Molecular phylogenetic studies focused on the genus Phyllanthus L. (Phyllanthaceae) showed that Sauropus Blume (including Synostemon F.Muell.) and its related genera Breynia J.R.Forst. & G... Show moreMolecular phylogenetic studies focused on the genus Phyllanthus L. (Phyllanthaceae) showed that Sauropus Blume (including Synostemon F.Muell.) and its related genera Breynia J.R.Forst. & G.Forst. and Glochidion J.R.Forst. & G.Forst. should be united with Phyllanthus to create a monophyletic genus. The relationships within Sauropus and its relationship with Breynia were studied to test/corroborate such a broad definition of Phyllanthus. The molecular phylogenetic analyses show that Sauropus in the broad sense is composed of two distinct groups, the former Australian Synostemon and the Southeast Asian Sauropus in the strict sense with the monophyletic Breynia embedded in the latter. As the phylogeny of the species rich Phyllanthus is still far from completed and the results here strongly support the distinction of monophyletic groups such as Glochidion, former Synostemon, and Sauropus/Breynia. These genera are recognisable, while union with Phyllanthus (suggested by Hoffmann and co-authors in 2006) will turn the latter into an unrecognisable monolithic giant of a genus. It is a much better strategy to use the complete phylogeny of Phyllanthus to render it into smaller, monophyletic genera that can be characterized. The present study shows Synostemon has to be recognised again on generic level. Breynia, the older name, is nested within Sauropus, leading us to transfer the latter to Breynia. Within this broadened Breynia, two subgenera and two sections are distinguished, subgenus Sauropus and subgenus Breynia with section Cryptogynium and section Breynia under the latter. Show less
Polar cell-to-cell transport of plant hormone auxin mediated by plasma membrane (PM)-localized PIN-FORMED (PIN) auxin efflux carriers generates auxin gradients that provide positional information... Show morePolar cell-to-cell transport of plant hormone auxin mediated by plasma membrane (PM)-localized PIN-FORMED (PIN) auxin efflux carriers generates auxin gradients that provide positional information for various plant developmental processes. The apical-basal polar localization of the PIN proteins that determines the direction of auxin flow is directed by reversible phosphorylation of the PIN hydrophilic loop (PINHL). Here, we identified three evolutionarily conserved TPRXS(N/S) motifs within the PINHL, and proved that the central serine residues located in three motifs were phosphorylated by the PINOID (PID) serine/threonine kinase protein and its closely related AGC3 kinases WAG1 and WAG2. Loss-of-phosphorylation PIN1 or PIN2 protein (serine to alanine mutation) induced auxin-related plant defects in inflorescence development or root gravity-response, respectively, correlating with their apical-to-basal polarity changing in their expressing plant tissues. Furthermore, phosphorylation at the conserved serine residues is important for PIN protein PM localization, as loss-of-phosphorylation PIN1 protein exhibited internalized signals in plant embryos and enhanced vacuolar accumulation in dark-incubated Arabidopsis protoplast cells. Our data indicate that phosphorylation of our identified conserved serine residues in the PIN1HL by AGC3 kinases is required for proper PIN polar localization, and is thus essential for generating the differential auxin distribution that directs plant development. Show less
The study of genomes is an active research area that raises much public interest. Since the sequencing of the human genome, numerous other genome projects were started and today we have sequence... Show moreThe study of genomes is an active research area that raises much public interest. Since the sequencing of the human genome, numerous other genome projects were started and today we have sequence information of over 1000 organisms. However, the function of approximately half of all genes in human and other vertebrate species is still unknown. Therefore, the functional annotation of genome sequences is now the major challenge. Functional annotation of the human genome can be supported by loss-of-function studies in model organisms and by the analysis of mutations that associate with human disorders. The work described in this thesis is focused on the investigation of Mpzl3, a novel gene with unknown function that was identified through mapping of the rough coat mutation in mice. The Mpzl3 gene is a member of the myelin protein zero family that consists of proteins containing immunoglobulin domains and with suggested roles related to immune function and cell adhesion. Functional studies of the Mpzl3 gene in two model organisms, mouse and zebrafish, and investigations of the human orthologue by in silico techniques, suggested that the product of this gene plays a role in the immune system and is a potential candidate gene for immune-related hereditary hair loss diseases in human. Show less
Analysis of the transcriptome, the total of all expressed RNA transcripts in a cell or an organism, contributes to our understanding of gene regulation during development and disease processes and... Show moreAnalysis of the transcriptome, the total of all expressed RNA transcripts in a cell or an organism, contributes to our understanding of gene regulation during development and disease processes and is therefore of great importance in the field of genomic research. This thesis focuses on the analysis of transcriptome complexity during infectious disease and cancer. The zebrafish was applied as an immunological model organism, due to the remarkable similarities of its immune system to that of human. The studies took advantage of novel opportunities for transcriptome profiling provided by recent developments in microarray and next generation sequencing technology that have made an enormous impact on biology. In addition to studying expression of protein coding genes, the work addressed regulatory functions of microRNAs, small non-coding RNAs playing important roles in the function of the immune system and other processes. The transcriptome data provide a valuable reference set of infection-responsive genes and microRNAs in zebrafish models and have identified microRNAs conserved between human and zebrafish liver cancer. These genomic data sets provide a strong basis for future applications of zebrafish as an infection and cancer model and contribute to the understanding of pathogenesis and the development of novel strategies for disease treatment. Show less
Jasmonic acid (JA) is a plant hormone that plays an important role in defense against wounding, insects and microbial pathogens. In defense responses against microbial pathogens JA acts... Show moreJasmonic acid (JA) is a plant hormone that plays an important role in defense against wounding, insects and microbial pathogens. In defense responses against microbial pathogens JA acts synergistically with the stress hormone ethylene. ORA59, belonging to the plant-specific class of AP2-domain transcription factors, is the main regulator of JA/ethylene-responsive defense gene expression in the model plant species Arabidopsis thaliana. The aim of the research described in this thesis was to study how the activity of ORA59 is regulated by JA. Studies on the promoter of the defense gene PDF1.2 showed that ORA59 regulates gene expression by interaction with GCCGCC motifs. Studies of ORA59 at the protein level indicated that JA controls ORA59 activity by promoting the nuclear localization and stabilization of the protein. Based on the findings it was postulated that there is an F-box protein that targets ORA59 for degradation, and a repressor protein that sequesters ORA59 in the cytoplasm. A protein interacting with ORA59 was identified by yeast two-hybrid screening. Further studies showed that this protein acts as a repressor of ORA59 by retaining it in the cytoplasm, which leads to fine-tuning of basal resistance against pathogens. Show less
Is there a good continued fraction approximation between every two bad ones? What is the entropy of the natural extension for alpha-Rosen fractions? How do you find multi-dimensional continued... Show moreIs there a good continued fraction approximation between every two bad ones? What is the entropy of the natural extension for alpha-Rosen fractions? How do you find multi-dimensional continued fractions with a guaranteed quality in polynomial time? These, and many more, questions are answered in this thesis. Show less
In this thesis, different speciation processes were studied that were involved in the origin of V. stagnina and its closest relatives. Phylogenetic analyses of the CHS intron showed that... Show moreIn this thesis, different speciation processes were studied that were involved in the origin of V. stagnina and its closest relatives. Phylogenetic analyses of the CHS intron showed that hybridization and polyploidisation played an important role during speciation and that Viola stagnina is one of the parental species of the alloploid species V. canina, V. lactea and V. pumila and the parental species of the autotetraploid V. elatior. The analyses also confirmed that the closest relatives of V. stagnina were the other arosulate violets V. canina, V. elatior, V. pumila and V. lactea. In an attempt to settle a debate among Dutch botanists about the taxonomic status of V. stagnina var. lacteoides, the morphological and genetic variation within V. stagnina were studied using AFLP, morphometrics analyses, a common garden experiment, and a crossing experiment. The genetic and morphological differences found support for the recognition of the infraspecific taxon V. stagnina var. lacteoides. The nomenclatural studies carried out resulted in a recommendation to formally reject the ambiguous name V. persicifolia for the European Fen Violet and use the name V. stagnina, instead. To bring the common name into line with the usage in Belgium, it is also recommended to change the Dutch common name from Melkviooltje into Vals melkviooltje. Show less
As the zebrafish, Danio rerio, has been increasingly used as an animal model for biomedical research, we aimed to establish zebrafish cell line models for inflammation and cancer studies in this... Show moreAs the zebrafish, Danio rerio, has been increasingly used as an animal model for biomedical research, we aimed to establish zebrafish cell line models for inflammation and cancer studies in this thesis. Several zebrafish cell lines were characterized and their genetic and physiological properties were compared. We also developed a set of tool methods to investigate cellular signaling events in zebrafish cell lines. Our case studies illustrated that zebrafish cell lines are as reliable models as the widely used mammalian cell cultures. Taking advantage of the transparency of zebrafish embryos and cell implantation protocols, zebrafish cell lines can serve as a bridge platform between in vitro, in silico, ex vivo and in vivo studies in order to enhance our understanding of molecular mechanisms underlying disease progression. Show less
In the last decade the study of the innate immune system has gained renewed scientific momentum as a result of the discovery of essential receptor families, such as the Toll-like receptor (TLR)... Show moreIn the last decade the study of the innate immune system has gained renewed scientific momentum as a result of the discovery of essential receptor families, such as the Toll-like receptor (TLR) family, that are required for pathogen recognition. These receptors detect specific molecular structures of microorganisms and in turn are able to trigger host immune responses. The work described in this thesis focuses on the use of the zebrafish embryo as a model to study the vertebrate immune system in order to gain new insights into the mechanisms of innate immune defence against bacterial infections and TLR signalling. Making use of a Salmonella infection model in combination with microarray technology and gene knock-down studies we were able to thoroughly characterize the embryonic host transcriptome response to a bacterial infection. Furthermore, we have demonstrated important functions for key signalling molecules in the innate immune response, including Tlr5, MyD88 and Traf6 and discovered new downstream targets of the TLR signalling pathway. The data presented here will enable in-depth functional follow-up studies that will provide new insights into the mechanisms of innate immune defence systems. This, in combination with future applications of zebrafish embryo infection models in high-throughput compound screens, holds much promise for the discovery of novel anti-microbial and anti-inflammatory drugs. Show less
In this thesis I studied the relationships between parasitoids, hosts and climate from an evolutionary point of view by using hymenopteran parasitoids as a model system. A comparative approach was... Show moreIn this thesis I studied the relationships between parasitoids, hosts and climate from an evolutionary point of view by using hymenopteran parasitoids as a model system. A comparative approach was used to study the variation in life-history traits of species or populations from different habitats. I showed that closely related species manipulate their host behaviour differently and allocate their essential resources to different life-history traits during development. Metabolic rate and energy reserves varied strongly between species. At the population level, energy reserves were found differ substantially between different climate zones. A molecular study revealed clear genetic divergence of these populations, which partially reflected the pattern in life-history variation. To conclude, I suggest that life-history traits of parasitoids are subject to natural selection pressures from both host and cli mate. Resource allocation and host manipulation in parasitoids is species specific and highly diverged among populations to fit habitat requirements. Show less
