Fons J. Verbeek

Knockdown of the glucocorticoid receptor alters functional integration of newborn neurons in the adult hippocampus and impairs fear-motivated behavior

Glucocorticoids (GCs) secreted after stress reduce adult hippocampal neurogenesis, a process that has been implicated in cognitive aspects of psychopathology, amongst others. Yet, the exact role of the GC receptor (GR), a key mediator of GC action, in regulating adult neurogenesis is largely unknown. Here, we show that GR knockdown, selectively in newborn cells of the hippocampal neurogenic niche, accelerates their neuronal differentiation and migration. Strikingly, GR knockdown induced ectopic positioning of a subset of the new granule cells, altered their dendritic complexity and increased their number of mature dendritic spines and mossy fiber boutons. Consistent with the increase in synaptic contacts, cells with GR knockdown exhibit increased basal excitability parallel to impaired contextual freezing during fear conditioning. Together, our data demonstrate a key role for the GR in newborn hippocampal cells in mediating their synaptic connectivity and structural as well as functional integration into mature hippocampal circuits involved in fear memory consolidation.

Digital Atlasing and Standardization in the Mouse Brain

Digital brain atlases are used in neuroscience to characterize the spatial organization of neuronal structures [1]–[3], for planning and guidance during neurosurgery [4], [5], and as a reference for interpreting other modalities such as gene expression or proteomic data [6]–[9]. The field of digital atlasing is extensive, and includes high quality brain atlases of the mouse [10], rat [11], rhesus macaque [12], human [13], [14], and several other model organisms. In addition to atlases based on histology, [11], [15], [16], magnetic resonance imaging [10], [17], and positron emission tomography [11], modern digital atlases often use probabilistic and multimodal techniques [18], [19], as well as sophisticated visualization software [20], [21]. Whether atlases involve detailed visualization of structures of a single or small group of specimens [6], [22], [23] or averages over larger populations [18], [24], much of the work in developing digital brain atlases is from the perspective of the user of a single resource. This is often due largely to the challenges of data generation, maintenance, and resources management [25], [26]. A more recent goal of many neuroscientists is to connect multiple and diverse resources to work in a collaborative manner using an atlas based framework [2], [19]. This vision is appealing as, ideally, researchers would be able to share their data and analyses with others, regardless of where they or the data are located. An important step in this direction is the specification of a common frame of reference across specimens and resources (either as coordinate, ontology, or region of interest) that is adopted by the community. In this perspective, we propose a collaborative digital atlasing framework for coordinating mouse brain research that allows access to data, tools, and analyses from multiple sources.

Zebrafish embryo screen for mycobacterial genes involved in the initiation of granuloma formation reveals a newly identified ESX-1 component

SUMMARY The hallmark of tuberculosis (TB) is the formation of granulomas, which are clusters of infected macrophages surrounded by additional macrophages, neutrophils and lymphocytes. Although it has long been thought that granulomas are beneficial for the host, there is evidence that mycobacteria also promote the formation of these structures. In this study, we aimed to identify new mycobacterial factors involved in the initial stages of granuloma formation. We exploited the zebrafish embryo Mycobacterium marinum infection model to study initiation of granuloma formation and developed an in vivo screen to select for random M. marinum mutants that were unable to induce granuloma formation efficiently. Upon screening 200 mutants, three mutants repeatedly initiated reduced granuloma formation. One of the mutants was found to be defective in the espL gene, which is located in the ESX-1 cluster. The ESX-1 cluster is disrupted in the Mycobacterium bovis BCG vaccine strain and encodes a specialized secretion system known to be important for granuloma formation and virulence. Although espL has not been implicated in protein secretion before, we observed a strong effect on the secretion of the ESX-1 substrates ESAT-6 and EspE. We conclude that our zebrafish embryo M. marinum screen is a useful tool to identify mycobacterial genes involved in the initial stages of granuloma formation and that we have identified a new component of the ESX-1 secretion system. We are confident that our approach will contribute to the knowledge of mycobacterial virulence and could be helpful for the development of new TB vaccines.

Longitudinal assessment of Alzheimer's β‐amyloid plaque development in transgenic mice monitored by in vivo magnetic resonance microimaging

To assess the development of β‐amyloid (Aβ) plaques in the brain with age in the transgenic mouse model of Alzheimers disease (AD) pathology by in vivo magnetic resonance microimaging (μMRI).

Gene expression and digit homology in the chicken embryo wing

Summary The bird wing is of special interest to students of homology and avian evolution. Fossil and developmental data give conflicting indications of digit homology if a pentadactyl “archetype” is assumed. Morphological signs of a vestigial digit I are seen in bird embryos, but no digit‐like structure develops in wild‐type embryos. To examine the developmental mechanisms of digit loss, we studied the expression of the high‐mobility group box containing Sox9 gene, and bone morphogenetic protein receptor 1b (bmpR‐1b)—markers for precondensation and prechondrogenic cells, respectively. We find an elongated domain of Sox9 expression, but no bmpR‐1b expression, anterior to digit II. We interpret this as a digit I domain that reaches precondensation, but not condensation or precartilage stages. It develops late, when the tissue in which it is lodged is being remodeled. We consider these findings in the light of previous Hoxd‐11 misexpression studies. Together, they suggest that there is a digit I vestige in the wing that can be rescued and undergo development if posterior patterning cues are enhanced. We observed Sox9 expression in the elusive “element X” that is sometimes stated to represent a sixth digit. Indeed, incongruity between digit domains and identities in theropods disappears if birds and other archosaurs are considered primitively polydactyl. Our study provides the first gene expression evidence for at least five digital domains in the chick wing. The failure of the first to develop may be plausibly linked to attenuation of posterior signals.

Septation and valvar formation in the outflow tract of the embryonic chick heart.

There is no agreement, in the chick, about the number of the endocardial cushions within the outflow tract or their pattern of fusion. Also, little is known of their relative contributions to the formation of the arterial valves, the subpulmonary infundibulum, and the arterial valvar sinuses. As the chick heart is an important model for studying septation of the outflow tract, our objective was to clarify these issues. Normal septation of the outflow tract was studied in a series of 60 staged chick hearts, by using stained whole‐mount preparations, serial sections, and scanning electron microscopy. A further six hearts were examined subsequent to hatching. At stage 21, two pairs of endocardial cushions were seen within the developing outflow tract. One pair was positioned proximally, with the other pair located distally. By stage 25, a third distal cushion had developed. This finding was before the appearance of two further, intercalated, endocardial cushions, also distally positioned, which were first seen at stage 29. In the arterial segment, the aortic and pulmonary channels were separated by the structure known as the aortopulmonary septum. The dorsal limb of this septum penetrated the distal dorsal cushion, whereas the ventral limb grew between the remaining two distal cushions, both of which were positioned ventrally. The three distal endocardial cushions, and the two intercalated endocardial cushions, contributed to the formation of the leaflets and sinuses of the arterial roots. The two proximal cushions gave rise to a transient septum, which later became transformed into the muscular component of the subpulmonary infundibulum. Concomitant with these changes, an extracardiac tissue plane was formed which separated this newly formed structure from the sinuses of the aortic root. Our study confirms that three endocardial cushions are positioned distally, and two proximally, within the developing outflow tract of the chick. The pattern of the distal cushions, and the position of the ventral limb of the aortopulmonary septum, differs significantly from that seen in mammals. Anat Rec 264:273–283, 2001.

Comparison and integration of target prediction algorithms for microRNA studies.

microRNAs are short RNA fragments that have the capacity of regulating hundreds of target gene expression. Currently, due to lack of high-throughput experimental methods for miRNA target identification, a collection of computational target prediction approaches have been developed. However, these approaches deal with different features or factors are weighted differently resulting in diverse range of predictions. The prediction accuracy remains uncertain. In this paper, three commonly used target prediction algorithms are evaluated and further integrated using algorithm combination, ranking aggregation and Bayesian Network classification. Our results revealed that each individual prediction algorithm displays its advantages as was shown on different test data sets. Among different integration strategies, the application of Bayesian Network classifier on the features calculated from multiple prediction methods significantly improved target prediction accuracy.

ZebraFISH: fluorescent in situ hybridization protocol and three-dimensional imaging of gene expression patterns

We present a method and protocol for fluorescent in situ hybridization (FISH) in zebrafish embryos to enable three-dimensional imaging of patterns of gene expression using confocal laser scanning microscopy. We describe the development of our protocol and the processing workflow of the three-dimensional images from the confocal microscope. We refer to this protocol as zebraFISH. FISH is based on the use of tyramide signal amplification (TSA), which results in highly sensitive and very localized fluorescent staining. The zebraFISH protocol was extensively tested and here we present a panel of five probes for genes expressed in different tissues or single cells. FISH in combination with confocal laser scanning microscopy provides an excellent tool to generate three-dimensional images of patterns of gene expression. We propose that such three-dimensional images are suitable for building a repository of gene expression patterns, complementary to our previously published three-dimensional anatomical atlas of zebrafish development (bio-imaging.liacs.nl/). Our methodology for image processing of three-dimensional confocal images allows an analytical approach to the definition of gene expression domains based on the three-dimensional anatomical atlas.

Magnetic resonance microscopy of the adult zebrafish.

Magnetic resonance microscopy (MRM) is an imaging modality that allows for noninvasive acquisition of high-resolution images in intact opaque animals. The zebrafish (Danio rerio) is an important model organism for the study of vertebrate biology. However, optical in vivo studies in zebrafish are restricted to very early developmental stages due to the opacity of the juvenile and adult stages. Application of high resolution MRM has not yet been explored in adult zebrafish. In this study we applied and optimized high resolution MRM methods to examine anatomical structures noninvasively in adult zebrafish. Clear morphological proton images were obtained by T(2)-weighted spin echo and rapid acquisition with rapid acquisition with relaxation enhancement (RARE) sequences which revealed many anatomical details in the entire intact zebrafish at a magnetic field strength of 9.4 T. In addition, in vivo imaging of adult zebrafish revealed sufficient anatomical details. To our knowledge this is the first report of the application of high resolution MRM to study detailed anatomical structures in adult zebrafish.

Underlying molecular mechanisms of DIO2 susceptibility in symptomatic osteoarthritis.

Objectives To investigate how the genetic susceptibility gene DIO2 confers risk to osteoarthritis (OA) onset in humans and to explore whether counteracting the deleterious effect could contribute to novel therapeutic approaches. Methods Epigenetically regulated expression of DIO2 was explored by assessing methylation of positional CpG-dinucleotides and the respective DIO2 expression in OA-affected and macroscopically preserved articular cartilage from end-stage OA patients. In a human in vitro chondrogenesis model, we measured the effects when thyroid signalling during culturing was either enhanced (excess T3 or lentiviral induced DIO2 overexpression) or decreased (iopanoic acid). Results OA-related changes in methylation at a specific CpG dinucleotide upstream of DIO2 caused significant upregulation of its expression (β=4.96; p=0.0016). This effect was enhanced and appeared driven specifically by DIO2 rs225014 risk allele carriers (β=5.58, p=0.0006). During in vitro chondrogenesis, DIO2 overexpression resulted in a significant reduced capacity of chondrocytes to deposit extracellular matrix (ECM) components, concurrent with significant induction of ECM degrading enzymes (ADAMTS5, MMP13) and markers of mineralisation (ALPL, COL1A1). Given their concurrent and significant upregulation of expression, this process is likely mediated via HIF-2α/RUNX2 signalling. In contrast, we showed that inhibiting deiodinases during in vitro chondrogenesis contributed to prolonged cartilage homeostasis as reflected by significant increased deposition of ECM components and attenuated upregulation of matrix degrading enzymes. Conclusions Our findings show how genetic variation at DIO2 could confer risk to OA and raised the possibility that counteracting thyroid signalling may be a novel therapeutic approach.