1
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van Os WL, Wielaert L, Alter C, Davidović D, Šachl R, Kock T, González UU, Arias-Alpizar G, Vigario FL, Knol RA, Kuster R, Romeijn S, Mora NL, Detampel P, Hof M, Huwyler J, Kros A. Lipid conjugate dissociation analysis improves the in vivo understanding of lipid-based nanomedicine. J Control Release 2024; 371:85-100. [PMID: 38782063 DOI: 10.1016/j.jconrel.2024.05.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/14/2024] [Accepted: 05/19/2024] [Indexed: 05/25/2024]
Abstract
Lipid conjugates have advanced the field of lipid-based nanomedicine by promoting active-targeting (ligand, peptide, antibody), stability (PEGylation), controlled release (lipoid prodrug), and probe-based tracking (fluorophore). Recent findings indicate lipid conjugates dissociating from nanomedicine upon encountering a biological environment. Yet, implications for (pre)clinical outcomes remain unclear. In this study, using the zebrafish model (Danio rerio), we investigated the fate of liposome-incorporated lipid fluorophore conjugates (LFCs) after intravenous (IV) administration. LFCs having a bilayer mismatch and relatively polar fluorophore revealed counter-predictive outcomes for Caelyx/Doxil (clearance vs. circulating) and AmBisome-like liposomes (scavenger endothelial cell vs. macrophage uptake). Findings on LFC (mis)match for Caelyx/Doxil-like liposomes were supported by translational intravital imaging studies in mice. Importantly, contradicting observations suggest to originate from LFC dissociation in vivo, which was investigated by Asymmetric Flow Field-Flow Fractionation (AF4) upon liposome-serum incubation in situ. Our data suggests that LFCs matching with the liposome bilayer composition - that did not dissociate upon serum incubation - revealed improved predictive outcomes for liposome biodistribution profiles. Altogether, this study highlights the critical importance of fatty acid tail length and headgroup moiety when selecting lipid conjugates for lipid-based nanomedicine.
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Affiliation(s)
- Winant L van Os
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Laura Wielaert
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Claudio Alter
- Division of Pharmaceutical Technology, Department of Pharmaceutical Science, University of Basel, Switzerland
| | - David Davidović
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Radek Šachl
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Thomas Kock
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Urimare Ugueto González
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Gabriela Arias-Alpizar
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Fernando Lozano Vigario
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Renzo A Knol
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Rick Kuster
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Stefan Romeijn
- Division of BioTherapeutics, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Nestor Lopez Mora
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Pascal Detampel
- Division of Pharmaceutical Technology, Department of Pharmaceutical Science, University of Basel, Switzerland
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jörg Huwyler
- Division of Pharmaceutical Technology, Department of Pharmaceutical Science, University of Basel, Switzerland
| | - Alexander Kros
- Department of Supramolecular and Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
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2
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Sofyantoro F, Septriani NI, Yudha DS, Wicaksono EA, Priyono DS, Putri WA, Primahesa A, Raharjeng ARP, Purwestri YA, Nuringtyas TR. Zebrafish as Versatile Model for Assessing Animal Venoms and Toxins: Current Applications and Future Prospects. Zebrafish 2024; 21:231-242. [PMID: 38608228 DOI: 10.1089/zeb.2023.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Abstract
Animal venoms and toxins hold promise as sources of novel drug candidates, therapeutic agents, and biomolecules. To fully harness their potential, it is crucial to develop reliable testing methods that provide a comprehensive understanding of their effects and mechanisms of action. However, traditional rodent assays encounter difficulties in mimicking venom-induced effects in human due to the impractical venom dosage levels. The search for reliable testing methods has led to the emergence of zebrafish (Danio rerio) as a versatile model organism for evaluating animal venoms and toxins. Zebrafish possess genetic similarities to humans, rapid development, transparency, and amenability to high-throughput assays, making it ideal for assessing the effects of animal venoms and toxins. This review highlights unique attributes of zebrafish and explores their applications in studying venom- and toxin-induced effects from various species, including snakes, jellyfish, cuttlefish, anemones, spiders, and cone snails. Through zebrafish-based research, intricate physiological responses, developmental alterations, and potential therapeutic interventions induced by venoms are revealed. Novel techniques such as CRISPR/Cas9 gene editing, optogenetics, and high-throughput screening hold great promise for advancing venom research. As zebrafish-based insights converge with findings from other models, the comprehensive understanding of venom-induced effects continues to expand, guiding the development of targeted interventions and promoting both scientific knowledge and practical applications.
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Affiliation(s)
- Fajar Sofyantoro
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | | | - Ega Adhi Wicaksono
- Faculties of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Dwi Sendi Priyono
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Alfian Primahesa
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Anita Restu Puji Raharjeng
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Science and Technology, Universitas Islam Negeri Raden Fatah Palembang, South Sumatera, Indonesia
| | - Yekti Asih Purwestri
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Tri Rini Nuringtyas
- Faculties of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Research Center for Biotechnology, Universitas Gadjah Mada, Yogyakarta, Indonesia
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3
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Zhang Y, Li Y, Quan Z, Xiao P, Duan JA. New Insights into Antioxidant Peptides: An Overview of Efficient Screening, Evaluation Models, Molecular Mechanisms, and Applications. Antioxidants (Basel) 2024; 13:203. [PMID: 38397801 PMCID: PMC10886007 DOI: 10.3390/antiox13020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/03/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Antioxidant peptides are currently a hotspot in food science, pharmaceuticals, and cosmetics. In different fields, the screening, activity evaluation, mechanisms, and applications of antioxidant peptides are the pivotal areas of research. Among these topics, the efficient screening of antioxidant peptides stands at the forefront of cutting-edge research. To this end, efficient screening with novel technologies has significantly accelerated the research process, gradually replacing the traditional approach. After the novel antioxidant peptides are screened and identified, a time-consuming activity evaluation is another indispensable procedure, especially in in vivo models. Cellular and rodent models have been widely used for activity evaluation, whilst non-rodent models provide an efficient solution, even with the potential for high-throughput screening. Meanwhile, further research of molecular mechanisms can elucidate the essence underlying the activity, which is related to several signaling pathways, including Keap1-Nrf2/ARE, mitochondria-dependent apoptosis, TGF-β/SMAD, AMPK/SIRT1/PGC-1α, PI3K/Akt/mTOR, and NF-κB. Last but not least, antioxidant peptides have broad applications in food manufacture, therapy, and the cosmetics industry, which requires a systematic review. This review introduces novel technologies for the efficient screening of antioxidant peptides, categorized with a new vision. A wide range of activity evaluation assays, encompassing cellular models, as well as rodent and non-rodent models, are provided in a comprehensive manner. In addition, recent advances in molecular mechanisms are analyzed with specific cases. Finally, the applications of antioxidant peptides in food production, therapy, and cosmetics are systematically reviewed.
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Affiliation(s)
| | | | | | - Ping Xiao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China; (Y.Z.); (Y.L.); (Z.Q.)
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, and Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China; (Y.Z.); (Y.L.); (Z.Q.)
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4
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Zappa F, Intartaglia D, Guarino AM, De Cegli R, Wilson C, Salierno FG, Polishchuk E, Sorrentino NC, Conte I, De Matteis MA. Role of trafficking protein particle complex 2 in medaka development. Traffic 2024; 25:e12924. [PMID: 37963679 DOI: 10.1111/tra.12924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/16/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023]
Abstract
The skeletal dysplasia spondyloepiphyseal dysplasia tarda (SEDT) is caused by mutations in the TRAPPC2 gene, which encodes Sedlin, a component of the trafficking protein particle (TRAPP) complex that we have shown previously to be required for the export of type II collagen (Col2) from the endoplasmic reticulum. No vertebrate model for SEDT has been generated thus far. To address this gap, we generated a Sedlin knockout animal by mutating the orthologous TRAPPC2 gene (olSedl) of Oryzias latipes (medaka) fish. OlSedl deficiency leads to embryonic defects, short size, diminished skeletal ossification and altered Col2 production and secretion, resembling human defects observed in SEDT patients. Moreover, SEDT knock-out animals display photoreceptor degeneration and gut morphogenesis defects, suggesting a key role for Sedlin in the development of these organs. Thus, by studying Sedlin function in vivo, we provide evidence for a mechanistic link between TRAPPC2-mediated membrane trafficking, Col2 export, and developmental disorders.
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Affiliation(s)
- Francesca Zappa
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
| | - Daniela Intartaglia
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
| | - Andrea M Guarino
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Rossella De Cegli
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
| | - Cathal Wilson
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | | | - Elena Polishchuk
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
| | - Nicolina Cristina Sorrentino
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Ivan Conte
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine, TIGEM, Pozzuoli (Naples), Italy
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
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5
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Kumar N, Marée R, Geurts P, Muller M. Recent Advances in Bioimage Analysis Methods for Detecting Skeletal Deformities in Biomedical and Aquaculture Fish Species. Biomolecules 2023; 13:1797. [PMID: 38136667 PMCID: PMC10742266 DOI: 10.3390/biom13121797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Detecting skeletal or bone-related deformities in model and aquaculture fish is vital for numerous biomedical studies. In biomedical research, model fish with bone-related disorders are potential indicators of various chemically induced toxins in their environment or poor dietary conditions. In aquaculture, skeletal deformities are affecting fish health, and economic losses are incurred by fish farmers. This survey paper focuses on showcasing the cutting-edge image analysis tools and techniques based on artificial intelligence that are currently applied in the analysis of bone-related deformities in aquaculture and model fish. These methods and tools play a significant role in improving research by automating various aspects of the analysis. This paper also sheds light on some of the hurdles faced when dealing with high-content bioimages and explores potential solutions to overcome these challenges.
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Affiliation(s)
- Navdeep Kumar
- Department of Computer Science and Electrical Engineering, Montefiore Institute, University of Liège, 4000 Liège, Belgium; (R.M.); (P.G.)
| | - Raphaël Marée
- Department of Computer Science and Electrical Engineering, Montefiore Institute, University of Liège, 4000 Liège, Belgium; (R.M.); (P.G.)
| | - Pierre Geurts
- Department of Computer Science and Electrical Engineering, Montefiore Institute, University of Liège, 4000 Liège, Belgium; (R.M.); (P.G.)
| | - Marc Muller
- Laboratory for Organogenesis and Regeneration (LOR), GIGA Institute, University of Liège, 4000 Liège, Belgium;
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6
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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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7
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Fan YL, Hsu FR, Wang Y, Liao LD. Unlocking the Potential of Zebrafish Research with Artificial Intelligence: Advancements in Tracking, Processing, and Visualization. Med Biol Eng Comput 2023; 61:2797-2814. [PMID: 37558927 DOI: 10.1007/s11517-023-02903-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023]
Abstract
Zebrafish have become a widely accepted model organism for biomedical research due to their strong cortisol stress response, behavioral strain differences, and sensitivity to both drug treatments and predators. However, experimental zebrafish studies generate substantial data that must be analyzed through objective, accurate, and repeatable analysis methods. Recently, advancements in artificial intelligence (AI) have enabled automated tracking, image recognition, and data analysis, leading to more efficient and insightful investigations. In this review, we examine key AI applications in zebrafish research, including behavior analysis, genomics, and neuroscience. With the development of deep learning technology, AI algorithms have been used to precisely analyze and identify images of zebrafish, enabling automated testing and analysis. By applying AI algorithms in genomics research, researchers have elucidated the relationship between genes and biology, providing a better basis for the development of disease treatments and gene therapies. Additionally, the development of more effective neuroscience tools could help researchers better understand the complex neural networks in the zebrafish brain. In the future, further advancements in AI technology are expected to enable more extensive and in-depth medical research applications in zebrafish, improving our understanding of this important animal model. This review highlights the potential of AI technology in achieving the full potential of zebrafish research by enabling researchers to efficiently track, process, and visualize the outcomes of their experiments.
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Affiliation(s)
- Yi-Ling Fan
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County, 35053, Taiwan
- Department of Information Engineering and Computer Science, Feng Chia University, Taichung, 407, Taiwan
| | - Fang-Rong Hsu
- Department of Information Engineering and Computer Science, Feng Chia University, Taichung, 407, Taiwan
| | - Yuhling Wang
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County, 35053, Taiwan
- Department of Electrical Engineering, National United University, 2, Lien-Da, Nan-Shih Li, Miaoli, 360302, Taiwan
| | - Lun-De Liao
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, 35, Keyan Road, Zhunan Town, Miaoli County, 35053, Taiwan.
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8
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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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9
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Dash SN, Patnaik L. Flight for fish in drug discovery: a review of zebrafish-based screening of molecules. Biol Lett 2023; 19:20220541. [PMID: 37528729 PMCID: PMC10394424 DOI: 10.1098/rsbl.2022.0541] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 07/13/2023] [Indexed: 08/03/2023] Open
Abstract
Human disease and biological practices are modelled in zebrafish (Danio rerio) at various phases of drug development as well as toxicity evaluation. The zebrafish is ideal for in vivo pathological research and high-resolution investigation of disease progress. Zebrafish has an advantage over other mammalian models, it is cost-effective, it has external development and embryo transparency, easy to apply genetic manipulations, and open to both forward and reverse genetic techniques. Drug screening in zebrafish is suitable for target identification, illness modelling, high-throughput screening of compounds for inhibition or prevention of disease phenotypes and developing new drugs. Several drugs that have recently entered the clinic or clinical trials have their origins in zebrafish. The sophisticated screening methods used in zebrafish models are expected to play a significant role in advancing drug development programmes. This review highlights the current developments in drug discovery processes, including understanding the action of drugs in the context of disease and screening novel candidates in neurological diseases, cardiovascular diseases, glomerulopathies and cancer. Additionally, it summarizes the current techniques and approaches for the selection of small molecules and current technical limitations on the execution of zebrafish drug screening tests.
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Affiliation(s)
- Surjya Narayan Dash
- Institute of Biotechnology, Biocenter 2. Viikinkaari, University of Helsinki, Viikinkaari 5D, 00790 Helsinki, Finland
| | - Lipika Patnaik
- Environmental Science Laboratory, Department of Zoology, COE in Environment and Public Health, Ravenshaw University, Cuttack 751003, Odisha, India
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10
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Shen Y, Sheng R, Guo R. Application of Zebrafish as a Model for Anti-Cancer Activity Evaluation and Toxicity Testing of Natural Products. Pharmaceuticals (Basel) 2023; 16:827. [PMID: 37375774 DOI: 10.3390/ph16060827] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/27/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
Developing natural product-based anti-cancer drugs/agents is a promising way to overcome the serious side effects and toxicity of traditional chemotherapeutics for cancer treatment. However, rapid assessment of the in vivo anti-cancer activities of natural products is a challenge. Alternatively, zebrafish are useful model organisms and perform well in addressing this challenging issue. Nowadays, a growing number of studies have utilized zebrafish models to evaluate the in vivo activities of natural compounds. Herein, we reviewed the application of zebrafish models for evaluating the anti-cancer activity and toxicity of natural products over the past years, summarized its process and benefits, and provided future outlooks for the development of natural product-based anti-cancer drugs.
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Affiliation(s)
- Yifan Shen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Ruilong Sheng
- CQM-Centro de Química da Madeira, Campus da Penteada, Universidade da Madeira, 9000-390 Funchal, Portugal
| | - Ruihua Guo
- College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai 201306, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai 201306, China
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11
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Rude CI, Tidwell LG, Tilton SC, Waters KM, Anderson KA, Tanguay RL. Coupling Environmental Whole Mixture Toxicity Screening with Unbiased RNA-Seq Reveals Site-Specific Biological Responses in Zebrafish. TOXICS 2023; 11:201. [PMID: 36976966 PMCID: PMC10053777 DOI: 10.3390/toxics11030201] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Passive sampling device (PSD) extracts paired with developmental toxicity assays in Danio Rerio (zebrafish) are excellent sensors for whole mixture toxicity associated with the bioavailable non-polar organics at environmental sites. We expand this concept by incorporating RNA-Seq in 48-h post fertilization zebrafish statically exposed to PSD extracts from two Portland Harbor Superfund Site locations: river mile 6.5W (RM 6.5W) and river mile 7W (RM 7W). RM 6.5W contained higher concentrations of polycyclic aromatic hydrocarbons (PAHs), but the diagnostic ratios of both extracts indicated similar PAH sourcing and composition. Developmental screens determined RM 6.5W to be more toxic with the most sensitive endpoint being a "wavy" notochord malformation. Differential gene expression from exposure to both extracts was largely parallel, although more pronounced for RM 6.5W. When compared to the gene expression associated with individual chemical exposures, PSD extracts produced some gene signatures parallel to PAHs but were more closely matched by oxygenated-PAHs. Additionally, differential expression, reminiscent of the wavy notochord phenotype, was not accounted for by either class of chemical, indicating the potential of other contaminants driving mixture toxicity. These techniques offer a compelling method for non-targeted hazard characterization of whole mixtures in an in vivo vertebrate system without requiring complete chemical characterization.
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Affiliation(s)
- Christian I. Rude
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Lane G. Tidwell
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Susan C. Tilton
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Katrina M. Waters
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
- Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA 99354, USA
| | - Kim A. Anderson
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
| | - Robyn L. Tanguay
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
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12
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Everson JL, Tseng YC, Eberhart JK. High-throughput detection of craniofacial defects in fluorescent zebrafish. Birth Defects Res 2023; 115:371-389. [PMID: 36369674 PMCID: PMC9898129 DOI: 10.1002/bdr2.2127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/20/2022] [Accepted: 10/28/2022] [Indexed: 11/14/2022]
Abstract
Losses and malformations of cranial neural crest cell (cNCC) derivatives are a hallmark of several common brain and face malformations. Nevertheless, the etiology of these cNCC defects remains unknown for many cases, suggesting a complex basis involving interactions between genetic and/or environmental factors. However, the sheer number of possible factors (thousands of genes and hundreds of thousands of toxicants) has hindered identification of specific interactions. Here, we develop a high-throughput analysis that will enable faster identification of multifactorial interactions in the genesis of craniofacial defects. Zebrafish embryos expressing a fluorescent marker of cNCCs (fli1:EGFP) were exposed to a pathway inhibitor standard or environmental toxicant, and resulting changes in fluorescence were measured in high-throughput using a fluorescent microplate reader to approximate cNCC losses. Embryos exposed to the environmental Hedgehog pathway inhibitor piperonyl butoxide (PBO), a Hedgehog pathway inhibitor standard, or alcohol (ethanol) exhibited reduced fli1:EGFP fluorescence at one day post fertilization, which corresponded with craniofacial defects at five days post fertilization. Combining PBO and alcohol in a co-exposure paradigm synergistically reduced fluorescence, demonstrating a multifactorial interaction. Using pathway reporter transgenics, we show that the plate reader assay is sensitive at detecting alterations in Hedgehog signaling, a critical regulator of craniofacial development. We go on to demonstrate that this technique readily detects defects in other important cell types, namely neurons. Together, these findings demonstrate this novel in vivo platform can predict developmental abnormalities and multifactorial interactions in high-throughput.
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Affiliation(s)
- Joshua L. Everson
- Department of Molecular Biosciences, School of Natural Sciences, University of Texas at Austin, Austin, Texas, USA,Waggoner Center for Alcohol and Addiction Research, School of Pharmacy, University of Texas at Austin, Austin, Texas, USA
| | - Yung-Chia Tseng
- Department of Molecular Biosciences, School of Natural Sciences, University of Texas at Austin, Austin, Texas, USA
| | - Johann K. Eberhart
- Department of Molecular Biosciences, School of Natural Sciences, University of Texas at Austin, Austin, Texas, USA,Waggoner Center for Alcohol and Addiction Research, School of Pharmacy, University of Texas at Austin, Austin, Texas, USA
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13
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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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14
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Abstract
Heart disease is the leading cause of death worldwide. Despite decades of research, most heart pathologies have limited treatments, and often the only curative approach is heart transplantation. Thus, there is an urgent need to develop new therapeutic approaches for treating cardiac diseases. Animal models that reproduce the human pathophysiology are essential to uncovering the biology of diseases and discovering therapies. Traditionally, mammals have been used as models of cardiac disease, but the cost of generating and maintaining new models is exorbitant, and the studies have very low throughput. In the last decade, the zebrafish has emerged as a tractable model for cardiac diseases, owing to several characteristics that made this animal popular among developmental biologists. Zebrafish fertilization and development are external; embryos can be obtained in high numbers, are cheap and easy to maintain, and can be manipulated to create new genetic models. Moreover, zebrafish exhibit an exceptional ability to regenerate their heart after injury. This review summarizes 25 years of research using the zebrafish to study the heart, from the classical forward screenings to the contemporary methods to model mutations found in patients with cardiac disease. We discuss the advantages and limitations of this model organism and introduce the experimental approaches exploited in zebrafish, including forward and reverse genetics and chemical screenings. Last, we review the models used to induce cardiac injury and essential ideas derived from studying natural regeneration. Studies using zebrafish have the potential to accelerate the discovery of new strategies to treat cardiac diseases.
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Affiliation(s)
- Juan Manuel González-Rosa
- Cardiovascular Research Center, Massachusetts General Hospital Research Institute, Harvard Medical School, Charlestown, MA
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15
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Zeng M, Pi C, Li K, Sheng L, Zuo Y, Yuan J, Zou Y, Zhang X, Zhao W, Lee RJ, Wei Y, Zhao L. Patient-Derived Xenograft: A More Standard "Avatar" Model in Preclinical Studies of Gastric Cancer. Front Oncol 2022; 12:898563. [PMID: 35664756 PMCID: PMC9161630 DOI: 10.3389/fonc.2022.898563] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/21/2022] [Indexed: 11/23/2022] Open
Abstract
Despite advances in diagnosis and treatment, gastric cancer remains the third most common cause of cancer-related death in humans. The establishment of relevant animal models of gastric cancer is critical for further research. Due to the complexity of the tumor microenvironment and the genetic heterogeneity of gastric cancer, the commonly used preclinical animal models fail to adequately represent clinically relevant models of gastric cancer. However, patient-derived models are able to replicate as much of the original inter-tumoral and intra-tumoral heterogeneity of gastric cancer as possible, reflecting the cellular interactions of the tumor microenvironment. In addition to implanting patient tissues or primary cells into immunodeficient mouse hosts for culture, the advent of alternative hosts such as humanized mouse hosts, zebrafish hosts, and in vitro culture modalities has also facilitated the advancement of gastric cancer research. This review highlights the current status, characteristics, interfering factors, and applications of patient-derived models that have emerged as more valuable preclinical tools for studying the progression and metastasis of gastric cancer.
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Affiliation(s)
- Mingtang Zeng
- Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China.,Central Nervous System Drug Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Chao Pi
- Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China.,Central Nervous System Drug Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Ke Li
- Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China.,Central Nervous System Drug Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Lin Sheng
- Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China.,Central Nervous System Drug Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Ying Zuo
- Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China.,Department of Comprehensive Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Jiyuan Yuan
- Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China.,Clinical Trial Center, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Yonggen Zou
- Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China.,Department of Spinal Surgery, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Xiaomei Zhang
- Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, Institute of Medicinal Chemistry of Chinese Medicine, Chongqing Academy of Chinese MateriaMedica, Chongqing, China
| | - Wenmei Zhao
- Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, China.,Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China.,Central Nervous System Drug Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Robert J Lee
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, OH, United States
| | - Yumeng Wei
- Key Laboratory of Medical Electrophysiology, Ministry of Education, School of Pharmacy of Southwest Medical University, Luzhou, China.,Central Nervous System Drug Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China
| | - Ling Zhao
- Luzhou Key Laboratory of Traditional Chinese Medicine for Chronic Diseases Jointly Built by Sichuan and Chongqing, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China.,Central Nervous System Drug Key Laboratory of Sichuan Province, Southwest Medical University, Luzhou, China
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Otterstrom JJ, Lubin A, Payne EM, Paran Y. Technologies bringing young Zebrafish from a niche field to the limelight. SLAS Technol 2022; 27:109-120. [PMID: 35058207 DOI: 10.1016/j.slast.2021.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fundamental life science and pharmaceutical research are continually striving to provide physiologically relevant context for their biological studies. Zebrafish present an opportunity for high-content screening (HCS) to bring a true in vivo model system to screening studies. Zebrafish embryos and young larvae are an economical, human-relevant model organism that are amenable to both genetic engineering and modification, and direct inspection via microscopy. The use of these organisms entails unique challenges that new technologies are overcoming, including artificial intelligence (AI). In this perspective article, we describe the state-of-the-art in terms of automated sample handling, imaging, and data analysis with zebrafish during early developmental stages. We highlight advances in orienting the embryos, including the use of robots, microfluidics, and creative multi-well plate solutions. Analyzing the micrographs in a fast, reliable fashion that maintains the anatomical context of the fluorescently labeled cells is a crucial step. Existing software solutions range from AI-driven commercial solutions to bespoke analysis algorithms. Deep learning appears to be a critical tool that researchers are only beginning to apply, but already facilitates many automated steps in the experimental workflow. Currently, such work has permitted the cellular quantification of multiple cell types in vivo, including stem cell responses to stress and drugs, neuronal myelination and macrophage behavior during inflammation and infection. We evaluate pro and cons of proprietary versus open-source methodologies for combining technologies into fully automated workflows of zebrafish studies. Zebrafish are poised to charge into HCS with ever-greater presence, bringing a new level of physiological context.
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Affiliation(s)
| | - Alexandra Lubin
- Research Department of Hematology, Cancer Institute, University College London, London, UK
| | - Elspeth M Payne
- Research Department of Hematology, Cancer Institute, University College London, London, UK
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First person – Alexandra Lubin. Biol Open 2021. [DOI: 10.1242/bio.058924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ABSTRACT
First Person is a series of interviews with the first authors of a selection of papers published in Biology Open, helping early-career researchers promote themselves alongside their papers. Alexandra Lubin is first author on ‘ A versatile, automated and high-throughput drug screening platform for zebrafish embryos’, published in BiO. Alexandra is a postdoctoral research associate in the lab of Elspeth Payne at University College London (UCL), London, UK, investigating high-throughput automated drug screening in live zebrafish to discover novel therapeutics for myelodysplastic syndrome (MDS) and acute myeloid leukaemia (AML).
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