Targeted screening and validation of copy number variations.

The accessibility of genome-wide screening technologies considerably facilitated the identification and characterization of copy number variations (CNVs). The increasing amount of available data describing these variants, clearly demonstrates their abundance in the human genome. This observation shows that not only SNPs, but also CNVs and other structural variants strongly contribute to genetic variation.

Development of a microarray for Enchytraeus albidus (Oligochaeta): preliminary tool with diverse applications.

Standard bioassays allow hazard assessment at the population level, but much remains to be learned about the molecular level response of organisms to stressors. The main aim of this study was the development of a DNA microarray for Enchytraeus albidus, a common soil worm species. Further, this microarray was tested using worms exposed to Cu, phenmedipham, and different soil types.

miRNA genes and the brain: implications for psychiatric disorders.

MicroRNAs (miRNAs) are a class of nonprotein coding genes with a growing importance in regulatory mechanisms of gene expression related to brain function and plasticity. Considering the relative lack of success of the analysis of variations in candidate protein coding genes and of genome-wide association studies to identify strong risk factors for common psychiatric disorders (PDs), miRNA genes are of particular interest for the field of psychiatric genetics as deregulation of the rate of transcription or translation of a normal gene may be phenotypically similar to disruption of the gene itself. In this article we review the current knowledge on the contribution of miRNAs in basic mechanisms of brain development and plasticity and their possible involvement in the pathogenesis of several PDs.

An integrated transcriptomic and proteomic approach characterizing estrogenic and metabolic effects of 17 alpha-ethinylestradiol in zebrafish (Danio rerio).

Nowadays there is much concern about the presence of endocrine disrupting compounds (EDCs) in the environment due to their ability to interfere with the endocrine system. In the presented study, adult zebrafish (Danio rerio) were exposed to 30 ng L(-1) 17alpha-ethinylestradiol (EE2) for 4 and 28 days. The underlying molecular mechanisms of EE2 were studied in the zebrafish liver by applying a combined transcriptomics and proteomics approach.

Sublethal effects of waterborne uranium exposures on the zebrafish brain: transcriptional responses and alterations of the olfactory bulb ultrastructure.

The toxic action modes of uranium (U) in fish are still scarcely known. U is known to modify the acetylcholinesterase activity in the fish brain. To gain further insight into U neurotoxicity in fish, we examined transcriptional responses in the brain of the zebrafish, Danio rerio, exposed to 15 microg L(-1) and 100 microg L(-1) of waterborne U for 3 and 10 days.

Nickel and binary metal mixture responses in Daphnia magna: molecular fingerprints and (sub)organismal effects.

The recent development of a custom cDNA microarray platform for one of the standard organisms in aquatic toxicology, Daphnia magna, opened up new ways to mechanistic insights of toxicological responses. In this study, the mRNA expression of several genes and (sub)organismal responses (Cellular Energy Allocation, growth) were assayed after short-term waterborne metal exposure. Microarray analysis of Ni-exposed daphnids revealed several affected functional gene classes, of which the largest ones were involved in different metabolic processes (mainly protein and chitin related processes), cuticula turnover, transport and signal transduction.

Molecular targets of TBBPA in zebrafish analysed through integration of genomic and proteomic approaches.

Tetrabromobisphenol-A (TBBPA) is nowadays one of the most frequently used brominated flame retardants (BFRs) and can be considered as a high production volume chemical. Over the last decade, numerous reports of increasing concentrations of BFRs in the environment and humans have been published. However, the toxicological knowledge on TBBPA, and more specifically its molecular mode of action, is rather fragmentary.

Ecotoxicological risk assessment using DNA chips and cellular reporters.

Ecotoxicological risk assessment has long been based on (acute) effective concentration and lethal concentration (EC/LC50) endpoints in organisms from different trophic levels. These tests are insufficient adequately to assess the risk associated with many chemical classes. The introduction of advanced molecular techniques is leading to improved risk assessment and is also providing an alternative to the massive use of animal testing.

Molecular responses during cadmium-induced stress in Daphnia magna: integration of differential gene expression with higher-level effects.

DNA microarrays offer great potential in revealing insight into mechanistic toxicity of contaminants. The aim of the present study was (i) to gain insight in concentration- and time-dependent cadmium-induced molecular responses by using a customized Daphnia magna microarray, and (ii) to compare the gene expression profiles with effects at higher levels of biological organization (e.g.

Use of suppression subtractive hybridization PCR for the development of cDNA arrays for the detection of endocrine disruption in carp (Cyprinus carpio).

The potential of a variety of xenobiotic compounds to modulate or disrupt the endocrine system of humans and wildlife is now widely recognized. In the present study, we developed a molecular tool for the evaluation of endocrine disruption in common carp (Cyprinus carpio). Suppression Subtractive Hybridization PCR was applied for the isolation of a relevant gene set, consisting of gender- and hormone-responsive gene fragments.

Effluent impact assessment using microarray-based analysis in common carp: a systems toxicology approach.

Effluents are a main source of direct and continuous input of pollutants to the aquatic environment, and can cause ecotoxicological effects at different levels of biological organization. Since gene expression responses represent the primary interaction site between environmental contaminants and biota, they provide essential clues to understand how chemical exposure can affect organismal health. The aim of the present study was to investigate the applicability of a microarray approach for unraveling modes of action of whole effluent toxicity and impact assessment.

Daphnia magna and ecotoxicogenomics: gene expression profiles of the anti-ecdysteroidal fungicide fenarimol using energy-, molting- and life stage-related cDNA libraries.

In the present study, the existing life stage-specific cDNA library was extended with energy- and molting-related genes using Suppression Subtractive Hybridization PCR and a microarray for the aquatic test organism Daphnia magna was created. A gene set of 2455 fragments was produced belonging to different pathways such as carbohydrate and lipid metabolism, O2 transport and heme metabolism, immune response, embryo development, cuticula metabolism and visual perception pathways. Using this custom microarray, gene expression profiles were generated from neonates exposed to three concentrations of the anti-ecdysteroidal fungicide fenarimol (0.

Effect of copper exposure on gene expression profiles in Chlamydomonas reinhardtii based on microarray analysis.

Copper is a naturally occurring trace metal with toxic properties for man and environment. It is assumed that toxicity is primarily caused by oxidative damage, generated through the production of reactive oxygen species. Copper is, however, also an essential element, which means trace amounts are necessary for biological processes to function properly.

Patterns of gene expression in carp liver after exposure to a mixture of waterborne and dietary cadmium using a custom-made microarray.

Gene expression changes in carp liver tissue were studied after acute (3 and 24h) and subchronic (7 and 28 days) exposure to a mixture of waterborne (9, 105 and 480 microg/l) and dietary (9.5, 122 and 144 microg/g) cadmium, using a custom-made microarray. Suppression subtractive hybridization-PCR (SSH-PCR) was applied to isolate a set of 643 liver genes, involved in multiple biological pathways, such as energy metabolism (e.

Neuropharmaceuticals in the environment: mianserin-induced neuroendocrine disruption in zebrafish (Danio rerio) using cDNA microarrays.

Because of their environmental occurrence and high biological activity, human pharmaceuticals have received increasing attention from environmental and health agencies. A major bottleneck in their risk assessment is the lack of relevant and specific effect data. We developed an approach using gene expression analysis in quantifying adverse effects of neuroendocrine pharmaceuticals in the environment.

Expression profiling of endocrine-disrupting compounds using a customized Cyprinus carpio cDNA microarray.

Exposure to a variety of anthropogenic compounds has been shown to interfere with normal development, physiology, and reproduction in a wide range of organisms, both in laboratory studies and wildlife. We have developed a Cyprinus carpio cDNA microarray consisting of endocrine-related genes. In the current study, we investigated the applicability of this microarray (1) to study the molecular effects induced by exposure to a variety of endocrine-disrupting compounds (EDCs) in fish and (2) to discriminate the specific transcriptional profiles associated with these compounds.

Effects of the antidepressant mianserin in zebrafish: molecular markers of endocrine disruption.

Due to their environmental occurrence and intrinsic biological activity, human pharmaceuticals have received increasing attention from environmental and health agencies. Of particular, ecotoxicological concern are drugs that affect nervous- and endocrine-systems. Zebrafish genome-wide oligo arrays are used to collect mechanistic information on mianserin-induced changes in gene expression in zebrafish.

Molecular impact of propiconazole on Daphnia magna using a reproduction-related cDNA array.

We have developed a first version cDNA microarray of the cladoceran Daphnia magna. Through Suppression Subtractive Hybridisation PCR (SSH-PCR) 855 life stage-specific cDNAs were collected and used to document the toxicological mode of action of the pesticide propiconazole. DNA sequencing analysis revealed gene fragments related to important functional classes such as embryo development, energy metabolism, molting and cell cycle.

Development and application of a brain-specific cDNA microarray for effect evaluation of neuro-active pharmaceuticals in zebrafish (Danio rerio).

The environmental fate and ecotoxicological effect of pharmaceuticals are poorly understood, and standardized tests to detect and evaluate their potential effects in the environment are not available. We developed a zebrafish brain-specific microarray containing 682 neurologically relevant cDNA-fragments. To investigate the applicability of this microarray for studying neurotoxic modes-of-action and impact assessment of neuro-active pharmaceuticals in zebrafish, chlorpromazine was used as a model compound.

Determination of diazepam in aquatic samples by capillary liquid chromatography-electrospray tandem mass spectrometry.

In recent years growing attention has been paid toward the discharge, presence and potential adverse effects of pharmaceuticals in the environment. Using different existing analytical methods several studies have already identified a variety of drugs in waste-, surface- and drinking water. The monitoring of surface waters for drugs is of great importance because drugs are designed to be biological very active substances.