.; Wellmer, F.; Grosse, I.; Quint, M. Post-embryonic hourglass patterns mark ontogenetic transitions in plant development BioRxiv (2015) DOI: 10.1101/035527

The historic developmental hourglass concept depicts the convergence of animal embryos to a common form during the phylotypic period. Recently, it has been shown that a transcriptomic hourglass is associated with this morphological pattern, consistent with the idea of underlying selective constraints due to intense molecular interactions during body plan establishment. Although plants do not exhibit a morphological hourglass during embryogenesis, a transcriptomic hourglass has nevertheless been identified in the model plant Arabidopsis thaliana. Here, we investigated whether plant hourglass patterns are also found post-embryonically. We found that the two main phase changes during the life cycle of Arabidopsis, from embryonic to vegetative and from vegetative to reproductive development, are associated with transcriptomic hourglass patterns. In contrast, flower development, a process dominated by organ formation, is not. This suggests that plant hourglass patterns are decoupled from organogenesis and body plan establishment. Instead, they may reflect general transitions through organizational checkpoints.
Bücher und Buchkapitel

Tissier, A.; Ziegler, J.; Vogt, T. Specialized Plant Metabolites: Diversity and Biosynthesis (Krauss, G.-J. & Nies, D. H., eds.). 14-37, (2015) ISBN: 978-3-527-31650-2 DOI: 10.1002/9783527686063.ch2

Plant secondary metabolites, also termed specialized plant metabolites, currently comprise more than 200 000 natural products that are all based on a few biosynthetic pathways and key primary metabolites. Some pathways like flavonoid and terpenoid biosynthesis are universally distributed in the plant kingdom, whereas others like alkaloid or cyanogenic glycoside biosynthesis are restricted to a limited set of taxa. Diversification is achieved by an array of mechanisms at the genetic and enzymatic level including gene duplications, substrate promiscuity of enzymes, cell‐specific regulatory systems, together with modularity and combinatorial aspects. Specialized metabolites reflect adaptations to a specific environment. The observed diversity illustrates the heterogeneity and multitude of ecological habitats and niches that plants have colonized so far and constitutes a reservoir of potential new metabolites that may provide adaptive advantage in the face of environmental changes. The code that connects the observed chemical diversity to this ecological diversity is largely unknown. One way to apprehend this diversity is to realize its tremendous plasticity and evolutionary potential. This chapter presents an overview of the most widespread and popular secondary metabolites, which provide a definite advantage to adapt to or to colonize a particular environment, making the boundary between the “primary” and the “secondary” old fashioned and blurry.
Bücher und Buchkapitel

Wasternack, C. Jasmonates in plant growth and stress responses. (Tran, L.-S.; Pal, S.). Springer, 221-264, (2014) ISBN: 978-1-4939-0490-7 (hardcover) 978-1-4939-4814-7 (softcover) DOI: 10.1007/978-1-4939-0491-4_8

Abiotic and biotic stresses adversely affect plant growth and productivity. The phytohormones regulate key physiological events under normal and stressful conditions for plant development. Accumulative research efforts have discovered important roles of phytohormones and their interactions in regulation of plant adaptation to numerous stressors. Intensive molecular studies have elucidated various plant hormonal pathways; each of which consist of many signaling components that link a specific hormone perception to the regulation of downstream genes. Signal transduction pathways of auxin, abscisic acid, cytokinins, gibberellins and ethylene have been thoroughly investigated. More recently, emerging signaling pathways of brassinosteroids, jasmonates, salicylic acid and strigolactones offer an exciting gateway for understanding their multiple roles in plant physiological processes.At the molecular level, phytohormonal crosstalks can be antagonistic or synergistic or additive in actions. Additionally, the signal transduction component(s) of one hormonal pathway may interplay with the signaling component(s) of other hormonal pathway(s). Together these and other research findings have revolutionized the concept of phytohormonal studies in plants. Importantly, genetic engineering now enables plant biologists to manipulate the signaling pathways of plant hormones for development of crop varieties with improved yield and stress tolerance.This book, written by internationally recognized scholars from various countries, represents the state-of-the-art understanding of plant hormones’ biology, signal transduction and implications. Aimed at a wide range of readers, including researchers, students, teachers and many others who have interests in this flourishing research field, every section is concluded with biotechnological strategies to modulate hormone contents or signal transduction pathways and crosstalk that enable us to develop crops in a sustainable manner. Given the important physiological implications of plant hormones in stressful environments, our book is finalized with chapters on phytohormonal crosstalks under abiotic and biotic stresses. 
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