Applications & Publications
Technical Notes
3D Tomographic Visualization of Zebrafish Larvae Using the VAST BioImager™ (QTN-026)
March 13, 2020
High-Throughput Craniofacial Development Phenotyping in Zebrafish using VAST BioImager (QTN-024)
January 04, 2017
D. rerio Analysis and Sorting: High throughput screening of innate immune responses in zebrafish embryos
Profiling of live D. reriolarvae using the COPAS XL instrument. Work performed in collaboration with the Spaink Laboratory, University of Leiden (ANXL-02)
Zebra Fish Sorting: Live embryos vs. Dead eggs
Automated Detection and Sorting of live D. rerio embryos from dead D. rerio eggs using the COPAS XL instrument (ANXL-01)
Publications
RNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS
Dharmadhikari et al. February 17, 2025 Nat Commun. 2025; 16: 1703. Published online 2025 Feb 17. doi 10.1038/s41467-025-56876-w
View AbstractRNA methyltransferase SPOUT1/CENP-32 links mitotic spindle organization with the neurodevelopmental disorder SpADMiSS
SPOUT1/CENP-32 encodes a putative SPOUT RNA methyltransferase previously identified as a mitotic chromosome associated protein. SPOUT1/CENP-32 depletion leads to centrosome detachment from the spindle poles and chromosome misalignment. Aided by gene matching platforms, here we identify 28 individuals with neurodevelopmental delays from 21 families with bi-allelic variants in SPOUT1/CENP-32 detected by exome/genome sequencing. Zebrafish spout1/cenp-32 mutants show reduction in larval head size with concomitant apoptosis likely associated with altered cell cycle progression. In vivo complementation assays in zebrafish indicate that SPOUT1/CENP-32 missense variants identified in humans are pathogenic. Crystal structure analysis of SPOUT1/CENP-32 reveals that most disease-associated missense variants are located within the catalytic domain. Additionally, SPOUT1/CENP-32 recurrent missense variants show reduced methyltransferase activity in vitro and compromised centrosome tethering to the spindle poles in human cells. Thus, SPOUT1/CENP-32 pathogenic variants cause an autosomal recessive neurodevelopmental disorder: SpADMiSS (SPOUT1 Associated Development delay Microcephaly Seizures Short stature) underpinned by mitotic spindle organization defects and consequent chromosome segregation errors.
Functionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning
Mazzaferro et al. February 13, 2025 Sci Rep. 2025; 15: 5408. Published online 2025 Feb 13. doi: 10.1038/s41598-025-89823-2
View AbstractFunctionally characterizing obesity-susceptibility genes using CRISPR/Cas9, in vivo imaging and deep learning
m6A-mRNA Reader YTHDF2 Identified as a Potential Risk Gene in Autism With Disproportionate Megalencephaly
Nishizaki et al. January 30, 2025 https://doi.org/10.1002/aur.3314
View Abstractm6A-mRNA Reader YTHDF2 Identified as a Potential Risk Gene in Autism With Disproportionate Megalencephaly
Among autistic individuals, a subphenotype of disproportionate megalencephaly (ASD-DM) seen at three years of age is associated with co-occurring intellectual disability and poorer prognoses later in life. However, many of the genes contributing to ASD-DM have yet to be delineated. In this study, we identified additional ASD-DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD-DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection, totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD-DM genes harboring de novo protein-impacting variants. Our findings include 14 high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM, including CHD8 and PTEN. By performing functional network analysis, we expanded to additional candidate genes, including one previously implicated in ASD-DM (PIK3CA) as well as 184 additional genes connected with ASD or DM alone. Using zebrafish, we modeled a de novo tandem duplication impacting YTHDF2, encoding an N6-methyladenosine (m6A)-mRNA reader, in an ASD-DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size, while overexpressing YTHDF2 resulted in increased head/brain size matching that of the proband. Single-cell transcriptomes of YTHDF2 gain-of-function larvae point to reduced expression of Fragile-X-syndrome-associated FMRP-target genes globally and in the developing brain, providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader, YTHDC1, in our ASD-DM cohort. Though we highlight only two cases to date, our study provides support for the m6A-RNA modification pathway as potentially contributing to this severe form of autism.
A whole-animal phenotypic drug screen identifies suppressors of atherogenic lipoproteins
Kelpsch et al. November 15, 2024 Version 3. bioRxiv. Preprint. 2024 Nov 15 [revised 2025 Jan 16]. doi: 10.1101/2024.11.14.623618
View AbstractA whole-animal phenotypic drug screen identifies suppressors of atherogenic lipoproteins
Lipoproteins are essential for lipid transport in all bilaterians. A single Apolipoprotein B (ApoB) molecule is the inseparable structural scaffold of each ApoB-containing lipoprotein (B-lps), which are responsible for transporting lipids to peripheral tissues. The cellular mechanisms that regulate ApoB and B-lp production, secretion, transport, and degradation remain to be fully defined. In humans, elevated levels of vascular B-lps play a causative role in cardiovascular disease. Previously, we have detailed that human B-lp biology is remarkably conserved in the zebrafish using an in vivo chemiluminescent reporter of ApoB (LipoGlo) that does not disrupt ApoB function. Thus, the LipoGlo model is an ideal system for identifying novel mechanisms of ApoB modulation and, due to the ability of zebrafish to generate many progeny, is particularly amenable to large-scale phenotypic drug screening. Here, we report a screen of roughly 3000 compounds that identified 49 unique ApoB-lowering hits. Nineteen hits passed orthogonal screening criteria. A licorice root component, enoxolone, significantly lowered B-lps only in animals that express a functional allele of the nuclear hormone receptor Hepatocyte Nuclear Factor 4α (HNF4α). Consistent with this result, inhibitors of HNF4α also reduce B-lp levels. These data demonstrate that mechanism(s) of action can be rapidly determined from a whole animal zebrafish phenotypic screen. Given the well documented role of HNF4α in human B-lp biology, these data validate the LipoGlo screening platform for identifying small molecule modulators of B-lps that play a critical role in a leading cause of worldwide mortality.
Aurora kinase B is required for growth and expansion of medulloblastoma cells in the tissue context
Gries et al. November 08, 2024 Neoplasia. 2025 Jan; 59: 101078. Published online 2024 Nov 8. doi: 10.1016/j.neo.2024.101078
View AbstractAurora kinase B is required for growth and expansion of medulloblastoma cells in the tissue context
Gene expansions contributing to human brain evolution
Soto et al. September 26, 2024 Version 1. bioRxiv. Preprint. 2024 Sep 26. doi: 10.1101/2024.09.26.615256
View AbstractGene expansions contributing to human brain evolution
Genomic drivers of human-specific neurological traits remain largely undiscovered. Duplicated genes expanded uniquely in the human lineage likely contributed to brain evolution, including the increased complexity of synaptic connections between neurons and the dramatic expansion of the neocortex. Discovering duplicate genes is challenging because the similarity of paralogs makes them prone to sequence-assembly errors. To mitigate this issue, we analyzed a complete telomere-to-telomere human genome sequence (T2T-CHM13) and identified 213 duplicated gene families likely containing human-specific paralogs (>98% identity). Positing that genes important in universal human brain features should exist with at least one copy in all modern humans and exhibit expression in the brain, we narrowed in on 362 paralogs with at least one copy across thousands of ancestrally diverse genomes and present in human brain transcriptomes. Of these, 38 paralogs co-express in gene modules enriched for autism-associated genes and potentially contribute to human language and cognition. We narrowed in on 13 duplicate gene families with human-specific paralogs that are fixed among modern humans and show convincing brain expression patterns. Using long-read DNA sequencing revealed hidden variation across 200 modern humans of diverse ancestries, uncovering signatures of selection not previously identified, including possible balancing selection of CD8B. To understand the roles of duplicated genes in brain development, we generated zebrafish CRISPR "knockout" models of nine orthologs and transiently introduced mRNA-encoding paralogs, effectively "humanizing" the larvae. Morphometric, behavioral, and single-cell RNA-seq screening highlighted, for the first time, a possible role for GPR89B in dosage-mediated brain expansion and FRMPD2B function in altered synaptic signaling, both hallmark features of the human brain. Our holistic approach provides important insights into human brain evolution as well as a resource to the community for studying additional gene expansion drivers of human brain evolution.
An explainable map of human gastruloid morphospace reveals gastrulation failure modes and predicts teratogens
Rufo et al. September 23, 2024 Version 1. bioRxiv. Preprint. 2024 Sep 23. doi:Â 10.1101/2024.09.20.614192
View AbstractAn explainable map of human gastruloid morphospace reveals gastrulation failure modes and predicts teratogens
Human gastrulation is a critical stage of development where many pregnancies fail due to poorly understood mechanisms. Using the 2D gastruloid, a stem cell model of human gastrulation, we combined high-throughput drug perturbations and mathematical modelling to create an explainable map of gastruloid morphospace. This map outlines patterning outcomes in response to diverse perturbations and identifies variations in canonical patterning and failure modes. We modeled morphogen dynamics to embed simulated gastruloids into experimentally-determined morphospace to explain how developmental parameters drive patterning. Our model predicted and validated the two greatest sources of patterning variance: cell density-based modulations in Wnt signaling and SOX2 stability. Assigning these parameters as axes of morphospace imparted interpretability. To demonstrate its utility, we predicted novel teratogens that we validated in zebrafish. Overall, we show how stem cell models of development can be used to build a comprehensive and interpretable understanding of the set of developmental outcomes.
Zebrafish models of human-duplicated SRGAP2 reveal novel functions in microglia and visual system development
Uribe-Salazar et al. September 11, 2024 Version 2. bioRxiv. Preprint. 2024 Sep 11 [revised 2024 Sep 27]. doi: 10.1101/2024.09.11.612570
View AbstractZebrafish models of human-duplicated SRGAP2 reveal novel functions in microglia and visual system development
The expansion of the human SRGAP2 family, resulting in a human-specific paralog SRGAP2C, likely contributed to altered evolutionary brain features. The introduction of SRGAP2C in mouse models is associated with changes in cortical neuronal migration, axon guidance, synaptogenesis, and sensory-task performance. Truncated SRGAP2C heterodimerizes with the full-length ancestral gene product SRGAP2A and antagonizes its functions. However, the significance of SRGAP2 duplication beyond neocortex development has not been elucidated due to the embryonic lethality of complete Srgap2 knockout in mice. Using zebrafish, we show that srgap2 knockout results in viable offspring and that these larvae phenocopy “humanized” SRGAP2C larvae, including altered morphometric features (i.e., reduced body length and inter-eye distance) and differential expression of synapse-, axonogenesis-, and vision-related genes. Through single-cell transcriptome analysis, we demonstrate a skewed balance of excitatory and inhibitory neurons that likely contribute to increased susceptibility to seizures displayed by Srgap2 mutant larvae, a phenotype resembling SRGAP2 loss-of-function in a child with early infantile epileptic encephalopathy. Single-cell data also shows strong endogenous expression of srgap2 in microglia with mutants exhibiting altered membrane dynamics and likely delayed maturation of microglial cells. Microglia cells expressing srgap2 were also detected in the developing eye together with altered expression of genes related to axonogenesis in mutant retinal cells. Consistent with the perturbed gene expression in the retina, we found that SRGAP2 mutant larvae exhibited increased sensitivity to broad and fine visual cues. Finally, comparing the transcriptomes of relevant cell types between human (+SRGAP2C) and non-human primates (–SRGAP2C) revealed significant overlaps of gene alterations with mutant cells in our zebrafish models; this suggests that SRGAP2C plays a similar role altering microglia and the visual system in modern humans. Together, our functional characterization of conserved ortholog Srgap2 and human SRGAP2C in zebrafish uncovered novel gene functions and highlights the strength of cross-species analysis in understanding the development of human-specific features.
The zebrafish embryo as a model for chemically-induced steatosis: A case study with three pesticides
Heusinkveld et al. August 14, 2024 Toxicology,Volume 508,2024,153927,ISSN 0300-483X,https://doi.org/10.1016/j.tox.2024.153927.(https://www.sciencedirect.com/science/article/pii/S0300483X24002087)
The zebrafish embryo as a model for chemically-induced steatosis: A case study with three pesticides
In vivo multiscale analyses of spring viremia of carp virus (SVCV) infection: From model organism to target species
Souto et al. August 05, 2024 https://doi.org/10.1371/journal.ppat.1012328
In vivo multiscale analyses of spring viremia of carp virus (SVCV) infection: From model organism to target species
Adaptive Optics in an Oblique Plane Microscope
McFadden et al. March 22, 2024 bioRxiv 2024.03.21.586191; doi: https://doi.org/10.1101/2024.03.21.586191
Adaptive Optics in an Oblique Plane Microscope
A retroviral link to vertebrate myelination through retrotransposon-RNA-mediated control of myelin gene expression
Ghosh et al. February 15, 2024 Cell, Volume 187, Issue 4p814-830.e23,February 15, 2024
View AbstractA retroviral link to vertebrate myelination through retrotransposon-RNA-mediated control of myelin gene expression
Myelin, the insulating sheath that surrounds neuronal axons, is produced by oligodendrocytes in the central nervous system (CNS). This evolutionary innovation, which first appears in jawed vertebrates, enabled rapid transmission of nerve impulses, more complex brains, and greater morphological diversity. Here, we report that RNA-level expression of RNLTR12-int, a retrotransposon of retroviral origin, is essential for myelination. We show that RNLTR12-int-encoded RNA binds to the transcription factor SOX10 to regulate transcription of myelin basic protein (Mbp, the major constituent of myelin) in rodents. RNLTR12-int-like sequences (which we name RetroMyelin) are found in all jawed vertebrates, and we further demonstrate their function in regulating myelination in two different vertebrate classes (zebrafish and frogs). Our study therefore suggests that retroviral endogenization played a prominent role in the emergence of vertebrate myelin.
Analysis of vascular disruption in zebrafish embryos as an endpoint to predict developmental toxicity
Nöth et al. December 21, 2023 Reproductive Toxicology, Open access, Published: 21 December 2023, Volume 98, pages 537–549, (2024)
View AbstractAnalysis of vascular disruption in zebrafish embryos as an endpoint to predict developmental toxicity
Inhibition of angiogenesis is an important mode of action for the teratogenic effect of chemicals and drugs. There is a gap in the availability of simple, experimental screening models for the detection of angiogenesis inhibition. The zebrafish embryo represents an alternative test system which offers the complexity of developmental differentiation of an entire organism while allowing for small-scale and high-throughput screening. Here we present a novel automated imaging-based method to detect the inhibition of angiogenesis in early life stage zebrafish. Video subtraction was used to identify the location and number of functional intersegmental vessels according to the detection of moving blood cells. By exposing embryos to multiple tyrosine kinase inhibitors including SU4312, SU5416, Sorafenib, or PTK787, we confirmed that this method can detect concentration-dependent inhibition of angiogenesis. Parallel assessment of arterial and venal aorta ruled out a potential bias by impaired heart or blood cell development. In contrast, the histone deacetylase inhibitor valproic acid did not affect ISV formation supporting the specificity of the angiogenic effects. The new test method showed higher sensitivity, i.e. lower effect concentrations, relative to a fluorescent reporter gene strain (Tg(KDR:EGFP)) exposed to the same tyrosine kinase inhibitors indicating that functional effects due to altered tubulogenesis or blood transport can be detected before structural changes of the endothelium are visible by fluorescence imaging. Comparison of exposure windows indicated higher specificity for angiogenesis when exposure started at later embryonic stages (24 h post-fertilization). One of the test compounds was showing particularly high specificity for angiogenesis effects (SU4312) and was, therefore, suggested as a model compound for the identification of molecular markers of angiogenic disruption. Our findings establish video imaging in wild-type strains as viable, non-invasive, high-throughput method for the detection of chemical-induced angiogenic disruption in zebrafish embryos.
Grouping of chemicals into mode of action classes by automated effect pattern analysis using the zebrafish embryo toxicity test
Teixidó et al. March 07, 2022 Reproductive Toxicology, Open Access, Volume 96, pages 1353–1369, Published: 07 March 2022
View AbstractGrouping of chemicals into mode of action classes by automated effect pattern analysis using the zebrafish embryo toxicity test
Automated in vivo drug screen in zebrafish identifies synapse-stabilising drugs with relevance to spinal muscular atrophy
Oprisoreanu et al. April 26, 2021 Dis Model Mech (2021) 14 (4): dmm047761. https://doi.org/10.1242/dmm.047761
Automated in vivo drug screen in zebrafish identifies synapse-stabilising drugs with relevance to spinal muscular atrophy
Assessment of Autism Zebrafish Mutant Models Using a High-Throughput Larval Phenotyping Platform
Colón-Rodríguez A, et al. November 23, 2020 Front. Cell Dev. Biol. 8:586296.; doi: 10.3389/fcell.2020.586296
Assessment of Autism Zebrafish Mutant Models Using a High-Throughput Larval Phenotyping Platform
Morphometric analysis of developing zebrafish embryos allow predicting teratogenicity modes of action in higher vertebrates
Jarque et al. August 19, 2020 Reproductive Toxicology 96 (2020) 337-348; https://doi.org/10.1016/j.reprotox.2020.08.004
Morphometric analysis of developing zebrafish embryos allow predicting teratogenicity modes of action in higher vertebrates
The identification of dual protective agents against cisplatin-induced oto-and nephrotoxicity using the zebrafish model
Wertman JN, Melong N, Stoyek MR, et al. July 28, 2020 [published online ahead of print, 2020 Jul 28]. Elife. 2020;9:e56235. doi:10.7554/eLife.56235
The identification of dual protective agents against cisplatin-induced oto-and nephrotoxicity using the zebrafish model
Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/ Cas9-based approach
von der Heyde et al. July 16, 2020 Sci Rep 10, 11831 (2020). https://doi.org/10.1038/s41598-020-68567-1
Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/ Cas9-based approach
TCF12 haploinsufficiency causes autosomal dominant Kallmann syndrome and reveals network-level interactions between causal loci
Davis et al. July 03, 2020 Human Molecular Genetics, , ddaa120, https://doi.org/10.1093/hmg/ddaa120
TCF12 haploinsufficiency causes autosomal dominant Kallmann syndrome and reveals network-level interactions between causal loci
Integrative discovery of treatments for high-risk neuroblastoma
Almstedt et al. January 03, 2020 Nat Commun. 2020 Jan 3;11(1):71. doi: 10.1038/s41467-019-13817-8.
Integrative discovery of treatments for high-risk neuroblastoma
The ALK-1/SMAD/ATOH8 axis attenuates hypoxic responses and protects against the development of pulmonary arterial hypertension
Morikawa et al. November 12, 2019 Science Signaling 12 Nov 2019: Vol. 12, Issue 607, eaay4430 DOI: 10.1126/scisignal.aay4430
The ALK-1/SMAD/ATOH8 axis attenuates hypoxic responses and protects against the development of pulmonary arterial hypertension
Comparison of Zebrafish Larvae and hiPSC Cardiomyocytes for Predicting Drug-Induced Cardiotoxicity in Humans
Sylvia Dyballa et al. October 01, 2019 Toxicological Sciences, Volume 171, Issue 2, October 2019, Pages 283–295, https://doi.org/10.1093/toxsci/kfz165
Comparison of Zebrafish Larvae and hiPSC Cardiomyocytes for Predicting Drug-Induced Cardiotoxicity in Humans
TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish
Gudmundsson et al. September 01, 2019 Sci Rep. 2019; 9: 10730. Published online 2019 Jul 24. doi: 10.1038/s41598-019-46632-8
TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish
Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis
Bandaru et al. June 11, 2019 bioRxiv 502674; doi: https://doi.org/10.1101/502674
Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis
Bi-allelic Variants in DYNC1I2 Cause Syndromic Microcephaly with Intellectual Disability, Cerebral Malformations, and Dysmorphic Facial Features
Ansar et al. May 09, 2019 https://doi.org/10.1016/j.ajhg.2019.04.002
Bi-allelic Variants in DYNC1I2 Cause Syndromic Microcephaly with Intellectual Disability, Cerebral Malformations, and Dysmorphic Facial Features
An automated screening method for detecting compounds with goitrogenic activity using transgenic zebrafish embryos’
Jarque et al. August 29, 2018 PLOS ONE | https://doi.org/10.1371/journal.pone.0203087 August 29, 2018
An automated screening method for detecting compounds with goitrogenic activity using transgenic zebrafish embryos’
An automated high-resolution in vivo screen in zebrafish to identify chemical regulators of myelination
Early et al. July 06, 2018 DOI: 10.7554/eLife.35136 DOI: 10.7554/eLife.35136
An automated high-resolution in vivo screen in zebrafish to identify chemical regulators of myelination
Three-dimensional reconstruction and measurements of zebrafish larvae from high-throughput axial-view in vivo imaging
Guo et al. April 26, 2017 https://doi.org/10.1364/BOE.8.002611; Received 9 Nov 2016; revised 31 Jan 2017; accepted 31 Jan 2017; published 26 Apr 2017
Three-dimensional reconstruction and measurements of zebrafish larvae from high-throughput axial-view in vivo imaging
A truncating mutation in CEP55 is the likely cause of MARCH, a novel syndrome affecting neuronal mitosis.
Frosk et al. March 06, 2017 J Med Genet. 2017 Mar 6. pii: jmedgenet-2016-104296. doi: 10.1136/jmedgenet-2016-104296. [Epub ahead of print]
A truncating mutation in CEP55 is the likely cause of MARCH, a novel syndrome affecting neuronal mitosis.
SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome
Shaw et al. January 09, 2017 Nature Genetics (2017) doi:10.1038/ng.3743
SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome
De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder
Kury et al. January 03, 2017 http://dx.doi.org/10.1016/j.ajhg.2017.01.003
De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder
ARQiv-HTS, a versatile whole-organism screening platform enabling in vivo drug discovery at high-throughput rates
David T White, Arife Unal Eroglu, Guohua Wang, Liyun Zhang, Sumitra Sengupta, Ding Ding, Surendra K Rajpurohit, Steven L Walker, Hongkai Ji, Jiang Qian & Jeff S Mumm November 10, 2016 Nature Protocols 11, 2432–2453 (2016) doi:10.1038/nprot.2016.142
ARQiv-HTS, a versatile whole-organism screening platform enabling in vivo drug discovery at high-throughput rates
Developing systems for high-throughput screening of infectious diseases using zebrafish
Veneman, Wouter Jurjen December 05, 2015 Department of Animal Sciences and Health, Institute of Biology, Faculty of Science, Leiden University
Developing systems for high-throughput screening of infectious diseases using zebrafish
Mutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type.
Mala Isrie 1,2 et al. October 14, 2015 Am J Hum Genet. 2015 Dec 3;97(6):790-800. doi: 10.1016/j.ajhg.2015.10.014.
View AbstractMutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type.
1Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium; 2Laboratory for Genetics of Cognition, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
First quantitative high-throughput screen in zebrafish identifies novel pathways for increasing pancreatic ß-cell mass
Wang et al. July 28, 2015 eLife. 2015; 4: e08261. Published online 2015 Jul 28. doi: 10.7554/eLife.08261
First quantitative high-throughput screen in zebrafish identifies novel pathways for increasing pancreatic ß-cell mass
Semi-automated detection of goitrogenic compounds using transgenic zebrafish embryos and the VAST BioImager platform
SETAC Europe 25th Annual Meeting
Sergio Jarque¹, Eva Fetter², Marek Pípal¹, Marie Smutná¹, Ludek Blaha¹, Stefan Scholz².
May 03, 2015
Semi-automated detection of goitrogenic compounds using transgenic zebrafish embryos and the VAST BioImager platform
1RECETOX, Masaryk University, Faculty of Science, Kamenice 753/5, 625 00, Brno
2Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research – UFZ, Permoserstraße 15, 04318 Leipzig, Germany
Establishment and optimization of a high throughput setup to study Staphylococcus epidermidis and Mycobacterium marinum infection as a model for drug discovery.
Veneman WJ¹, Marín-Juez R², de Sonneville J³, Ordas A4, Jong-Raadsen S², Meijer AH4, Spaink HP5. June 26, 2014 JOVE
View AbstractEstablishment and optimization of a high throughput setup to study Staphylococcus epidermidis and Mycobacterium marinum infection as a model for drug discovery.
1Institute of Biology, Leiden University; w.j.veneman@biology.leidenuniv.nl. 2ZF-screens BV. 3Life Science Methods BV. 4Institute of Biology, Leiden University. 5Institute of Biology, Leiden University
Robotic injection of zebrafish embryos for high-throughput screening in disease models
Herman P. Spainka, Chao Cuib, Malgorzata I. Wiwegera, b, Hans J. Jansenb, Wouter J. Venemana, Rubén Marín-Juezb, Jan de Sonnevillec, Anita Ordasa, Vincenzo Torracaa, Wietske van der Enta, William P. Leendersd, Annemarie H. Meijer,a, B. Ewa Snaar-Jagalskaa, Ron P. Dirksb, August 15, 2013 Volume 62, Issue 3, 15 August 2013, Methods 62: 246–254
View AbstractRobotic injection of zebrafish embryos for high-throughput screening in disease models
a Department of Molecular Cell Biology, Institute of Biology, Leiden University, The Netherlands, b ZF-screens B.V., Leiden, The Netherlands, c Life Science Methods B.V., Leiden, The Netherlands, d Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
A zebrafish high throughput screening system used for Staphylococcus epidermidis infection marker discovery
Wouter J Veneman, Oliver W Stockhammer, Leonie de Boer, Sebastian A Zaat, Annemarie H Meijer and Herman P Spaink April 15, 2013 BMC Genomics 2013, 14:255 doi:10.1186/1471-2164-14-255
View AbstractA zebrafish high throughput screening system used for Staphylococcus epidermidis infection marker discovery
Background
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 in the context of infection of biomaterials. In order to better understand the factors involved in this process, a whole animal model with high throughput screening possibilities and markers for studying the host response to S. epidermidis infection are required.
Results
We have used a zebrafish yolk injection system to study bacterial proliferation and the host response in a time course experiment of S. epidermidis infection. By combining an automated microinjection system with complex object parametric analysis and sorting (COPAS) technology we have quantified bacterial proliferation. This system was used together with transcriptome analysis at several time points during the infection period. We show that bacterial colony forming unit (CFU) counting can be replaced by high throughput flow-based fluorescence analysis of embryos enabling high throughput readout. Comparison of the host transcriptome response to S. epidermidis and Mycobacterium marinum infection in the same system showed that M. marinum has a far stronger effect on host gene regulation than S. epidermidis. However, multiple genes responded differently to S. epidermidis infection than to M. marinum, including a cell adhesion gene linked to specific infection by staphylococci in mammals.
Conclusions
Our zebrafish embryo infection model allowed (i) quantitative assessment of bacterial proliferation, (ii) identification of zebrafish genes serving as markers for infection with the opportunistic pathogen S. epidermidis, and (iii) comparison of the transcriptome response of infection with S. epidermidis and with the pathogen M. marinum. As a result we have identified markers that can be used to distinguish common and specific responses to S. epidermidis. These markers enable the future integration of our high throughput screening technology with functional analyses of immune response genes and immune modulating factors.
High-throughput hyperdimensional vertebrate phenotyping
Carlos Pardo-Martin, Amin Allalou, Jaime Medina, Peter M. Eimon, Carolina Wählby Mehmet Fatih Yanik February 12, 2013 Nature Communications 4, Article number:1467, doi:10.1038/ncomms2475
High-throughput hyperdimensional vertebrate phenotyping
Presenting VAST BioImager™: A new modular, expandable platform to automate the orientation of 2-7 day old zebrafish larvae for imaging
The Nordic Countries Zebrafish Meeting on the Zebrafish as a model for Development and Disease
Union Biometrica, Geel, Belgium, Union Biometrica, Holliston, MA, USA
Yanik lab, MIT, Boston, MA, USA
November 21, 2012
Presenting VAST BioImager™: A new modular, expandable platform to automate the orientation of 2-7 day old zebrafish larvae for imaging
Development and Validation of an Automated High-Throughput System for Zebrafish In Vivo Screenings
Ainhoa Letamendia¹, Celia Quevedo¹, Izaskun Ibarbia¹, Juan M. Virto¹, Olaia Holgado¹, Maria Diez¹, Juan Carlos Izpisua Belmonte²,³, Carles Callol-Massot¹ May 15, 2012 PLoS ONE 7(5): e36690. doi:10.1371/journal.pone.0036690
View AbstractDevelopment and Validation of an Automated High-Throughput System for Zebrafish In Vivo Screenings
1Biobide S.L., San Sebastian, Guipuzcoa, Spain, 2Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, California, United States of America, 3Center of Regenerative Medicine in Barcelona, Barcelona, Spain
Fully automated cellular-resolution vertebrate screening platform with parallel animal processing
Chang TY, Pardo-Martin C, Allalou A, Wählby C, Yanik MF. February 01, 2012 Lab Chip. 2012 Feb 21;12(4):711-6. doi: 10.1039/c1lc20849g. Epub 2011 Dec 8.
Fully automated cellular-resolution vertebrate screening platform with parallel animal processing
A High-Throughput Screen for Tuberculosis Progression
Ralph Carvalho¹,³* Jan de Sonneville,² Oliver W. Stockhammer,³ Nigel D. L. Savage,4 Wouter J. Veneman,³ Tom H. M. Ottenhoff,4 Ron P. Dirks¹ Annemarie H. Meijer,³ and Herman P. Spaink ³ February 16, 2011 PLoS One. 2011; 6(2): e16779. 1) F-screens B.V., Leiden, The Netherlands, 2) Institute of Chemistry, Leiden University, Leiden, The Netherlands, 3) Institute of Biology, Leiden University, Leiden, The Netherlands,4) Department of Immunohematology and Blood Transfusion, Leiden University Medical Centre, Leiden, The Netherlands
View AbstractA High-Throughput Screen for Tuberculosis Progression
One-third of the world population is infected with Mycobacterium tuberculosis and multi-drug resistant strains are rapidly evolving. The noticeable absence of a whole organism high-throughput screening system for studying the progression of tuberculosis is fast becoming the bottleneck in tuberculosis research. We successfully developed such a system using the zebrafish Mycobacterium marinum infection model, which is a well-characterized model for tuberculosis progression with biomedical significance, mimicking hallmarks of human tuberculosis pathology. Importantly, we demonstrate the suitability of our system to directly study M. tuberculosis, showing for the first time that the human pathogen can propagate in this vertebrate model, resulting in similar early disease symptoms to those observed upon M. marinum infection. Our system is capable of screening for disease progression via robotic yolk injection of early embryos and visual flow screening of late-stage larvae. We also show that this system can reliably recapitulate the standard caudal vein injection method with a throughput level of 2,000 embryos per hour. We additionally demonstrate the possibility of studying signal transduction leading to disease progression using reverse genetics at high-throughput levels. Importantly, we use reference compounds to validate our system in the testing of molecules that prevent tuberculosis progression, making it highly suited for investigating novel anti-tuberculosis compounds in vivo.
Zebrafish high throughput screening using robotic injection technology
The zebrafish embryo model in toxicology and teratology: Karlsruhe, Germany 2nd-3rd September 2010
Herman Spaink¹, Ron Dirks², Jan de Sonneville¹, Ralph Carvalho², Oliver Stockhammer¹,², Ewa Snaar-Jagalska¹, Annemarie Meijer¹
September 02, 2010
Zebrafish high throughput screening using robotic injection technology
1Leiden University, Leiden The Netherlands; 2ZF-screens B.V. Leiden, The Netherlands
High-throughput in vivo vertebrate screening.
Pardo-Martin C, Chang TY, Koo BK, Gilleland CL, Wasserman SC, Yanik MF. August 01, 2010 Nat Methods. 2010 Aug;7(8):634-6. doi: 10.1038/nmeth.1481. Epub 2010 Jul 18.
High-throughput in vivo vertebrate screening.
Zebrafish High-Throughput Screening of Innate Immune Responses.
Zebrafish Disease Modeling III, June 21-24, 2010 Dana-Farber Cancer Institute, Boston, MA
Herman Spaink¹, Ron Dirks², Jan de Sonneville¹, Ralph Carvalho², Oliver Stockhammer¹,², Ewa Snaar-Jagalska¹, Annemarie Meijer¹
June 21, 2010
Zebrafish High-Throughput Screening of Innate Immune Responses.
1Leiden University, Leiden The Netherlands; 2ZF-screens B.V. Leiden, The Netherlands
Zebrafish are an excellent model for studying the mechanisms of the innate immune defense against pathogens. A high throughput approach is described for a study of the innate immunity in response to bacterial pathogens. The COPAS flow cytometer provided the data analysis in a quick, unbiased and high throughput manner.
A High-Throughput Assay To Measure Whole Body Metabolic Rate Using Zebrafish Larvae.
2009 Lab Automation, January 25-28, Palm Springs, CA
Khadijah Makky1, Petar Duvnjak1, Kallal Pramanik2, Ramani Ramchandran2, and Alan N. Mayer1
January 25, 2009
A High-Throughput Assay To Measure Whole Body Metabolic Rate Using Zebrafish Larvae.
Department of Pediatrics, Gastroenterology1 and Developmental Biology Sections2, Medical College of Wisconsin and Children’s Research Institute, Milwaukee, WI 53226
Whole animal acid secretion can be used as readout for energy metabolism, thus enabling high-throughput chemical and genetic screens for regulators of metabolic rate in a vertebrate. The COPAS sorter was critical for automation.
A Whole-Animal Microplate Assay for Metabolic Rate Using Zebrafish
Makky K, Duvnjak P, Pramanik K, Ramchandran R, Mayer AN
November 18, 2008
Journal of Biomolecular Screening, Vol. 13, No. 10, 960-967 (2008)
DOI: 10.1177/1087057108326080
A Whole-Animal Microplate Assay for Metabolic Rate Using Zebrafish
Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
To study genetics and drugs that impact metabolic rates, whole-animal acid secretion was used as an indicator for energy metabolism. Because of rapid kinetics, COPAS was used for large-scale screening of zebrafish.
Multiparametric analysis of neuromast hair cells in intact early larvae using a large particle sorter.
2005 West Coast Zebrafish Meeting, September 9 – 10
Bo Wang, Julia Thompson and Rock Pulak
September 09, 2005
Multiparametric analysis of neuromast hair cells in intact early larvae using a large particle sorter.
Union Biometrica Inc., 84 October Hill Rd, Holliston, MA 01746 USA
Drug Discovery - Automated Drug Screening Using Zebrafish: COPAS XL Allows for Increased Throughput
September 01, 2002 Genetic Engineering News Volume 22, Number 15, September 1, 2002, pp. 32, 35.