A5006242811- Zebrafish Biomedical Research Applications
- Aquaculture disease management and microbiota
- Immune Response and Inflammation
- Metabolomics and Mass Spectrometry Studies
- Selenium in Biological Systems
- Metabolism and Genetic Disorders
- Chemical synthesis and alkaloids
- Effects and risks of endocrine disrupting chemicals
- Diet and metabolism studies
- Alkaloids: synthesis and pharmacology
- Advanced Vision and Imaging
- Pluripotent Stem Cells Research
- Mycobacterium research and diagnosis
- Laser-Ablation Synthesis of Nanoparticles
- Microplastics and Plastic Pollution
- Nanoparticles: synthesis and applications
- Genomics and Phylogenetic Studies
- Environmental Toxicology and Ecotoxicology
- Reproductive biology and impacts on aquatic species
- Tuberculosis Research and Epidemiology
- Plant Virus Research Studies
- Vibrio bacteria research studies
- CRISPR and Genetic Engineering
- Medical Image Segmentation Techniques
- Computational Drug Discovery Methods
Cancer Genomics Centre
2024
Leiden University
2011-2020
One-third of the world population is infected with Mycobacterium tuberculosis and multi-drug resistant strains are rapidly evolving. The noticeable absence a whole organism high-throughput screening system for studying progression fast becoming bottleneck in research. We successfully developed such using zebrafish marinum infection model, which well-characterized model biomedical significance, mimicking hallmarks human pathology. Importantly, we demonstrate suitability our to directly study...
The increasing use of zebrafish larvae for biomedical research applications is resulting in versatile models a variety human diseases. These exploit the optical transparency and availability large genetic tool box. Here we present detailed protocols robotic injection embryos at very high accuracy with speed up to 2000 per hour. are benchmarked several applications: (1) DNA obtaining transgenic animals, (2) antisense morpholinos that can be used gene knock-down, (3) microbes studying...
Microbial reduction of selenium (Se) oxyanions to elemental Se is a promising technology for bioremediation and treatment wastewaters. But fraction biogenic nano-Selenium (nano-Seb) formed in bioreactors remains suspended the treated waters, thus entering aquatic environment. The present study investigated toxicity nano-Seb by anaerobic granular sludge biofilms on zebrafish embryos comparison with selenite chemogenic nano-Se (nano-Sec). showed LC50 value 1.77 mg/L, which was 3.2-fold less...
Staphylococcus epidermidis bacteria are a major cause of biomaterial-associated infections in modern medicine. Yet there is little known about the host responses against this normally innocent bacterium context infection biomaterials. In order to better understand factors involved process, whole animal model with high throughput screening possibilities and markers for studying response S. required.We have used zebrafish yolk injection system study bacterial proliferation time course...
High-throughput imaging is applied to provide observations for accurate statements on phenomena in biology and this has been successfully the domain of cells, i.e. cytomics.In whole organisms, we need take hurdles ensure that can be accomplished with a sufficient throughput reproducibility.For vertebrate biology, zebrafish popular model system high-throughput applications.The development Vertebrate Automated Screening Technology (VAST BioImager), microscope mounted system, enables...
The knowledge on environmentally relevant chemicals that may interfere with thyroid signaling is scarce. Here, we present a method for the screening of goitrogens, compounds disrupt gland function, based automatic orientation zebrafish in glass capillary and subsequent imaging reporter gene fluorescence embryos transgenic line tg(tg:mCherry). tg(tg:mCherry) indicates compensatory upregulation thyroglobulin, hormone precursor, response to inhibition synthesis. Fish were exposed negative...
Zebrafish are becoming a valuable tool in the preclinical phase of drug discovery screenings as whole animal model with high throughput screening possibilities. They can be used to bridge gap between cell based assays at earlier stages and vivo validation mammalian models, reducing, this way, number compounds passing through testing on much more expensive rodent models. In light, present manuscript is described new pipeline using zebrafish system for study Staphylococcus epidermidis...
Abstract Tuberculosis is a highly infectious and potentially fatal disease accompanied by wasting symptoms, which cause severe metabolic changes in infected people. In this study we have compared the effect of mycobacteria infection on level metabolites blood humans mice whole zebrafish larvae using one standardized mass spectrometry pipeline, ensuring technical comparability results. Quantification range circulating small amines showed that levels majority these compounds were significantly...
We present a RNA deep sequencing (RNAseq) analysis of comparison the transcriptome responses to infection zebrafish larvae with Staphylococcus epidermidis and Mycobacterium marinum bacteria. show how our developed GeneTiles software can improve RNAseq approaches by more confidently identifying large set markers upon these For data currently, programs such as Bowtie2 Samtools are indispensable. However, that designed for LINUX environment require some dedicated programming skills have no...
Good estimations of volume and surface area are important to biological systems measurement. In this paper we develop a 3D reconstruction from evenly sampled axial views in order enable the We system for high throughput applications with zebrafish model system. The VAST BioImager is specifically developed purpose can be produced. Silhouettes derived sequence shape priors which directly used solve camera calibration problem that required accurate reconstruction. Nonlinear optimisation...
Abstract Monoterpene indole alkaloids (MIAs) from Mitragyna speciosa (“kratom”), such as mitragynine and speciogynine, are promising novel scaffolds for opioid receptor ligands treatment of pain, addiction, depression. While kratom leaves have been used centuries in South-East Asia stimulant pain management substance, the biosynthetic pathway these psychoactives only recently partially elucidated. Here, we demonstrate de novo production speciogynine Saccharomyces cerevisiae through...
The taxa Ixodes ricinus and inopinatus are sympatric in Tunisia. genetics underlying their morphological differences unresolved. In this study, ticks collected Jouza-Amdoun, Tunisia, were morphologically identified sequenced using Oxford Nanopore Technologies. Three complete genome assemblies of I. three with BUSCO scores ∼98% generated, including the reconstruction mitochondrial genomes separation both alleles TRPA1, TROSPA calreticulin genes. Deep sequencing allowed first descriptions...
Zebrafish are becoming a valuable tool in the preclinical phase of drug discovery screenings as whole animal model with high throughput screening possibilities. They can be used to bridge gap between cell based assays at earlier stages and vivo validation mammalian models, reducing, this way, number compounds passing through testing on much more expensive rodent models. In light, present manuscript is described new pipeline using zebrafish system for study Staphylococcus epidermidis...
Abstract Tuberculosis is a highly infectious and potentially fatal disease accompanied by wasting symptoms, which cause severe metabolic changes in infected people. In this study we have compared the effect of mycobacteria infection on level metabolites blood humans mice whole zebrafish larvae using one standardized mass spectrometry pipeline, ensuring technical comparability results. Quantification range circulating small amines showed that levels majority these compounds were significantly...