Wouter Houthoofd

Bio: Wouter Houthoofd is an academic researcher from Ghent University. The author has contributed to research in topics: Macrostomum lignano & Caenorhabditis elegans. The author has an hindex of 13, co-authored 27 publications receiving 713 citations.

The embryonic cell lineage of the nematode Halicephalobus gingivalis (Nematoda: Cephalobina: Panagrolaimoidea)

Abstract: This paper describes the nearly complete embryonic cell lineage of the terrestrial nematode, Halicephalobus gingivalis, up to somatic muscle contraction, resulting in the formation of 536 cells, of which 24 undergo programmed cell death. Halicephalobus gingivalis has a 94% lineage homology with both Caenorhabditis elegans and Pellioditis marina, and a fate homology of only 86% and 78%, respectively. Although H. gingivalis belongs to a different superfamily than C. elegans and P. marina, its cell lineage is remarkably consistent with them. Variations in the fate distribution of cells among the different species were only observed at the end of the cell lineage. The data presented here show that the polyclonal cell specification is much more widespread in clades 9 and 10 and is not a highly derived trait that is specifically linked to the fast development of the model organism C. elegans.

The embryonic cell lineage of the nematode Rhabditophanes sp.

Abstract: One of the unique features of the model organism Caenorhabditis elegans is its invariant development, where a stereotyped cell lineage generates a fixed number of cells with a fixed cell type. It remains unclear how embryonic development evolved within the nematodes to give rise to the complex, invariant cell lineage of C. elegans. Therefore, we determined the embryonic cell lineage of the nematode, Rhabditophanes sp. (family Alloionematidae) and made detailed cell-by-cell comparison with the known cell lineages of C. elegans, Pellioditis marina and Halicephalobus gingivalis. This gave us a unique data set of four embryonic cell lineages, which allowed a detailed comparison between these cell lineages at the level of each individual cell. This lineage comparison revealed a similar complex polyclonal fate distribution in all four nematode species (85% of the cells have the same fate). It is striking that there is a conservation of a 'C. elegans' like polyclonal cell lineage with strong left-right asymmetry. We propose that an early symmetry-breaking event in nematodes of clade IV-V is a major developmental constraint which shapes their asymmetric cell lineage.

The simplicity of metazoan cell lineages

Abstract: Developmental processes are thought to be highly complex, but there have been few attempts to measure and compare such complexity across different groups of organisms. Here we introduce a measure of biological complexity based on the similarity between developmental and computer programs. We define the algorithmic complexity of a cell lineage as the length of the shortest description of the lineage based on its constituent sublineages. We then use this measure to estimate the complexity of the embryonic lineages of four metazoan species from two different phyla. We find that these cell lineages are significantly simpler than would be expected by chance. Furthermore, evolutionary simulations show that the complexity of the embryonic lineages surveyed is near that of the simplest lineages evolvable, assuming strong developmental constraints on the spatial positions of cells and stabilizing selection on cell number. We propose that selection for decreased complexity has played a major role in moulding metazoan cell lineages.

Mononchoides composticola n. sp. (Nematoda:Diplogastridae) associated with composting processes: morphological, molecular and autecological characterisation

Abstract: Mononchoides composticola n. sp. was isolated from compost and is described based on light and scanning electron microscopy, supplemented with SSU rDNA sequence data. It is characterised by the following features: a denticulate ridge in addition to the dorsal claw-like tooth, a small tooth-like swelling at the stegostom base, ca 26 longitudinal ridges on the female body, a uterine sac associated with two dumb-bell-shaped pouches, relatively small spicules (30-38 µm long), a simple gubernaculum shorter than half the spicule length, the genital subventral papillae (v6) consisting of three very small papillae, and a long filiform tail (female: 391-550 µm, 18-26 anal body diam.; male: 304-548 µm, 19-30 anal body diam.). Phylogenetic analyses placed the new species together with M. striatus, sister to Tylopharynx foetida. Since the use of nematodes as functional indicators often relies on the allocation of nematodes to feeding groups, experiments were performed to elucidate the feeding strategy of the new species. Both its ability to move actively to bacterial food sources and to prey on other compost nematodes were tested. Mononchoides composticola n. sp. actively moved towards the compost bacterium Achromobacter, a taxis that was temperature dependent, and also preyed on other nematodes. Predation was selective, with a higher predation rate on the relatively small and slow-moving Rhabditella sp. than on the considerably larger and more motile Rhabditis (Poikilolaimus) sp. Adults of M. composticola n. sp. have a dual feeding behaviour and can apparently alternate between bacterial and nematode prey

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.

Single-cell sequencing-based technologies will revolutionize whole-organism science

Abstract: The unabated progress in next-generation sequencing technologies is fostering a wave of new genomics, epigenomics, transcriptomics and proteomics technologies. These sequencing-based technologies are increasingly being targeted to individual cells, which will allow many new and longstanding questions to be addressed. For example, single-cell genomics will help to uncover cell lineage relationships; single-cell transcriptomics will supplant the coarse notion of marker-based cell types; and single-cell epigenomics and proteomics will allow the functional states of individual cells to be analysed. These technologies will become integrated within a decade or so, enabling high-throughput, multi-dimensional analyses of individual cells that will produce detailed knowledge of the cell lineage trees of higher organisms, including humans. Such studies will have important implications for both basic biological research and medicine.

Human organoids: model systems for human biology and medicine.

Abstract: The historical reliance of biological research on the use of animal models has sometimes made it challenging to address questions that are specific to the understanding of human biology and disease. But with the advent of human organoids - which are stem cell-derived 3D culture systems - it is now possible to re-create the architecture and physiology of human organs in remarkable detail. Human organoids provide unique opportunities for the study of human disease and complement animal models. Human organoids have been used to study infectious diseases, genetic disorders and cancers through the genetic engineering of human stem cells, as well as directly when organoids are generated from patient biopsy samples. This Review discusses the applications, advantages and disadvantages of human organoids as models of development and disease and outlines the challenges that have to be overcome for organoids to be able to substantially reduce the need for animal experiments.