Wim Cornelis De Leeuw

University of Amsterdam | UVA · Swammerdam Institute for Life Sciences

Beta-lactam antibiotics are the most applied antimicrobials in human and veterinarian health care. Hence, beta-lactam resistance is a major health problem. Gene amplification of AmpC beta-lactamase is a main contributor to de novo β-lactam resistance in E. coli. However, the time course of amplification and the accompanying DNA mutations are unclea...

Seaweeds are increasingly recognized as sustainable food sources; however, their large-scale cultivation faces challenges similar to land crops, including susceptibility to pathogens. Plant viruses pose a significant threat to global food security, yet little is known about the diversity of viruses in seaweeds. This study investigates virus-associa...

The stringent response of bacteria to starvation and stress also fulfills a role in addressing the threat of antibiotics. Within this stringent response, (p)ppGpp, synthesized by RelA or SpoT, functions as a global alarmone. However, the effect of this (p)ppGpp on resistance development is poorly understood. Here, we show that knockout of relA or r...

Resistance evolution during exposure to non-lethal levels of antibiotics is influenced by various stress responses of bacteria which are known to affect growth rate. Here, we aim to disentangle how the interplay between resistance development and associated fitness costs is affected by stress responses. We performed de novo resistance evolution of...

This study explores the genomic diversity of three novel Konjac mosaic virus (KoMV) variants, originating from distinct Zantedeschia (calla lily) commercial cultivars. Virus-derived small RNA sequencing was performed and the complete KoMV variant genome sequences were determined by de novo assembly of short reads. All KoMV variants showed substanti...

Resistance evolution during exposure to non-lethal levels of antibiotics is influenced by various stress responses of bacteria which are known to affect growth rate. Here, we aim to disentangle how the interplay between resistance development and associated fitness costs is affected by stress responses. We performed de novo resistance evolution of...

The stringent response of bacteria to starvation and stress, also fulfils a role in addressing the threat of antibiotics. Within this stringent response, (p)ppGpp, synthesized by RelA or SpoT, functions as a global alarmone. However, the effect of this stringent response and (p)ppGpp on resistance development is poorly understood. Here, we show tha...

Reactive oxygen species (ROS) produced as a secondary effect of bactericidal antibiotics are hypothesized to play a role in killing bacteria. If correct, ROS may play a role in development of de novo resistance. Here we report that single-gene knockout strains with reduced ROS scavenging exhibited enhanced ROS accumulation and more rapid acquisitio...

Here, we report the genome sequences of 10 Carnation mottle virus variants. Six variants originated from a single proprietary carnation cultivar, and four were derived from four different proprietary cultivars. All variants showed nucleotide differences, but the last four did not show any variation at the amino acid level.

Reactive oxygen species (ROS) produced as a secondary effect of bactericidal antibiotics are hypothesized to play a role in killing bacteria. However, the role of ROS in the development of de novo resistance as a result of sublethal levels of bactericidal antibiotics has barely been investigated. Here, we report that single-gene knockout strains wi...

Here, we report the genome sequence of a new circular viroid-like RNA (CarSV-1) derived from Dianthus caryophyllus (carnation) leaves. The CarSV-1 genome has notable sequence similarity (62%) to the well-studied CarSV viroid-like RNA and comprises the complete hammerhead consensus sequences involved in self-cleavage. CarSV-1 co-occurs with carnatio...

At gastrulation in the zebrafish embryogenesis, the embryonic genome is switched on to produce transcripts that are used for the maintenance and development of the embryo. In a previous study from late blastula to mid gastrula on the transcriptomes of 179 individual embryos, we capture the transcriptome dynamics via ten gene-expression types. Here...

Cellular translation relies heavily on the involvements of several types of non-coding RNAs. In previous studies we have identified a dual translation system in zebrafish development, involving maternal-type and somatic-type rRNAs, snoRNAs, and snRNAs. In this study we focused on several remaining non-coding RNAs involved in the translation system;...

Small nucleolar RNAs (snoRNAs) are non-coding RNAs that play an important role in the complex maturation process of ribosomal RNAs (rRNAs). SnoRNAs are categorized in classes, with each class member having several variants present in a genome. Similar to our finding of specific rRNA expression types in zebrafish embryogenesis, we discovered prefere...

Splicing removes intronic RNA sequences are removed from pre-mRNA molecules and enables, by alternative splicing, the generation of multiple unique RNA molecules from a single gene. As such, splicing is an essential part of the whole translation system of a cell. The spliceosome is a ribonucleoprotein complex in which five small nuclear RNAs (snRNA...

Background Huntington’s disease (HD) is a fatal neurodegenerative disorder caused by a CAG expansion in the Huntingtin (HTT) gene. Proteolytic cleavage of mutant huntingtin (Htt) protein with an expanded polyglutamine (polyQ) stretch results in production of Htt fragments that aggregate and induce impaired ubiquitin proteasome, mitochondrial functi...

Background Recently, much progress has been made in the field of gene-expression in early embryogenesis. However, the dynamic behaviour of transcriptomes in individual embryos has hardly been studied yet and the time points at which pools of embryos are collected are usually still quite far apart. Here, we present a high-resolution gene-expression...

Maternal mRNA that is present in the mature oocyte plays an important role in the proper development of the early embryo. The composition of the maternal transcriptome is unknown at the individual egg level. Here we present a microarray study on individual zebrafish eggs from five different clutches from sibling mothers. This experimental design al...

We have collected several valuable lessons learned that will help improve transcriptomics experimentation. These lessons relate to design for experimentation, experiment execution and analysis. The cautions, but also the pointers may help biologists to avoid common pitfalls in transcriptomics experimentation and achieve better results with their tr...

There is an increasing interest in complementing RNA-seq experiments with small-RNA (sRNA) expression data to obtain a comprehensive view of a transcriptome. Currently, two main experimental challenges concerning sRNA-seq exist: how to check the size distribution of isolated sRNAs, given the sensitive size-selection steps in the protocol; and how t...

Structural variations in genomes are commonly studied by (micro)array-based comparative genomic hybridization. The data analysis methods to infer copy number variation in model organisms (human, mouse) are established. In principle, the procedures are based on signal ratios between test and reference samples and the order of the probe targets in th...

Cellular stress responses are frequently presumed to be more sensitive than traditional ecotoxicological life cycle endpoints such as survival and growth. Yet, the focus to reduce test duration and to generate more sensitive endpoints has caused transcriptomics studies to be performed at low doses during short exposures, separately and independentl...

Whole-transcriptome gene-expression analyses are commonly performed in species that have a sequenced genome and for which microarrays are commercially available. To do such analyses in species with no or limited genome data, i.e. non-model organisms, necessary transcriptomics resources, i.e. an annotated transcriptome and a validated gene-expressio...

Detailed C. riparius sample list. (DOCX)

blastx results using different e-value cut-offs. (DOCX)

Additional information to the Materials and Methods. (DOCX)

aCGH signal intensities of the control probes according to GC-content. Box- and-whisker plot showing the log2 A. gambiae signal intensity distributions of the positive control probes (light grey) and the negative control probes (dark grey) for 20 GC-bins, each bin corresponding to a GC-content increase of 5%. (TIFF)

MA-plots of the aCGH experiment obtained for the various dipteran probe collections. The grey dots represent the entire probe library, except the negative control probes. The black are the probes targeting the ESTs of respectively (A) Chironomus spp., (B) Anopeheles darlingi, (C) Anopheles funestus, (D), Aedes aegypti and (E) Culex quinquefasciatus...

The C. riparius transcriptome annotation. (7Z)

User interfaces and visualisations are part of group problem solving. Technology is already a part of daily decision-making in multidisplay environments, both as communication tools and information devices. As these devices, such as large displays and visualisation tools become more accessible, there is an increasing opportunity to develop applicat...

Zebrafish Microarray Design - Perfect hit only cross-hybridizing probes. Tabulated are the probes that have an exclusive 100% similarity to the probes they cross-hybridize with. The probes are given together with the sequences they are designed on and between brackets the TCs they cross-hybridize with plus the sequence the TC has been designed on....

A complete gene-expression microarray should preferably detect all genomic sequences that can be expressed as RNA in an organism, i.e. the transcriptome. However, our knowledge of a transcriptome of any organism still is incomplete and transcriptome information is continuously being updated. Here, we present a strategy to integrate heterogeneous se...

RIDGES in HTM. RIDGES in a human transcriptome map [2].

ROCAGEs on p-values. ROCAGEs in Down Syndrome Brain expression data [4] for all chromosomes calculated by p-values on the Null Hypothesis of no differential expression between Down and control samples.

Zebrafish Microarray Design - Non Cross-hybridizing Probes. All non cross-hybridizing probes are tabulated together with their sequences, the TC-id, the transcript the probe is designed on, whether the probe is designed on the sequence given by the sequence resource or is designed on the reverse complement, start of the probe on the transcript, inf...

An exact formula for the probability function. An exact formula for calculating the probability given a median, window size and sequence length for even and uneven window sizes.

Zebrafish Microarray Design - Cross-hybridizing Probes. all cross-hybridizing probes are tabulated together with their sequences, the TC-id, the transcript the probe is designed on, whether the probe is designed on the sequence given by the sequence resource or is designed on the reverse complement, start of the probe on the transcript, information...

Our SigWin-detector discovers significantly enriched windows of (genomic) elements in any sequence of values (genes or other genomic elements in a DNA sequence) in a fast and reproducible way. However, since it is grid based, only (life) scientists with access to the grid can use this tool. Therefore and on request, we have developed the SigWinR pa...

Genome function in higher eukaryotes involves major changes in the spatial organization of the chromatin fiber. Nevertheless, our understanding of chromatin folding is remarkably limited. Polymer models have been used to describe chromatin folding. However, none of the proposed models gives a satisfactory explanation of experimental data. In partic...

Affymetrix GeneChips can be re-annotated at the probe-level by breaking up the original probe-sets and recomposing new probe-sets based on up-to-date genomic knowledge, such as available in Entrez Gene. This results in custom Chip Description Files (CDF). Using these custom CDFs improves the quality of the data and thus the results of related gene...

The three-dimensional (3D) organization of the chromosomal fiber in the human interphase nucleus is an important but poorly understood aspect of gene regulation. Here we quantitatively analyze and compare the 3D structures of two types of genomic domains as defined by the human transcriptome map. While ridges are gene dense and show high expression...

Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D physical distance between pairwise labeled genomic positions in gene-dense, highly transcribed domains and gene-...

In this paper we propose an approach in which interactive visualization and analysis are combined with batch tools for the processing of large data collections. Large and heterogeneous data collections are difficult to analyze and pose specific problems to interactive visualization. Application of the traditional interactive processing and visualiz...

In this paper we propose an approach in which interactive visualization and analysis are combined with batch tools for the processing of large data collections. Large and heterogeneous data collections are difficult to analyze and pose specific problems to interactive visualization. Application of the traditional interactive processing and visualiz...

Packaging of the eukaryotic genome into higher order chromatin structures is tightly related to gene expression. Pericentromeric heterochromatin is typified by accumulations of heterochromatin protein 1 (HP1), methylation of histone H3 at lysine 9 (MeH3K9) and global histone deacetylation. HP1 interacts with chromatin by binding to MeH3K9 through t...

Changes in chromatin structure are a key aspect in the epigenetic regulation of gene expression. We have used a lac operator array system to visualize by light microscopy the effect of heterochromatin protein 1 (HP1) α (HP1α) and HP1β on large-scale chromatin structure in living mammalian cells. The structure of HP1, containing a chromodomain, a ch...

This paper introduces GraphSplatting, a technique which transforms a graph into a two-dimensional scalar field. The scalar field can be rendered as a color coded map, a height field, or a set of contours. Splat fields allow for the visualization of arbitrarily large graphs without cluttering. They provide density information which can be used to de...

In this paper we present a distributed blackboard architecture for scientific visualzation. We discuss our motivation, design and application of the architecture. The main advantages of the architecure is twofold. First, it allows visualization tools to be tightly intergrated with simulations. Second, it allows qualitative and quantitative analysis...

The technique for visualizing topological information in fluid flows is well known. However, when applied to turbulent flows, the result will be a cluttered image which is difficult to interpret. This paper presents a technique for collapsing topologies. The governing idea is to classify the importance of the critical points in the topology. By onl...

In this case study, we compare two methods for filtering external motion in time dependent volume data sets acquired from confocal microscopy. The pros and cons of a landmark based and a voxel based method are discussed.

The design and implementation of an interactive spot noise algorithm is presented. Spot noise is a technique which utilizes texture for the visualization of flow fields. Various design tradeoffs are discussed that allow an optimal implementation on a range of high end graphical workstations.

Mass Conservative Motion Reconstruction is a new method for estimating motion in time dependent volume data.

Modern computational fluid dynamics simulations are capable of the detailed simulation of fluid flow. The output data sets of these simulations are very large and information rich. The importance of data visualization is clearly recognized for the presentation of these data sets. For gaining new insight in the nature of flow, interactive visualizat...

Analysing structure in complex time dependent flow fields is a challenging problem. Spot noise is a technique which utilizes texture for the visualization of flow fields. In this paper, two extensions of spot noise are discussed. These extensions allow spot noise to be used for very detailed analysis of time dependent flow fields.

This paper introduces GraphSplatting, a technique which transforms a graph into a two-dimensional scalar field. The scalar field can be rendered as a color coded map, a height field, or a set of contours. Splat fields allow for the visualization of arbitrarily large graphs without cluttering. They provide density information which can be used to de...

Large-scale chromatin organization is likely to play an important role in epigenetic control of gene expression. This implies that after mitosis the correct chromatin organization must be re-established in the nuclei of the two daughter cells. Here we analyze the dynamic behavior of chromatin during the transition from late anaphase to G1 in dividi...

In this case study, we compare two methods for filtering external motion in time dependent volume data sets acquired from confocal microscopy. The pros and cons of a landmark based and a voxel based method are discussed. We show that filtering external motion is an essential first step for the visualization of confocal data.

Mass Conservative Motion Reconstruction is a new method for estimating motion in time dependent volume data. A time dependent vector field representing the movement of the data is computed from a sequence of scalar volume data sets. The principle of mass conservation in a continuum is used during the reconstruction. Standard fiow visualization tech...

Multi Dimensional Scaling is a structure preserving projection method that allows for the visualization of multidimensional data. In this paper we discuss our practical experience in using MDS as a projection method in three different application scenarios. Various reasons are given why structure preserving projection methods are useful for the ana...

This paper describes BM3D: a method for the analysis of motion in time dependent volume data. From a sequence of volume data sets a sequence of vector data sets representing the movement of the data is computed. A block matching technique is used for the reconstruction of data movement. The derived vector field can be used for the visualization of...

Confocal microscopes have recently allowed biologists and biomedical researchers to obtain time dependent 3D data sets of biological. objects, such as cells and tissues. Scientific visualization can provide visual presentations of structural characteristics of these data sets. This paper addresses the role of virtual reality in gaining insight in t...

In this paper we present an overview for the interactive visualization of structural information in tabular multidimensional data. We first provide an overview of methods for layout of high dimensional data. Then we discuss a number of interactive visualization methods that can be used to present the structure of these high dimensional spaces. We d...

In this paper we describe techniques for the visualization of data defined on curvilinear grids. This type of grid poses some difficulties for visualization techniques not found in regular grids. First we will describe some basic techniques taht are useful for many visualization techniques if the are applied to curvilinear grids: grid transformatio...

In this case study we discuss an interactive feature tracking system and its use for the analysis of chromatin decondensation. Features are described as points in a multidimensional attribute space. Distances between points are used as a measure for feature correspondence. Users can interactively experiment with the correspondence measure in order...

In this case study we discuss an interactive feature tracking system and its use for the analysis of chromatin decondensation. Features are described as points in a multidimensional attribute space. Distances between points are used as a measure for feature correspondence. Users can interactively experiment with the correspondence measure in order...

Analyzing structure in complex time dependent flow fields is a challenging problem. This paper describes the use of spot noise for the visualization of this type of fields. Spot noise is a technique which utilizes texture for the visualization of flow fields. In this paper, two extensions of spot noise are discussed. These extensions allow spot noi...

The technique for visualizing topological information in fluid flows is well known. However, when the technique is used in complex and information-rich data sets, the result will be a cluttered image which is difficult to interpret. This paper presents a technique for the visualization of multi-level topology in flow data sets. It provides the user...

. Comparative visualization of data from different sources provides useful presentations to highlight similarities or differences. Such methods are valuable for comparing results from numerical flow simulation with images taken during windtunnel experiments. The experimental flow visualization technique represents the surface flow field with oil st...

Spot noise is a technique for texture synthesis, which is very useful for vector field visualization. This paper describes improvements and extensions of the basic principle of spot noise. First, better visualization of highly curved vector fields with spot noise is achieved, by adapting the shape of the spots to the local velocity field. Second, f...