Godelieve Gheysen

Bio: Godelieve Gheysen is an academic researcher from Ghent University. The author has contributed to research in topics: Gene & Root-knot nematode. The author has an hindex of 55, co-authored 205 publications receiving 9070 citations. Previous affiliations of Godelieve Gheysen include Flanders Institute for Biotechnology & University of Antwerp.

Gene expression in nematode feeding sites

Abstract: The feeding sites induced by sedentary root-endoparasitic nematodes have long fascinated researchers. Nematode feeding sites are constructed from plant cells, modified by the nematode to feed itself. Powerful new techniques are allowing us to begin to elucidate the molecular mechanisms that produce the ultrastructural features in nematode feeding cells. Many plant genes that are expressed in feeding sites produced by different nematodes have been identified in several plant species. Nematode-responsive plant genes can now be grouped in categories related to plant developmental pathways and their roles in the making of a feeding site can be illuminated. The black box of how nematodes bring about such elaborate cell differentiation in the plant is also starting to open. Although the information is far from complete, the groundwork is set so that the functions of the plant and nematode genes in feeding site development can begin to be assessed.

Suppression of beta-1,3-glucanase transgene expression in homozygous plants.

Abstract: A chimeric construct containing the Nicotiana plumbaginifolia beta-1,3-glucanase gn1 gene was introduced into Nicotiana tabacum SR1 to produce high levels of the enzyme constitutively. We determined that the GN1 protein represents a basic beta-1,3-glucanase isoform which accumulates into the vacuoles of the transgenic plants. Analysis of the progeny of the transgenic plant with the highest levels of gn1 expression revealed an unexpected phenomenon of gene suppression. Plants hemizygous for the T-DNA locus contained high levels of gn1 mRNA and exhibited a 14-fold higher beta-1,3-glucanase activity than untransformed plants. However, the expression of gn1 was completely suppressed in the homozygous plants: no corresponding mRNA or protein could be detected. This suppression mechanism occurs at a post-transcriptional level and is under developmental control. In addition, by generating haploid plants we found that this silencing phenomenon is not dependent on allelic interaction between T-DNA copies present at the same locus of homologous chromosomes, but rather is correlated with the transgene dose in the plant genome. We postulate that high doses of GN1 protein relative to the level(s) of other still unknown plant products could trigger the cellular processes directed to suppress gn1 expression.

The Jasmonate Pathway Is a Key Player in Systemically Induced Defense against Root Knot Nematodes in Rice

Abstract: Complex defense signaling pathways, controlled by different hormones, are involved in the reaction of plants to a wide range of biotic and abiotic stress factors. We studied the ability of salicylic acid, jasmonate (JA), and ethylene (ET) to induce systemic defense in rice (Oryza sativa) against the root knot nematode Meloidogyne graminicola. Exogenous ET (ethephon) and JA (methyl jasmonate) supply on the shoots induced a strong systemic defense response in the roots, exemplified by a major up-regulation of pathogenesis-related genes OsPR1a and OsPR1b, while the salicylic acid analog BTH (benzo-1,2,3-thiadiazole-7-carbothioic acid S-methyl ester) was a less potent systemic defense inducer from shoot to root. Experiments with JA biosynthesis mutants and ET-insensitive transgenics showed that ET-induced defense requires an intact JA pathway, while JA-induced defense was still functional when ET signaling was impaired. Pharmacological inhibition of JA and ET biosynthesis confirmed that JA biosynthesis is needed for ET-induced systemic defense, and quantitative real-time reverse transcription-polymerase chain reaction data revealed that ET application onto the shoots strongly activates JA biosynthesis and signaling genes in the roots. All data provided in this study point to the JA pathway to play a pivotal role in rice defense against root knot nematodes. The expression of defense-related genes was monitored in root galls caused by M. graminicola. Different analyzed defense genes were attenuated in root galls caused by the nematode at early time points after infection. However, when the exogenous defense inducers ethephon and methyl jasmonate were supplied to the plant, the nematode was less effective in counteracting root defense pathways, hence making the plant more resistant to nematode infection.

Genomics and Molecular Genetics of Plant-Nematode Interactions

Abstract: Part I - Introductory Chapters. 1. Introduction to Plant-parasitic Nematodes Modes of Parasitism. 1.1. Introduction to Nematodes. 1.2. Evolution of Plant Parasitism. 1.3. Hatching. 1.4. Attraction to Plants. 1.5. Penetration and Feeding. 1.6. Moulting. 1.7. Reproduction. 1.8. Survival. 1.9. Conclusions. 2. Current nematode threats to world agriculture. 2.1 Key nematodes threatening major agricultural crops of importance worldwide. 2.2 Quarantine nematodes of global importance. 2.3 Key nematodes on food staples for food security in developing countries. 3. Phylogeny and evolution of nematodes. 3.1 Introduction. 3.2 Backbone of nematode phylogeny. 3.3 Phylogeny of Tylenchomorpha. 3.4 Tylenchomorpha - top end plant parasites. 3.5 Concluding remarks. 4. Cyst nematodes and syncytia. 4.1 Introduction. 4.2 Root invasion and selection of the initial syncytial cell. 4.3 Syncytium development. 4.4 Syncytium ultrastructure. 4.5 Defence responses. 4.6 Concluding remarks. 5. Root-knot nematodes and giant cells. 5.1 Introduction. 5.2 Root invasion and migration. 5.3 Giant cell formation and function. 5.4 Giant cell induction - a deliberate controlled event. 5.5 Host resistance to root-knot nematodes. 5.6 Concluding remarks. Part II - Resources for functional analysis of plant-nematode interactions. 6. Genome analysis of plant parasitic nematodes. 6.1 Introduction. 6.2 Sequencing strategies. 6.3 Genome organization. 6.4 Plant parasitism. 6.5 Gene family and pathway conservation and diversification among plant parasitic and free-living nematodes. 6.6 Tools for functional genomics and genetics. 6.7 Future prospects sequencing of parasitic nematode genomes. 7. Transcriptomes of plant-parasitic nematodes. 7.1 Introduction. 7.2 Intra-specific transcriptomics has proven a powerful approach to identify parasitism-related genes. 7.3 Expressed sequence tags, the most versatile source of molecular data for plant parasitic nematodes. 7.4 Web-Based Access to Plant Parasitic Nematode EST data and tools to support analysis. 7.5 Functional and structural characterization of ESTs: understanding the molecular basis of parasitism. 7.6 Pan-phylum transcriptomics: an approach that reveals broadly conserved and taxonomically restricted molecular features in Nematoda. 7.7 The future of plant parasitic nematode transcriptomics. 8. Arabidopsis as a tool for the study of plant-nematode interactions. 8.1. Why Arabidopsis was the best choice for molecular approaches to plant-nematode interactions: a historical perspective. 8.2. Findings that were possible because of Arabidopsis. 8.3. High expectations that never quite made true. 8.4. When it would be better to use other model systems. 8.5. Future prospects: will Arabidopsis still be the best or only choice?. 9. Transcriptomic and proteomic analysis of the plant response to nematode infection. 9.1. Parasitic nematode interaction with plants. 9.2. A historical view of methods used to study transcriptional changes during plant-nematode interactions. 9.3. Microarray analysis of nematode-infected root tissues. 9.4. Next generation sequencing technology to study plant responses to nematode infection. 9.5. Proteomic analysis of the plant response to nematode infection. 9.6. Conclusions. 10. C. elegans as a resource for studies on plant parasitic nematodes. 10.2. C. elegans as a model nematode. 10.3. Application of RNAi in C. elegans and parasitic nematodes. 10.4. General conclusion and future perspectives. 11. Parallels between plant and animal parasitic nematodes. 11.1 Introduction. 11.2 Morphology. 11.3 Life Histories. 11.4. Neuronal Signalling Systems. 11.5. Endosymbionts. 11.6. Host-Parasite Interactions. 11.7. Concluding Remarks. Part III - Molecular genetics and cell biology of plant-nematode interactions. 12. Degradation of the plant cell wall by nematodes. 12.1 Introduction. 12.2 Enzymatic degradation of plant cell walls. 12.3 Non-enzymatic modification of plant cell walls. 12.4 Degradation of fungal cell walls. 12.5 Evolutionary aspects of cell wall modifying proteins. 12.6 Concluding remarks. 13. Suppression of plant defences by nematodes. 13.1 Plant parasitic nematodes as biotrophic pathogens. 13.2 Protection of the feeding site (biotrophy). 13.3 Protection of the nematode. 13.4 Conclusions and future prospects. 14. Other nematode effectors and evolutionary constraints. 14.1 A wide range of effectors are secreted during parasitism. 14.2 Signalling and protection at the plant-nematode interface. 14.3 Stylet secretions are major parasitism effectors. 14.4 Nematode effectors can trigger plant resistance. 14.5 Evolution of nematode effectors. 15. Disease resistance-genes and defense responses during incompatible interactions. 15.1 Introduction. 15.2 Nematode resistance genes. 15.3 Defense responses during incompatible interactions. 15.4 Resistance mechanisms. 15.5 Concluding remarks. 16. The role of plant hormones in nematode feeding cell formation. 16.1 Introduction. 16.2 Phytohormone-associated gene expression profiles in feeding cell formation. 16.3 Auxin. 16.4 Ethylene. 16.5 Cytokinin. 16.6. Peptide hormones. 16.7. Perspectives. 17. Unravelling the plant cell cycle in nematode induced feeding sites. 17.1 Introduction. 17.2. Transcriptional activity and transcript levels of cell cycle genes in nematode feeding sites. 17.3 In situ profiling of cell cycle genes in uninfected Arabidopsis: a useful source of information for nematode feeding sites. 17.4 DNA synthesis and the endocycle in the multinucleate giant cells and syncytia. 17.5 Cell Cycle inhibitors influence DNA synthesis and mitosis in feeding cells. 17.6 Concluding remarks. 18. The plant cytoskeleton remodelling in nematode induced feeding sites. 18.1. Introduction. 18.2. Actin and tubulin genes are highly expressed in nematode feeding sites. 18.3. Cytoskeleton rearrangements in nematode feeding sites. 18.4 The effects of cytoskeleton-disrupting drugs on nematode feeding sites. 18.5. Cytoskeleton interacting proteins and their putative role in feeding site development. 18.6. Closing remarks. 19. Cell wall modifications induced by nematodes. 19.1 Introduction. 19.2 Ultrastructure of feeding site wall in susceptible interactions. 19.3 Expression of genes involved in cell wall extension and remodeling. 19.4 Expression of genes involved in cell wall degradation in NFS. 19.5 Expression of genes involved in cell wall biosynthesis in NFS. 19.6 Ultrastructure of feeding site wall in resistant interactions. 19.7 Nematode development and cell wall modifications in plants with silenced expression of cell wall-related genes. 19.8 Summary. 20. Water and nutrient transport in nematode feeding sites.- 20.1 Nematodes as obligate parasites depend on plant water and solute supply.- 20.2 Water transport.- 20.3 Solute supply of nematode-induced feeding structures.- 20.4 Other plant-nematode interactions.- 20.5 Nematode feeding.- 20.6 Nutrient cycling and limited nutrient supply.- 20.7 Conclusions.- Part IV - Applied aspects of molecular plant nematology: exploiting genomics for practical outputs. 21. Molecular tools for diagnostics. 21.1 Introduction. 21.2 Markers for PCR diagnostics. 21.3 Other diagnostic methods. 21.4 Soil PCR. 21.5. Validation and troubleshooting. 21.6. Future research and perspectives. 21.7. Conclusions. 22. Breeding for nematode resistance: use of genomic information. 22.1 Introduction. 22.2: Mapped nematode resistance genes and QTLs. 22.3: Molecular marker-assisted breeding for resistance to nematodes. 22.4: Genes underlying resistance to nematodes. 22.5: Breeding for durable resistance to nematodes. 22.6 Conclusions. 23. Biological Control of Plant-Parasitic Nematodes: Towards Understanding Field Variation Through Molecular Mechanisms. 23.1 Introduction. 23.2 Ecological Context. 23.3 Molecular approaches for assessing field biodiversity. 23.4 Towards understanding field variation through molecular mechanisms: three models. 23.5 Future developments. 24. Nematode resistant GM crops in industrialised and developing countries. 24.1 Introduction. 24.2 Manipulation of Plant Resistance. 24.3 Development of biotechnological solutions to nematode control. 24.4 Progress towards transgenic resistance in crop plants. 24.5 Future developments. 24.6 Prospects for implementation of biotechnological control.

Integrative Genomics Viewer

Abstract: Rapid improvements in sequencing and array-based platforms are resulting in a flood of diverse genome-wide data, including data from exome and whole-genome sequencing, epigenetic surveys, expression profiling of coding and noncoding RNAs, single nucleotide polymorphism (SNP) and copy number profiling, and functional assays. Analysis of these large, diverse data sets holds the promise of a more comprehensive understanding of the genome and its relation to human disease. Experienced and knowledgeable human review is an essential component of this process, complementing computational approaches. This calls for efficient and intuitive visualization tools able to scale to very large data sets and to flexibly integrate multiple data types, including clinical data. However, the sheer volume and scope of data pose a significant challenge to the development of such tools.

Image Processing

Abstract: MUCKE aims to mine a large volume of images, to structure them conceptually and to use this conceptual structuring in order to improve large-scale image retrieval. The last decade witnessed important progress concerning low-level image representations. However, there are a number problems which need to be solved in order to unleash the full potential of image mining in applications. The central problem with low-level representations is the mismatch between them and the human interpretation of image content. This problem can be instantiated, for instance, by the incapability of existing descriptors to capture spatial relationships between the concepts represented or by their incapability to convey an explanation of why two images are similar in a content-based image retrieval framework. We start by assessing existing local descriptors for image classification and by proposing to use co-occurrence matrices to better capture spatial relationships in images. The main focus in MUCKE is on cleaning large scale Web image corpora and on proposing image representations which are closer to the human interpretation of images. Consequently, we introduce methods which tackle these two problems and compare results to state of the art methods. Note: some aspects of this deliverable are withheld at this time as they are pending review. Please contact the authors for a preview.

Hormonal Modulation of Plant Immunity

Abstract: Plant hormones have pivotal roles in the regulation of plant growth, development, and reproduction. Additionally, they emerged as cellular signal molecules with key functions in the regulation of immune responses to microbial pathogens, insect herbivores, and beneficial microbes. Their signaling pathways are interconnected in a complex network, which provides plants with an enormous regulatory potential to rapidly adapt to their biotic environment and to utilize their limited resources for growth and survival in a cost-efficient manner. Plants activate their immune system to counteract attack by pathogens or herbivorous insects. Intriguingly, successful plant enemies evolved ingenious mechanisms to rewire the plant’s hormone signaling circuitry to suppress or evade host immunity. Evidence is emerging that beneficial root-inhabiting microbes also hijack the hormone-regulated immune signaling network to establish a prolonged mutualistic association, highlighting the central role of plant hormones in the regulation of plant growth and survival.