Steven Vercruysse

The Cyclin-Dependent Kinase Inhibitor KRP2 Controls the Onset of the Endoreduplication Cycle during Arabidopsis Leaf Development through Inhibition of Mitotic CDKA;1 Kinase Complexes

Exit from the mitotic cell cycle and initiation of cell differentiation frequently coincides with the onset of endoreduplication, a modified cell cycle during which DNA continues to be duplicated in the absence of mitosis. Although the mitotic cell cycle and the endoreduplication cycle share much of the same machinery, the regulatory mechanisms controlling the transition between both cycles remain poorly understood. We show that the A-type cyclin-dependent kinase CDKA;1 and its specific inhibitor, the Kip-related protein, KRP2 regulate the mitosis-to-endocycle transition during Arabidopsis thaliana leaf development. Constitutive overexpression of KRP2 slightly above its endogenous level only inhibited the mitotic cell cycle–specific CDKA;1 kinase complexes, whereas the endoreduplication cycle-specific CDKA;1 complexes were unaffected, resulting in an increase in the DNA ploidy level. An identical effect on the endoreduplication cycle could be observed by overexpressing KRP2 exclusively in mitotically dividing cells. In agreement with a role for KRP2 as activator of the mitosis-to-endocycle transition, KRP2 protein levels were more abundant in endoreduplicating than in mitotically dividing tissues. We illustrate that KRP2 protein abundance is regulated posttranscriptionally through CDK phosphorylation and proteasomal degradation. KRP2 phosphorylation by the mitotic cell cycle–specific CDKB1;1 kinase suggests a mechanism in which CDKB1;1 controls the level of CDKA;1 activity through regulating KRP2 protein abundance. In accordance with this model, KRP2 protein levels increased in plants with reduced CDKB1;1 activity. Moreover, the proposed model allowed a dynamical simulation of the in vivo observations, validating the sufficiency of the regulatory interactions between CDKA;1, KRP2, and CDKB1;1 in fine-tuning the mitosis-to-endocycle transition.

Genome-Wide Analysis of Gene Expression Profiles Associated with Cell Cycle Transitions in Growing Organs of Arabidopsis

Organ growth results from the progression of component cells through subsequent phases of proliferation and expansion before reaching maturity. We combined kinematic analysis, flowcytometry, and microarray analysis to characterize cell cycle regulation during the growth process of leaves 1 and 2 of Arabidopsis (Arabidopsis thaliana). Kinematic analysis showed that the epidermis proliferates until day 12; thereafter, cells expand until day 19 when leaves reach maturity. Flowcytometry revealed that endoreduplication occurs from the time cell division rates decline until the end of cell expansion. Analysis of 10 time points with a 6k-cDNA microarray showed that transitions between the growth stages were closely reflected in the mRNA expression data. Subsequent genome-wide microarray analysis on the three main stages allowed us to categorize known cell cycle genes into three major classes: constitutively expressed, proliferative, and inhibitory. Comparison with published expression data obtained from root zones corresponding to similar developmental stages and from synchronized cell cultures supported this categorization and enabled us to identify a high confidence set of 131 proliferation genes. Most of those had an M phase-dependent expression pattern and, in addition to many known cell cycle-related genes, there were at least 90 that were unknown or previously not associated with proliferation.

The Arabidopsis leaf as a model system for investigating the role of cell cycle regulation in organ growth

The role of cell cycle regulation and cell division in plant growth and organ development is controversial. Some experimental data are most easily interpreted from the ‘cellular perspective’ that cell division drives growth, whereas other observations are more consistent with the ‘organismal perspective’ that cell division is merely a consequence of growth, and to a large extent facultative. Here we develop a model of cell cycle regulation in the context of leaf development based on literature, published kinematic analysis, flow-cytometric and transcriptomic data obtained from growing Arabidopsis leaves. We tested this model by comparing the in silico inhibition of the cell cycle progression with the experimental observations of transgenic plants overexpressing the cell cycle inhibitor Arath;KRP2. The model simulates the behaviour of proliferating cells quite well, but is inadequate in describing the effects on expanding cells. This may point to a difference in the nature of the expansion process during the proliferating and non-dividing phase of leaf development.

OLSVis: an animated, interactive visual browser for bio-ontologies

BackgroundMore than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS). Although OLS provides ample possibility for querying and browsing terms, the visualization of parts of the ontology graphs is rather limited and inflexible.ResultsWe created the OLSVis web application, a visualiser for browsing all ontologies available in the OLS database. OLSVis shows customisable subgraphs of the OLS ontologies. Subgraphs are animated via a real-time force-based layout algorithm which is fully interactive: each time the user makes a change, e.g. browsing to a new term, hiding, adding, or dragging terms, the algorithm performs smooth and only essential reorganisations of the graph. This assures an optimal viewing experience, because subsequent screen layouts are not grossly altered, and users can easily navigate through the graph. URL: http://ols.wordvis.comConclusionsThe OLSVis web application provides a user-friendly tool to visualise ontologies from the OLS repository. It broadens the possibilities to investigate and select ontology subgraphs through a smooth visualisation method.

Gene regulation knowledge commons: community action takes care of DNA binding transcription factors

A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge in databases is crucial for exploiting existing background knowledge, both for designing follow-up experiments and for interpreting new experimental data. Structured resources also underpin the computational integration and modeling of regulatory pathways, which further aids our understanding of regulatory dynamics. We argue how cooperation between the scientific community and professional curators can increase the capacity of capturing precise knowledge from literature. We demonstrate this with a project in which we mobilize biological domain experts who curate large amounts of DNA binding transcription factors, and show that they, although new to the field of curation, can make valuable contributions by harvesting reported knowledge from scientific papers. Such community curation can enhance the scientific epistemic process. Database URL: http://www.tfcheckpoint.org

WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary

Today’s data needs flexible visualization, and the advent of new tech-nologies defined under HTML5 has opened up new possibilities for rich web-applications. We used JavaScript and the new HTML5 ‘canvas’ element, to create a software module GraphVis for online visualization and exploration of large relationship networks. As a first test-case we applied the module to Princeton’s WordNet English thesaurus, and made the result available as the web-application WordVis. WordVis is an exceptionally agile, online synonym-dictionary explorer. It shows a customizable graph of interlinked words and meanings, which are arranged by real-time animation, and behave like repelling magnets that are also rearrangeable by the user. WordVis shows the merits of using JavaScript: the visualizer can be fully integrated inside a web page, and that enables communication with other HTML elements in the page. It demonstrates the latest developments in web technology, and its agility may serve as an inspiration for other web-applications. As an intuitive, online synonym-dictionary explorer, it helps to ‘find the right word’ while writing English texts. It offers an online, free and more powerful browsing experience than any existing word-network visualizer.

Jointly creating digital abstracts: dealing with synonymy and polysemy

BackgroundIdeally each Life Science article should get a ‘structured digital abstract’. This is a structured summary of the paper’s findings that is both human-verified and machine-readable. But articles can contain a large variety of information types and contextual details that all need to be reconciled with appropriate names, terms and identifiers, which poses a challenge to any curator. Current approaches mostly use tagging or limited entry-forms for semantic encoding.FindingsWe implemented a ‘controlled language’ as a more expressive representation method. We studied how usable this format was for wet-lab-biologists that volunteered as curators. We assessed some issues that arise with the usability of ontologies and other controlled vocabularies, for the encoding of structured information by ‘untrained’ curators. We take a user-oriented viewpoint, and make recommendations that may prove useful for creating a better curation environment: one that can engage a large community of volunteer curators.ConclusionsEntering information in a biocuration environment could improve in expressiveness and user-friendliness, if curators would be enabled to use synonymous and polysemous terms literally, whereby each term stays linked to an identifier.