1
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Efromson J, Ferrero G, Bègue A, Doman TJJ, Dugo C, Barker A, Saliu V, Reamey P, Kim K, Harfouche M, Yoder JA. Automated, high-throughput quantification of EGFP-expressing neutrophils in zebrafish by machine learning and a highly-parallelized microscope. PLoS One 2023; 18:e0295711. [PMID: 38060605 PMCID: PMC10703246 DOI: 10.1371/journal.pone.0295711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
Normal development of the immune system is essential for overall health and disease resistance. Bony fish, such as the zebrafish (Danio rerio), possess all the major immune cell lineages as mammals and can be employed to model human host response to immune challenge. Zebrafish neutrophils, for example, are present in the transparent larvae as early as 48 hours post fertilization and have been examined in numerous infection and immunotoxicology reports. One significant advantage of the zebrafish model is the ability to affordably generate high numbers of individual larvae that can be arrayed in multi-well plates for high throughput genetic and chemical exposure screens. However, traditional workflows for imaging individual larvae have been limited to low-throughput studies using traditional microscopes and manual analyses. Using a newly developed, parallelized microscope, the Multi-Camera Array Microscope (MCAM™), we have optimized a rapid, high-resolution algorithmic method to count fluorescently labeled cells in zebrafish larvae in vivo. Using transgenic zebrafish larvae, in which neutrophils express EGFP, we captured 18 gigapixels of images across a full 96-well plate, in 75 seconds, and processed the resulting datastream, counting individual fluorescent neutrophils in all individual larvae in 5 minutes. This automation is facilitated by a machine learning segmentation algorithm that defines the most in-focus view of each larva in each well after which pixel intensity thresholding and blob detection are employed to locate and count fluorescent cells. We validated this method by comparing algorithmic neutrophil counts to manual counts in larvae subjected to changes in neutrophil numbers, demonstrating the utility of this approach for high-throughput genetic and chemical screens where a change in neutrophil number is an endpoint metric. Using the MCAM™ we have been able to, within minutes, acquire both enough data to create an automated algorithm and execute a biological experiment with statistical significance. Finally, we present this open-source software package which allows the user to train and evaluate a custom machine learning segmentation model and use it to localize zebrafish and analyze cell counts within the segmented region of interest. This software can be modified as needed for studies involving other zebrafish cell lineages using different transgenic reporter lines and can also be adapted for studies using other amenable model species.
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Affiliation(s)
- John Efromson
- Ramona Optics Inc., Durham, NC, United States of America
| | - Giuliano Ferrero
- Department of Molecular Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Aurélien Bègue
- Ramona Optics Inc., Durham, NC, United States of America
| | | | - Clay Dugo
- Ramona Optics Inc., Durham, NC, United States of America
| | - Andi Barker
- Department of Molecular Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
| | - Veton Saliu
- Ramona Optics Inc., Durham, NC, United States of America
| | - Paul Reamey
- Ramona Optics Inc., Durham, NC, United States of America
| | - Kanghyun Kim
- Department of Biomedical Engineering, Duke University, Durham, NC, United States of America
| | - Mark Harfouche
- Ramona Optics Inc., Durham, NC, United States of America
| | - Jeffrey A. Yoder
- Department of Molecular Biological Sciences, North Carolina State University, Raleigh, NC, United States of America
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2
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Efromson J, Ferrero G, Bègue A, Doman TJJ, Dugo C, Barker A, Saliu V, Reamey P, Kim K, Harfouche M, Yoder JA. Automated, high-throughput quantification of EGFP-expressing neutrophils in zebrafish by machine learning and a highly-parallelized microscope. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.16.553550. [PMID: 37645798 PMCID: PMC10462042 DOI: 10.1101/2023.08.16.553550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Normal development of the immune system is essential for overall health and disease resistance. Bony fish, such as the zebrafish (Danio rerio), possess all the major immune cell lineages as mammals and can be employed to model human host response to immune challenge. Zebrafish neutrophils, for example, are present in the transparent larvae as early as 48 hours post fertilization and have been examined in numerous infection and immunotoxicology reports. One significant advantage of the zebrafish model is the ability to affordably generate high numbers of individual larvae that can be arrayed in multi-well plates for high throughput genetic and chemical exposure screens. However, traditional workflows for imaging individual larvae have been limited to low-throughput studies using traditional microscopes and manual analyses. Using a newly developed, parallelized microscope, the Multi-Camera Array Microscope (MCAM™), we have optimized a rapid, high-resolution algorithmic method to count fluorescently labeled cells in zebrafish larvae in vivo. Using transgenic zebrafish larvae, in which neutrophils express EGFP, we captured 18 gigapixels of images across a full 96-well plate, in 75 seconds, and processed the resulting datastream, counting individual fluorescent neutrophils in all individual larvae in 5 minutes. This automation is facilitated by a machine learning segmentation algorithm that defines the most in-focus view of each larva in each well after which pixel intensity thresholding and blob detection are employed to locate and count fluorescent cells. We validated this method by comparing algorithmic neutrophil counts to manual counts in larvae subjected to changes in neutrophil numbers, demonstrating the utility of this approach for high-throughput genetic and chemical screens where a change in neutrophil number is an endpoint metric. Using the MCAM™ we have been able to, within minutes, acquire both enough data to create an automated algorithm and execute a biological experiment with statistical significance. Finally, we present this open-source software package which allows the user to train and evaluate a custom machine learning segmentation model and use it to localize zebrafish and analyze cell counts within the segmented region of interest. This software can be modified as needed for studies involving other zebrafish cell lineages using different transgenic reporter lines and can also be adapted for studies using other amenable model species.
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Affiliation(s)
| | - Giuliano Ferrero
- Department of Molecular Biological Sciences, North Carolina State University, Raleigh, NC
| | | | | | | | - Andi Barker
- Department of Molecular Biological Sciences, North Carolina State University, Raleigh, NC
| | | | | | - Kanghyun Kim
- Department of Biomedical Engineering, Duke University, Durham, NC
| | | | - Jeffrey A. Yoder
- Department of Molecular Biological Sciences, North Carolina State University, Raleigh, NC
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3
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Wlodkowic D, Jansen M. High-throughput screening paradigms in ecotoxicity testing: Emerging prospects and ongoing challenges. CHEMOSPHERE 2022; 307:135929. [PMID: 35944679 DOI: 10.1016/j.chemosphere.2022.135929] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/09/2022] [Accepted: 07/31/2022] [Indexed: 06/15/2023]
Abstract
The rapidly increasing number of new production chemicals coupled with stringent implementation of global chemical management programs necessities a paradigm shift towards boarder uses of low-cost and high-throughput ecotoxicity testing strategies as well as deeper understanding of cellular and sub-cellular mechanisms of ecotoxicity that can be used in effective risk assessment. The latter will require automated acquisition of biological data, new capabilities for big data analysis as well as computational simulations capable of translating new data into in vivo relevance. However, very few efforts have been so far devoted into the development of automated bioanalytical systems in ecotoxicology. This is in stark contrast to standardized and high-throughput chemical screening and prioritization routines found in modern drug discovery pipelines. As a result, the high-throughput and high-content data acquisition in ecotoxicology is still in its infancy with limited examples focused on cell-free and cell-based assays. In this work we outline recent developments and emerging prospects of high-throughput bioanalytical approaches in ecotoxicology that reach beyond in vitro biotests. We discuss future importance of automated quantitative data acquisition for cell-free, cell-based as well as developments in phytotoxicity and in vivo biotests utilizing small aquatic model organisms. We also discuss recent innovations such as organs-on-a-chip technologies and existing challenges for emerging high-throughput ecotoxicity testing strategies. Lastly, we provide seminal examples of the small number of successful high-throughput implementations that have been employed in prioritization of chemicals and accelerated environmental risk assessment.
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Affiliation(s)
- Donald Wlodkowic
- The Neurotox Lab, School of Science, RMIT University, Melbourne, VIC, 3083, Australia.
| | - Marcus Jansen
- LemnaTec GmbH, Nerscheider Weg 170, 52076, Aachen, Germany
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4
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A low-molecular-weight chitosan fluorometric-based assay for evaluating antiangiogenic drugs. Int J Biol Macromol 2022; 224:927-937. [DOI: 10.1016/j.ijbiomac.2022.10.178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/13/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
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5
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Lubin A, Otterstrom J, Hoade Y, Bjedov I, Stead E, Whelan M, Gestri G, Paran Y, Payne E. A versatile, automated and high-throughput drug screening platform for zebrafish embryos. Biol Open 2021; 10:bio058513. [PMID: 34472582 PMCID: PMC8430230 DOI: 10.1242/bio.058513] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/28/2021] [Indexed: 12/29/2022] Open
Abstract
Zebrafish provide a unique opportunity for drug screening in living animals, with the fast-developing, transparent embryos allowing for relatively high-throughput, microscopy-based screens. However, the limited availability of rapid, flexible imaging and analysis platforms has limited the use of zebrafish in drug screens. We have developed an easy-to-use, customisable automated screening procedure suitable for high-throughput phenotype-based screens of live zebrafish. We utilised the WiScan® Hermes High Content Imaging System to rapidly acquire brightfield and fluorescent images of embryos, and the WiSoft® Athena Zebrafish Application for analysis, which harnesses an Artificial Intelligence-driven algorithm to automatically detect fish in brightfield images, identify anatomical structures, partition the animal into regions and exclusively select the desired side-oriented fish. Our initial validation combined structural analysis with fluorescence images to enumerate GFP-tagged haematopoietic stem and progenitor cells in the tails of embryos, which correlated with manual counts. We further validated this system to assess the effects of genetic mutations and X-ray irradiation in high content using a wide range of assays. Further, we performed simultaneous analysis of multiple cell types using dual fluorophores in high throughput. In summary, we demonstrate a broadly applicable and rapidly customisable platform for high-content screening in zebrafish. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Alexandra Lubin
- Research Department of Haematology, Cancer Institute, University College London, London WC1E 6DD, UK
| | | | - Yvette Hoade
- Research Department of Haematology, Cancer Institute, University College London, London WC1E 6DD, UK
| | - Ivana Bjedov
- Research Department of Cancer Biology, Cancer Institute, University College London, London WC1E 6DD, UK
| | - Eleanor Stead
- Research Department of Cancer Biology, Cancer Institute, University College London, London WC1E 6DD, UK
| | - Matthew Whelan
- Division of Infection and Immunity, University College London, London WC1E 6BT, UK
| | - Gaia Gestri
- Department of Cell and Developmental Biology, University College London, London WC1E 6AR, UK
| | - Yael Paran
- IDEA Bio-Medical Ltd., Rehovot 76705, Israel
| | - Elspeth Payne
- Research Department of Haematology, Cancer Institute, University College London, London WC1E 6DD, UK
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6
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Functional Roles of FGF Signaling in Early Development of Vertebrate Embryos. Cells 2021; 10:cells10082148. [PMID: 34440915 PMCID: PMC8391977 DOI: 10.3390/cells10082148] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/10/2021] [Accepted: 08/18/2021] [Indexed: 02/07/2023] Open
Abstract
Fibroblast growth factors (FGFs) comprise a large family of growth factors, regulating diverse biological processes including cell proliferation, migration, and differentiation. Each FGF binds to a set of FGF receptors to initiate certain intracellular signaling molecules. Accumulated evidence suggests that in early development and adult state of vertebrates, FGFs also play exclusive and context dependent roles. Although FGFs have been the focus of research for therapeutic approaches in cancer, cardiovascular disease, and metabolic syndrome, in this review, we mainly focused on their role in germ layer specification and axis patterning during early vertebrate embryogenesis. We discussed the functional roles of FGFs and their interacting partners as part of the gene regulatory network for germ layer specification, dorsal-ventral (DV), and anterior-posterior (AP) patterning. Finally, we briefly reviewed the regulatory molecules and pharmacological agents discovered that may allow modulation of FGF signaling in research.
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7
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Saydmohammed M, Vollmer LL, Onuoha EO, Maskrey TS, Gibson G, Watkins SC, Wipf P, Vogt A, Tsang M. A High-Content Screen Reveals New Small-Molecule Enhancers of Ras/Mapk Signaling as Probes for Zebrafish Heart Development. Molecules 2018; 23:molecules23071691. [PMID: 29997348 PMCID: PMC6099644 DOI: 10.3390/molecules23071691] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/09/2018] [Accepted: 07/09/2018] [Indexed: 12/11/2022] Open
Abstract
Zebrafish is the preferred vertebrate model for high throughput chemical screens to discover modulators of complex biological pathways. We adapted a transgenic zebrafish line, Tg(dusp6:EGFP), which reports on fibroblast growth factor (Fgf)/Ras/Mapk activity, into a quantitative, high-content chemical screen to identify novel Fgf hyperactivators as chemical probes for zebrafish heart development and regeneration. We screened 10,000 compounds from the TimTec ActiProbe library, and identified several structurally distinct classes of molecules that enhanced Fgf/Ras/Mapk signaling. We chose three agents—ST020101, ST011282, and ST006994—for confirmatory and functional studies based on potency, repeatability with repurchased material, favorable whole organism toxicity, and evidence of structure–activity relationships. Functional follow-up assays confirmed that all three compounds induced the expression of Fgf target genes during zebrafish embryonic development. Moreover, these compounds increased cardiac progenitor populations by effecting a fate change from endothelial to cardiac progenitors that translated into increased numbers of cardiomyocytes. Interestingly, ST006994 augmented Fgf/Ras/Mapk signaling without increasing Erk phosphorylation, suggesting a molecular mechanism of action downstream of Erk. We posit that the ST006994 pharmacophore could become a unique chemical probe to uncover novel mechanisms of Fgf signaling during heart development and regeneration downstream of the Mapk signaling node.
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Affiliation(s)
- Manush Saydmohammed
- Department of Developmental Biology, University of Pittsburgh, BST3, 3501 5th Avenue, Pittsburgh, PA 15213, USA.
| | - Laura L Vollmer
- The University of Pittsburgh Drug Discovery Institute, 200 Lothrop Street, Pittsburgh, PA 15260, USA.
| | - Ezenwa O Onuoha
- Department of Developmental Biology, University of Pittsburgh, BST3, 3501 5th Avenue, Pittsburgh, PA 15213, USA.
| | - Taber S Maskrey
- Department of Chemistry, 219 University Drive, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Gregory Gibson
- Department of Cell Biology, University of Pittsburgh, 3500 Terrace Street, Pittsburgh, PA 15213, USA.
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh, 3500 Terrace Street, Pittsburgh, PA 15213, USA.
| | - Peter Wipf
- Department of Chemistry, 219 University Drive, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | - Andreas Vogt
- The University of Pittsburgh Drug Discovery Institute, 200 Lothrop Street, Pittsburgh, PA 15260, USA.
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA.
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh, BST3, 3501 5th Avenue, Pittsburgh, PA 15213, USA.
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8
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Missinato MA, Saydmohammed M, Zuppo DA, Rao KS, Opie GW, Kühn B, Tsang M. Dusp6 attenuates Ras/MAPK signaling to limit zebrafish heart regeneration. Development 2018; 145:dev.157206. [PMID: 29444893 DOI: 10.1242/dev.157206] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/29/2018] [Indexed: 01/10/2023]
Abstract
Zebrafish regenerate cardiac tissue through proliferation of pre-existing cardiomyocytes and neovascularization. Secreted growth factors such as FGFs, IGF, PDGFs and Neuregulin play essential roles in stimulating cardiomyocyte proliferation. These factors activate the Ras/MAPK pathway, which is tightly controlled by the feedback attenuator Dual specificity phosphatase 6 (Dusp6), an ERK phosphatase. Here, we show that suppressing Dusp6 function enhances cardiac regeneration. Inactivation of Dusp6 by small molecules or by gene inactivation increased cardiomyocyte proliferation, coronary angiogenesis, and reduced fibrosis after ventricular resection. Inhibition of Erbb or PDGF receptor signaling suppressed cardiac regeneration in wild-type zebrafish, but had a milder effect on regeneration in dusp6 mutants. Moreover, in rat primary cardiomyocytes, NRG1-stimulated proliferation can be enhanced upon chemical inhibition of Dusp6 with BCI. Our results suggest that Dusp6 attenuates Ras/MAPK signaling during regeneration and that suppressing Dusp6 can enhance cardiac repair.
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Affiliation(s)
- Maria A Missinato
- Department of Developmental Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Manush Saydmohammed
- Department of Developmental Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Daniel A Zuppo
- Department of Developmental Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Krithika S Rao
- Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, Children's Hospital of Pittsburgh of UPMC and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Graham W Opie
- Department of Developmental Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
| | - Bernhard Kühn
- Pediatric Institute for Heart Regeneration and Therapeutics (I-HRT), Richard King Mellon Foundation Institute for Pediatric Research and Division of Cardiology, Children's Hospital of Pittsburgh of UPMC and Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA 15224, USA.,McGowan Institute of Regenerative Medicine, Pittsburgh, PA 15219, USA
| | - Michael Tsang
- Department of Developmental Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA 15213, USA
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9
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Abstract
Zebrafish are increasingly used to perform phenotypic screens to identify agents that can alter physiology in a whole organismal context. Here, we describe an automated high-content chemical screen using transgenic zebrafish embryos to identify small molecules that modulate Fibroblast Growth Factor Signaling. High content multi-well screening was further refined with a particular emphasis on automated imaging and quantification that increases sensitivity and throughput of whole organism chemical screens.
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Affiliation(s)
- Manush Saydmohammed
- Department of Developmental Biology, School of Medicine, University of Pittsburgh, 5062 Biomedical Science Tower 3, Pittsburgh, PA, 15260, USA
| | - Michael Tsang
- Department of Developmental Biology, School of Medicine, University of Pittsburgh, 5062 Biomedical Science Tower 3, Pittsburgh, PA, 15260, USA.
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10
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Shun T, Gough AH, Sanker S, Hukriede NA, Vogt A. Exploiting Analysis of Heterogeneity to Increase the Information Content Extracted from Fluorescence Micrographs of Transgenic Zebrafish Embryos. Assay Drug Dev Technol 2017; 15:257-266. [PMID: 28800244 DOI: 10.1089/adt.2017.793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Zebrafish embryos are a near-ideal animal model for drug discovery because of their high genetic and physiological similarity to mammals, small size, high fecundity, and optical transparency. The latter properties make zebrafish at larval stages especially suited for high-content analysis and high throughput screening (HTS). However, inherent biological complexity and the inability to screen multiple specimens in a single well present a challenge for HTS because limiting replicates and high variability often prevent assays from reaching the stringent performance criteria demanded of large-scale screening assays. In this report, we present methodology that overcomes these obstacles. We used our previously developed Tg(lhx1a:EGFP)pt303 line, which expresses a fluorescent transgene that enables live real-time measurements of kidney progenitor cell expansion. Since transgenes are expressed in specific cell populations, whose localization is precisely controlled, both spatially and temporally, we considered the developing embryo to be a "host" for a cell population, analogous to a well of a cell culture microplate, rather than a single specimen. By adopting this view, parameters routinely used to analyze cultured cells became applicable to characterize and quantify zebrafish transgene appearance beyond the overall intensity or area measurements, which are analogous to calculating well average data. Using the pixel-level distribution of transgene intensity as a proxy to cell-level data, we applied population-based intensity and heterogeneity measurements to quantitatively describe and characterize transgene expression in each embryo. Subsequent linear discriminant analysis on eight such parameters captured and condensed this information into a single assay parameter that maximizes the difference between positive and negative responses. The improvements in assay performance resulted in the Tg(lhx1a:EGFP)pt303 assay achieving HTS compatible assay performance in multi-day variability studies, documenting readiness for HTS of compounds that expand kidney progenitor cell populations.
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Affiliation(s)
- Tongying Shun
- 1 University of Pittsburgh Drug Discovery Institute , Pittsburgh, Pennsylvania
| | - Albert H Gough
- 1 University of Pittsburgh Drug Discovery Institute , Pittsburgh, Pennsylvania.,2 Department of Computational and Systems Biology, University of Pittsburgh Drug Discovery Institute , Pittsburgh, Pennsylvania
| | - Subramaniam Sanker
- 3 Department of Developmental Biology, University of Pittsburgh Drug Discovery Institute , Pittsburgh, Pennsylvania
| | - Neil A Hukriede
- 3 Department of Developmental Biology, University of Pittsburgh Drug Discovery Institute , Pittsburgh, Pennsylvania.,4 Center for Critical Care Nephrology, University of Pittsburgh , Pittsburgh, Pennsylvania
| | - Andreas Vogt
- 1 University of Pittsburgh Drug Discovery Institute , Pittsburgh, Pennsylvania.,2 Department of Computational and Systems Biology, University of Pittsburgh Drug Discovery Institute , Pittsburgh, Pennsylvania
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11
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Wiley DS, Redfield SE, Zon LI. Chemical screening in zebrafish for novel biological and therapeutic discovery. Methods Cell Biol 2016; 138:651-679. [PMID: 28129862 DOI: 10.1016/bs.mcb.2016.10.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Zebrafish chemical screening allows for an in vivo assessment of small molecule modulation of biological processes. Compound toxicities, chemical alterations by metabolism, pharmacokinetic and pharmacodynamic properties, and modulation of cell niches can be studied with this method. Furthermore, zebrafish screening is straightforward and cost effective. Zebrafish provide an invaluable platform for novel therapeutic discovery through chemical screening.
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Affiliation(s)
- D S Wiley
- Stem Cell Program and Division of Hematology and Oncology, Childrens' Hospital Boston, Dana-Farber Cancer Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, United States
| | - S E Redfield
- Stem Cell Program and Division of Hematology and Oncology, Childrens' Hospital Boston, Dana-Farber Cancer Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, United States
| | - L I Zon
- Stem Cell Program and Division of Hematology and Oncology, Childrens' Hospital Boston, Dana-Farber Cancer Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, United States
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12
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Fraietta I, Gasparri F. The development of high-content screening (HCS) technology and its importance to drug discovery. Expert Opin Drug Discov 2016; 11:501-14. [PMID: 26971542 DOI: 10.1517/17460441.2016.1165203] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
INTRODUCTION High-content screening (HCS) was introduced about twenty years ago as a promising analytical approach to facilitate some critical aspects of drug discovery. Its application has spread progressively within the pharmaceutical industry and academia to the point that it today represents a fundamental tool in supporting drug discovery and development. AREAS COVERED Here, the authors review some of significant progress in the HCS field in terms of biological models and assay readouts. They highlight the importance of high-content screening in drug discovery, as testified by its numerous applications in a variety of therapeutic areas: oncology, infective diseases, cardiovascular and neurodegenerative diseases. They also dissect the role of HCS technology in different phases of the drug discovery pipeline: target identification, primary compound screening, secondary assays, mechanism of action studies and in vitro toxicology. EXPERT OPINION Recent advances in cellular assay technologies, such as the introduction of three-dimensional (3D) cultures, induced pluripotent stem cells (iPSCs) and genome editing technologies (e.g., CRISPR/Cas9), have tremendously expanded the potential of high-content assays to contribute to the drug discovery process. Increasingly predictive cellular models and readouts, together with the development of more sophisticated and affordable HCS readers, will further consolidate the role of HCS technology in drug discovery.
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Affiliation(s)
- Ivan Fraietta
- a Department of Biology , Nerviano Medical Sciences S.r.l ., Nerviano , Milano , Italy
| | - Fabio Gasparri
- a Department of Biology , Nerviano Medical Sciences S.r.l ., Nerviano , Milano , Italy
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13
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Abstract
The zebrafish has become a prominent vertebrate model for disease and has already contributed to several examples of successful phenotype-based drug discovery. For the zebrafish to become useful in drug development more broadly, key hurdles must be overcome, including a more comprehensive elucidation of the similarities and differences between human and zebrafish biology. Recent studies have begun to establish the capabilities and limitations of zebrafish for disease modelling, drug screening, target identification, pharmacology, and toxicology. As our understanding increases and as the technologies for manipulating zebrafish improve, it is hoped that the zebrafish will have a key role in accelerating the emergence of precision medicine.
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Affiliation(s)
- Calum A MacRae
- Cardiovascular Medicine and Network Medicine Divisions, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Randall T Peterson
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
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14
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Rennekamp AJ, Peterson RT. 15 years of zebrafish chemical screening. Curr Opin Chem Biol 2014; 24:58-70. [PMID: 25461724 DOI: 10.1016/j.cbpa.2014.10.025] [Citation(s) in RCA: 195] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 10/28/2014] [Accepted: 10/30/2014] [Indexed: 12/13/2022]
Abstract
In 2000, the first chemical screen using living zebrafish in a multi-well plate was reported. Since then, more than 60 additional screens have been published describing whole-organism drug and pathway discovery projects in zebrafish. To investigate the scope of the work reported in the last 14 years and to identify trends in the field, we analyzed the discovery strategies of 64 primary research articles from the literature. We found that zebrafish screens have expanded beyond the use of developmental phenotypes to include behavioral, cardiac, metabolic, proliferative and regenerative endpoints. Additionally, many creative strategies have been used to uncover the mechanisms of action of new small molecules including chemical phenocopy, genetic phenocopy, mutant rescue, and spatial localization strategies.
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Affiliation(s)
- Andrew J Rennekamp
- Cardiovascular Research Center and Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA; Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - Randall T Peterson
- Cardiovascular Research Center and Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, 149 13th Street, Charlestown, MA 02129, USA; Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA; Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.
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15
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Bugel SM, Tanguay RL, Planchart A. Zebrafish: A marvel of high-throughput biology for 21 st century toxicology. Curr Environ Health Rep 2014; 1:341-352. [PMID: 25678986 DOI: 10.1007/s40572-014-0029-5] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The evolutionary conservation of genomic, biochemical and developmental features between zebrafish and humans is gradually coming into focus with the end result that the zebrafish embryo model has emerged as a powerful tool for uncovering the effects of environmental exposures on a multitude of biological processes with direct relevance to human health. In this review, we highlight advances in automation, high-throughput (HT) screening, and analysis that leverage the power of the zebrafish embryo model for unparalleled advances in our understanding of how chemicals in our environment affect our health and wellbeing.
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Affiliation(s)
- Sean M Bugel
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97333
| | - Robert L Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97333
| | - Antonio Planchart
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695
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16
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Korotchenko VN, Saydmohammed M, Vollmer LL, Bakan A, Sheetz K, Debiec KT, Greene KA, Agliori CS, Bahar I, Day BW, Vogt A, Tsang M. In vivo structure-activity relationship studies support allosteric targeting of a dual specificity phosphatase. Chembiochem 2014; 15:1436-45. [PMID: 24909879 DOI: 10.1002/cbic.201402000] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2014] [Indexed: 11/06/2022]
Abstract
Dual specificity phosphatase 6 (DUSP6) functions as a feedback attenuator of fibroblast growth factor signaling during development. In vitro high throughput chemical screening attempts to discover DUSP6 inhibitors have yielded limited success. However, in vivo whole-organism screens of zebrafish identified compound 1 (BCI) as an allosteric inhibitor of DUSP6. Here we designed and synthesized a panel of analogues to define the structure-activity relationship (SAR) of DUSP6 inhibition. In vivo high-content analysis in transgenic zebrafish, coupled with cell-based chemical complementation assays, identified structural features of the pharmacophore of 1 that were essential for biological activity. In vitro assays of DUSP hyperactivation corroborated the results from in vivo and cellular SAR. The results reinforce the notion that DUSPs are druggable through allosteric mechanisms and illustrate the utility of zebrafish as a model organism for in vivo SAR analyses.
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Affiliation(s)
- Vasiliy N Korotchenko
- Department of Pharmaceutical Sciences, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213 (USA); Present address: Walter Reed Army Institute of Research, 503 Forney Drive, Silver Spring, MD 20910 (USA)
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17
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Singh S, Carpenter AE, Genovesio A. Increasing the Content of High-Content Screening: An Overview. ACTA ACUST UNITED AC 2014; 19:640-50. [PMID: 24710339 PMCID: PMC4230961 DOI: 10.1177/1087057114528537] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 12/31/2013] [Indexed: 01/17/2023]
Abstract
Target-based high-throughput screening (HTS) has recently been critiqued for its relatively poor yield compared to phenotypic screening approaches. One type of phenotypic screening, image-based high-content screening (HCS), has been seen as particularly promising. In this article, we assess whether HCS is as high content as it can be. We analyze HCS publications and find that although the number of HCS experiments published each year continues to grow steadily, the information content lags behind. We find that a majority of high-content screens published so far (60−80%) made use of only one or two image-based features measured from each sample and disregarded the distribution of those features among each cell population. We discuss several potential explanations, focusing on the hypothesis that data analysis traditions are to blame. This includes practical problems related to managing large and multidimensional HCS data sets as well as the adoption of assay quality statistics from HTS to HCS. Both may have led to the simplification or systematic rejection of assays carrying complex and valuable phenotypic information. We predict that advanced data analysis methods that enable full multiparametric data to be harvested for entire cell populations will enable HCS to finally reach its potential.
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Affiliation(s)
- Shantanu Singh
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Anne E Carpenter
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Auguste Genovesio
- Imaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA École Normale Supérieure, 45, Rue d'Ulm, 75005 Paris
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18
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Mikut R, Dickmeis T, Driever W, Geurts P, Hamprecht FA, Kausler BX, Ledesma-Carbayo MJ, Marée R, Mikula K, Pantazis P, Ronneberger O, Santos A, Stotzka R, Strähle U, Peyriéras N. Automated processing of zebrafish imaging data: a survey. Zebrafish 2013; 10:401-21. [PMID: 23758125 PMCID: PMC3760023 DOI: 10.1089/zeb.2013.0886] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Due to the relative transparency of its embryos and larvae, the zebrafish is an ideal model organism for bioimaging approaches in vertebrates. Novel microscope technologies allow the imaging of developmental processes in unprecedented detail, and they enable the use of complex image-based read-outs for high-throughput/high-content screening. Such applications can easily generate Terabytes of image data, the handling and analysis of which becomes a major bottleneck in extracting the targeted information. Here, we describe the current state of the art in computational image analysis in the zebrafish system. We discuss the challenges encountered when handling high-content image data, especially with regard to data quality, annotation, and storage. We survey methods for preprocessing image data for further analysis, and describe selected examples of automated image analysis, including the tracking of cells during embryogenesis, heartbeat detection, identification of dead embryos, recognition of tissues and anatomical landmarks, and quantification of behavioral patterns of adult fish. We review recent examples for applications using such methods, such as the comprehensive analysis of cell lineages during early development, the generation of a three-dimensional brain atlas of zebrafish larvae, and high-throughput drug screens based on movement patterns. Finally, we identify future challenges for the zebrafish image analysis community, notably those concerning the compatibility of algorithms and data formats for the assembly of modular analysis pipelines.
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Affiliation(s)
- Ralf Mikut
- Karlsruhe Institute of Technology, Karlsruhe, Germany.
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19
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Sanker S, Cirio MC, Vollmer LL, Goldberg ND, McDermott LA, Hukriede NA, Vogt A. Development of high-content assays for kidney progenitor cell expansion in transgenic zebrafish. ACTA ACUST UNITED AC 2013; 18:1193-202. [PMID: 23832868 DOI: 10.1177/1087057113495296] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Reactivation of genes normally expressed during organogenesis is a characteristic of kidney regeneration. Enhancing this reactivation could potentially be a therapeutic target to augment kidney regeneration. The inductive events that drive kidney organogenesis in zebrafish are similar to the initial steps in mammalian kidney organogenesis. Therefore, quantifying embryonic signals that drive zebrafish kidney development is an attractive strategy for the discovery of potential novel therapeutic modalities that accelerate kidney regeneration. The Lim1 homeobox protein, Lhx1, is a marker of kidney development that is also expressed in the regenerating kidneys after injury. Using a fluorescent Lhx1a-EGFP transgene whose phenotype faithfully recapitulates that of the endogenous protein, we developed a high-content assay for Lhx1a-EGFP expression in transgenic zebrafish embryos employing an artificial intelligence-based image analysis method termed cognition network technology (CNT). Implementation of the CNT assay on high-content readers enabled automated real-time in vivo time-course, dose-response, and variability studies in the developing embryo. The Lhx1a assay was complemented with a kidney-specific secondary CNT assay that enables direct measurements of the embryonic renal tubule cell population. The integration of fluorescent transgenic zebrafish embryos with automated imaging and artificial intelligence-based image analysis provides an in vivo analysis system for structure-activity relationship studies and de novo discovery of novel agents that augment innate regenerative processes.
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Affiliation(s)
- Subramaniam Sanker
- 1Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
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20
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Abstract
Due to several inherent advantages, zebrafish are being utilized in increasingly sophisticated screens to assess the physiological effects of chemical compounds directly in living vertebrate organisms. Diverse screening platforms showcase these advantages. Morphological assays encompassing basic qualitative observations to automated imaging, manipulation, and data-processing systems provide whole organism to subcellular levels of detail. Behavioral screens extend chemical screening to the level of complex systems. In addition, zebrafish-based disease models provide a means of identifying new potential therapeutic strategies. Automated systems for handling/sorting, high-resolution imaging and quantitative data collection have significantly increased throughput in recent years. These advances will make it easier to capture multiple streams of information from a given sample and facilitate integration of zebrafish at the earliest stages of the drug-discovery process, providing potential solutions to current drug-development bottlenecks. Here we outline advances that have been made within the growing field of zebrafish chemical screening.
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21
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Terriente J, Pujades C. Use of Zebrafish Embryos for Small Molecule Screening Related to Cancer. Dev Dyn 2013. [DOI: 10.1002/dvdy.23912] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Javier Terriente
- Department of Experimental and Health Sciences; Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona; PRBB; Barcelona; Spain
| | - Cristina Pujades
- Department of Experimental and Health Sciences; Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona; PRBB; Barcelona; Spain
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22
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Agca Y. Genome resource banking of biomedically important laboratory animals. Theriogenology 2012; 78:1653-65. [PMID: 22981880 DOI: 10.1016/j.theriogenology.2012.08.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/10/2012] [Accepted: 08/12/2012] [Indexed: 01/12/2023]
Abstract
Genome resource banking is the systematic collection, storage, and redistribution of biomaterials in an organized, logistical, and secure manner. Genome cryobanks usually contain biomaterials and associated genomic information essential for progression of biomedicine, human health, and research. In that regard, appropriate genome cryobanks could provide essential biomaterials for both current and future research projects in the form of various cell types and tissues, including sperm, oocytes, embryos, embryonic or adult stem cells, induced pluripotent stem cells, and gonadal tissues. In addition to cryobanked germplasm, cryobanking of DNA, serum, blood products, and tissues from scientifically, economically, and ecologically important species has become a common practice. For revitalization of the whole organism, cryopreserved germplasm in conjunction with assisted reproductive technologies, offer a powerful approach for research model management, as well as assisting in animal production for agriculture, conservation, and human reproductive medicine. Recently, many developed and developing countries have allocated substantial resources to establish genome resources banks which are responsible for safeguarding scientifically, economically, and ecologically important wild type, mutant, and transgenic plants, fish, and local livestock breeds, as well as wildlife species. This review is dedicated to the memory of Dr. John K. Critser, who has made profound contributions to the science of cryobiology and establishment of genome research and resources centers for mice, rats, and swine. Emphasis will be given to application of genome resource banks to species with substantial contributions to the advancement of biomedicine and human health.
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Affiliation(s)
- Yuksel Agca
- College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA.
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Geldenhuys WJ, Allen DD, Bloomquist JR. Novel models for assessing blood–brain barrier drug permeation. Expert Opin Drug Metab Toxicol 2012; 8:647-53. [DOI: 10.1517/17425255.2012.677433] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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