201
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Amorim RR, Silva PF, Luchiari AC. Effects of Alcohol on Inhibitory Avoidance Learning in Zebrafish (Danio rerio). Zebrafish 2017; 14:430-437. [DOI: 10.1089/zeb.2017.1438] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | - Ana Carolina Luchiari
- Departamento de Fisiologia, Universidade Federal do Rio Grande do Norte, Natal, Brazil
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202
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Aksoy I, Utami KH, Winata CL, Hillmer AM, Rouam SL, Briault S, Davila S, Stanton LW, Cacheux V. Personalized genome sequencing coupled with iPSC technology identifies GTDC1 as a gene involved in neurodevelopmental disorders. Hum Mol Genet 2017; 26:367-382. [PMID: 28365779 DOI: 10.1093/hmg/ddw393] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 11/11/2016] [Indexed: 01/22/2023] Open
Abstract
The cellular and molecular mechanisms underlying neurodevelopmental conditions such as autism spectrum disorders have been studied intensively for decades. The ability to generate patient-specific induced pluripotent stem cells (iPSCs) now offers a novel strategy for modelling human diseases. Recent studies have reported the derivation of iPSCs from patients with neurological disorders. The key challenge remains the demonstration of disease-related phenotypes and the ability to model the disease. Here we report a case study with signs of neurodevelopmental disorders (NDDs) harbouring chromosomal rearrangements that were sequenced using long-insert DNA paired-end tag (DNA-PET) sequencing approach. We identified the disruption of a specific gene, GTDC1. By deriving iPSCs from this patient and differentiating them into neural progenitor cells (NPCs) and neurons we dissected the disease process at the cellular level and observed defects in both NPCs and neuronal cells. We also showed that disruption of GTDC1 expression in wild type human NPCs and neurons showed a similar phenotype as patient's iPSCs. Finally, we utilized a zebrafish model to demonstrate a role for GTDC1 in the development of the central nervous system. Our findings highlight the importance of combining sequencing technologies with the iPSC technology for NDDs modelling that could be applied for personalized medicine.
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Affiliation(s)
- Irene Aksoy
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore.,University of Lyon, University Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, 69500 Bron, France
| | - Kagistia H Utami
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore
| | - Cecilia L Winata
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore.,International Institute of Molecular and Cell Biology, Warsaw, Poland.,Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Axel M Hillmer
- Cancer Therapeutics & Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore
| | - Sigrid L Rouam
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore
| | - Sylvain Briault
- Service de Génétique INEM UMR7355 CNRS-University, Centre Hospitalier Régional d'Orléans, Orléans, France
| | - Sonia Davila
- Human Genetics, Genome Institute of Singapore, 60 Biopolis Street, Singapore, Singapore
| | - Lawrence W Stanton
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore.,School of Biological Sciences, Nanyang Technological University, 50 Nanyang Avenue, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Valere Cacheux
- Stem Cell and Regenerative Biology, Genome Institute of Singapore, 60 Biopolis St, Singapore
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203
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Kirchberger S, Sturtzel C, Pascoal S, Distel M. Quo natas, Danio? -Recent Progress in Modeling Cancer in Zebrafish. Front Oncol 2017; 7:186. [PMID: 28894696 PMCID: PMC5581328 DOI: 10.3389/fonc.2017.00186] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/09/2017] [Indexed: 12/30/2022] Open
Abstract
Over the last decade, zebrafish has proven to be a powerful model in cancer research. Zebrafish form tumors that histologically and genetically resemble human cancers. The live imaging and cost-effective compound screening possible with zebrafish especially complement classic mouse cancer models. Here, we report recent progress in the field, including genetically engineered zebrafish cancer models, xenotransplantation of human cancer cells into zebrafish, promising approaches toward live investigation of the tumor microenvironment, and identification of therapeutic strategies by performing compound screens on zebrafish cancer models. Given the recent advances in genome editing, personalized zebrafish cancer models are now a realistic possibility. In addition, ongoing automation will soon allow high-throughput compound screening using zebrafish cancer models to be part of preclinical precision medicine approaches.
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Affiliation(s)
- Stefanie Kirchberger
- St. Anna Kinderkrebsforschung, Children's Cancer Research Institute, Innovative Cancer Models, Vienna, Austria
| | - Caterina Sturtzel
- St. Anna Kinderkrebsforschung, Children's Cancer Research Institute, Innovative Cancer Models, Vienna, Austria
| | - Susana Pascoal
- St. Anna Kinderkrebsforschung, Children's Cancer Research Institute, Innovative Cancer Models, Vienna, Austria
| | - Martin Distel
- St. Anna Kinderkrebsforschung, Children's Cancer Research Institute, Innovative Cancer Models, Vienna, Austria
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204
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Feng Z, Nam S, Hamouri F, Aujard I, Ducos B, Vriz S, Volovitch M, Jullien L, Lin S, Weiss S, Bensimon D. Optical Control of Tumor Induction in the Zebrafish. Sci Rep 2017; 7:9195. [PMID: 28835665 PMCID: PMC5569104 DOI: 10.1038/s41598-017-09697-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/27/2017] [Indexed: 12/15/2022] Open
Abstract
The zebrafish has become an increasingly popular and valuable cancer model over the past few decades. While most zebrafish cancer models are generated by expressing mammalian oncogenes under tissue-specific promoters, here we describe a method that allows for the precise optical control of oncogene expression in live zebrafish. We utilize this technique to transiently or constitutively activate a typical human oncogene, kRASG12V, in zebrafish embryos and investigate the developmental and tumorigenic phenotypes. We demonstrate the spatiotemporal control of oncogene expression in live zebrafish, and characterize the different tumorigenic probabilities when kRASG12V is expressed transiently or constitutively at different developmental stages. Moreover, we show that light can be used to activate oncogene expression in selected tissues and single cells without tissue-specific promoters. Our work presents a novel approach to initiate and study cancer in zebrafish, and the high spatiotemporal resolution of this method makes it a valuable tool for studying cancer initiation from single cells.
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Affiliation(s)
- Zhiping Feng
- Department of Molecular, Cellular and Integrative Physiology, University of California at Los Angeles, Los Angeles, California, USA.
- Department of Chemical and Systems Biology, Stanford University, Stanford, California, USA.
| | - Suzy Nam
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California, USA
| | - Fatima Hamouri
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University, Paris, France
- IBENS, CNRS-UMR8197, INSERM-U1024, PSL Research University, Paris, France
| | - Isabelle Aujard
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, Paris, France
| | - Bertrand Ducos
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University, Paris, France
- IBENS, CNRS-UMR8197, INSERM-U1024, PSL Research University, Paris, France
| | - Sophie Vriz
- Center for Interdisciplinary Research in Biology (CIRB), College de France, and CNRS UMR 7241, and INSERM U1050, Paris, France
- Department of Life Sciences, Paris-Diderot University, Sorbonne-Paris-Cité, Paris, France
| | - Michel Volovitch
- Center for Interdisciplinary Research in Biology (CIRB), College de France, and CNRS UMR 7241, and INSERM U1050, Paris, France
- Department of Biology, Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Ludovic Jullien
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, Paris, France
| | - Shuo Lin
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, California, USA
| | - Shimon Weiss
- Department of Molecular, Cellular and Integrative Physiology, University of California at Los Angeles, Los Angeles, California, USA.
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California, USA.
| | - David Bensimon
- Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University, Paris, France.
- IBENS, CNRS-UMR8197, INSERM-U1024, PSL Research University, Paris, France.
- Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California, USA.
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205
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Brenz Y, Winther-Larsen HC, Hagedorn M. Expanding Francisella models: Pairing up the soil amoeba Dictyostelium with aquatic Francisella. Int J Med Microbiol 2017; 308:32-40. [PMID: 28843671 DOI: 10.1016/j.ijmm.2017.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/31/2017] [Accepted: 08/04/2017] [Indexed: 12/19/2022] Open
Abstract
The bacterial genus Francisella comprises highly pathogenic species that infect mammals, arthropods, fish and protists. Understanding virulence and host defense mechanisms of Francisella infection relies on multiple animal and cellular model systems. In this review, we want to summarize the most commonly used Francisella host model platforms and highlight novel, alternative model systems using aquatic Francisella species. Established mouse and macrophage models contributed extensively to our understanding of Francisella infection. However, murine and human cells display significant differences in their response to Francisella infection. The zebrafish and the amoeba Dictyostelium are well-established model systems for host-pathogen interactions and open up opportunities to investigate bacterial virulence and host defense. Comparisons between model systems using human and fish pathogenic Francisella species revealed shared virulence strategies and pathology between them. Hence, zebrafish and Dictyostelium might complement current model systems to find new vaccine candidates and contribute to our understanding of Francisella infection.
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Affiliation(s)
- Yannick Brenz
- Department of Parasitology, Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Straße 74, 20359 Hamburg, Germany.
| | - Hanne C Winther-Larsen
- Centre for Integrative Microbial Evolution (CIME) and Department of Pharmaceutical Biosciences, University of Oslo, Sem Sælands vei 3, 0371 Oslo, Norway.
| | - Monica Hagedorn
- Department of Life Sciences and Chemistry, Jacobs University, Campus Ring 1, 28759 Bremen, Germany.
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206
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van Rooijen E, Fazio M, Zon LI. From fish bowl to bedside: The power of zebrafish to unravel melanoma pathogenesis and discover new therapeutics. Pigment Cell Melanoma Res 2017; 30:402-412. [PMID: 28379616 PMCID: PMC6038924 DOI: 10.1111/pcmr.12592] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/22/2017] [Indexed: 12/28/2022]
Abstract
Melanoma is the most aggressive and deadliest form of skin cancer. A detailed knowledge of the cellular, molecular, and genetic events underlying melanoma progression is highly relevant to diagnosis, prognosis and risk stratification, and the development of new therapies. In the last decade, zebrafish have emerged as a valuable model system for the study of melanoma. Pathway conservation, coupled with the availability of robust genetic, transgenic, and chemical tools, has made the zebrafish a powerful model for identifying novel disease genes, visualizing cancer initiation, interrogating tumor-microenvironment interactions, and discovering new therapeutics that regulate melanocyte and melanoma development. In this review, we will give an overview of these studies, and highlight recent advancements that will help unravel melanoma pathogenesis and impact human disease.
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Affiliation(s)
- Ellen van Rooijen
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Maurizio Fazio
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
- PhD program in Biological and Biomedical Sciences, Harvard University, Boston, MA, USA
| | - Leonard I. Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana Farber Cancer Institute, Howard Hughes Medical Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
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207
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Sugano Y, Cianciolo Cosentino C, Loffing-Cueni D, Neuhauss SCF, Loffing J. Comparative transcriptomic analysis identifies evolutionarily conserved gene products in the vertebrate renal distal convoluted tubule. Pflugers Arch 2017; 469:859-867. [PMID: 28656378 DOI: 10.1007/s00424-017-2009-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/29/2017] [Accepted: 05/31/2017] [Indexed: 12/11/2022]
Abstract
Understanding the molecular basis of the complex regulatory networks controlling renal ion transports is of major physiological and clinical importance. In this study, we aimed to identify evolutionarily conserved critical players in the function of the renal distal convoluted tubule (DCT) by a comparative transcriptomic approach. We generated a transgenic zebrafish line with expression of the red fluorescent mCherry protein under the control of the zebrafish DCT-specific promoter of the thiazide-sensitive NaCl cotransporter (NCC). The mCherry expression was then used to isolate from the zebrafish mesonephric kidneys the distal late (DL) segments, the equivalent of the mammalian DCT, for subsequent RNA-seq analysis. We next compared this zebrafish DL transcriptome to the previously established mouse DCT transcriptome and identified a subset of gene products significantly enriched in both the teleost DL and the mammalian DCT, including SLCs and nuclear transcription factors. Surprisingly, several of the previously described regulators of NCC (e.g., SPAK, KLHL3, ppp1r1a) in the mouse were not found enriched in the zebrafish DL. Nevertheless, the zebrafish DL expressed enriched levels of related homologues. Functional knockdown of one of these genes, ppp1r1b, reduced the phosphorylation of NCC in the zebrafish pronephros, similar to what was seen previously in knockout mice for its homologue, Ppp1r1a. The present work is the first report on global gene expression profiling in a specific nephron portion of the zebrafish kidney, an increasingly used model system for kidney research. Our study suggests that comparative analysis of gene expression between phylogenetically distant species may be an effective approach to identify novel regulators of renal function.
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Affiliation(s)
- Yuya Sugano
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Chiara Cianciolo Cosentino
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Dominique Loffing-Cueni
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Stephan C F Neuhauss
- Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Johannes Loffing
- Institute of Anatomy, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
- Swiss National Center of Competence in Research "Kidney.CH", Zurich, Switzerland.
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208
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Cho SJ, Byun D, Nam TS, Choi SY, Lee BG, Kim MK, Kim S. Zebrafish as an animal model in epilepsy studies with multichannel EEG recordings. Sci Rep 2017; 7:3099. [PMID: 28596539 PMCID: PMC5465065 DOI: 10.1038/s41598-017-03482-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/28/2017] [Indexed: 12/31/2022] Open
Abstract
Despite recent interest in using zebrafish in human disease studies, sparked by their economics, fecundity, easy handling, and homologies to humans, the electrophysiological tools or methods for zebrafish are still inaccessible. Although zebrafish exhibit more significant larval–adult duality than any other animal, most electrophysiological studies using zebrafish are biased by using larvae these days. The results of larval studies not only differ from those conducted with adults but also are unable to delicately manage electroencephalographic montages due to their small size. Hence, we enabled non-invasive long-term multichannel electroencephalographic recording on adult zebrafish using custom-designed electrodes and perfusion system. First, we exploited demonstration of long-term recording on pentylenetetrazole-induced seizure models, and the results were quantified. Second, we studied skin–electrode impedance, which is crucial to the quality of signals. Then, seizure propagations and gender differences in adult zebrafish were exhibited for the first time. Our results provide a new pathway for future neuroscience research using zebrafish by overcoming the challenges for aquatic organisms such as precision, serviceability, and continuous water seepage.
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Affiliation(s)
- Sung-Joon Cho
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Donghak Byun
- School of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Tai-Seung Nam
- Department of Neurology, Chonnam National University Medical School, Gwangju, 61469, Republic of Korea
| | - Seok-Yong Choi
- Department of Biomedical Sciences, Chonnam National University Medical School, Gwangju, 61469, Republic of Korea
| | - Byung-Geun Lee
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Myeong-Kyu Kim
- Department of Neurology, Chonnam National University Medical School, Gwangju, 61469, Republic of Korea
| | - Sohee Kim
- Department of Robotics Engineering, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea.
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209
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Genome editing of factor X in zebrafish reveals unexpected tolerance of severe defects in the common pathway. Blood 2017; 130:666-676. [PMID: 28576875 DOI: 10.1182/blood-2017-02-765206] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/23/2017] [Indexed: 12/24/2022] Open
Abstract
Deficiency of factor X (F10) in humans is a rare bleeding disorder with a heterogeneous phenotype and limited therapeutic options. Targeted disruption of F10 and other common pathway factors in mice results in embryonic/neonatal lethality with rapid resorption of homozygous mutants, hampering additional studies. Several of these mutants also display yolk sac vascular defects, suggesting a role for thrombin signaling in vessel development. The zebrafish is a vertebrate model that demonstrates conservation of the mammalian hemostatic and vascular systems. We have leveraged these advantages for in-depth study of the role of the coagulation cascade in the developmental regulation of hemostasis and vasculogenesis. In this article, we show that ablation of zebrafish f10 by using genome editing with transcription activator-like effector nucleases results in a major embryonic hemostatic defect. However, widespread hemorrhage and subsequent lethality does not occur until later stages, with absence of any detectable defect in vascular development. We also use f10-/- zebrafish to confirm 5 novel human F10 variants as causative mutations in affected patients, providing a rapid and reliable in vivo model for testing the severity of F10 variants. These findings as well as the prolonged survival of f10-/- mutants will enable us to expand our understanding of the molecular mechanisms of hemostasis, including a platform for screening variants of uncertain significance in patients with F10 deficiency and other coagulation disorders. Further study as to how fish tolerate what is an early lethal mutation in mammals could facilitate improvement of diagnostics and therapeutics for affected patients with bleeding disorders.
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210
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Lutfi E, Babin PJ, Gutiérrez J, Capilla E, Navarro I. Caffeic acid and hydroxytyrosol have anti-obesogenic properties in zebrafish and rainbow trout models. PLoS One 2017; 12:e0178833. [PMID: 28570659 PMCID: PMC5453583 DOI: 10.1371/journal.pone.0178833] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 05/19/2017] [Indexed: 12/18/2022] Open
Abstract
Some natural products, known sources of bioactive compounds with a wide range of properties, may have therapeutic values in human health and diseases, as well as agronomic applications. The effect of three compounds of plant origin with well-known dietary antioxidant properties, astaxanthin (ATX), caffeic acid (CA) and hydroxytyrosol (HT), on zebrafish (Danio rerio) larval adiposity and rainbow trout (Onchorynchus mykiss) adipocytes was assessed. The zebrafish obesogenic test (ZOT) demonstrated the anti-obesogenic activity of CA and HT. These compounds were able to counteract the obesogenic effect produced by the peroxisome proliferator-activated receptor gamma (PPARγ) agonist, rosiglitazone (RGZ). CA and HT suppressed RGZ-increased PPARγ protein expression and lipid accumulation in primary-cultured rainbow trout adipocytes. HT also significantly reduced plasma triacylglycerol concentrations, as well as mRNA levels of the fasn adipogenic gene in the adipose tissue of HT-injected rainbow trout. In conclusion, in vitro and in vivo approaches demonstrated the anti-obesogenic potential of CA and HT on teleost fish models that may be relevant for studying their molecular mode of action. Further studies are required to evaluate the effect of these bioactive components as food supplements for modulating adiposity in farmed fish.
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Affiliation(s)
- Esmail Lutfi
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Patrick J. Babin
- Maladies Rares: Génétique et Métabolisme (MRGM), University of Bordeaux, INSERM, U12211, Pessac, France
- * E-mail: (IN); (PJB)
| | - Joaquim Gutiérrez
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Encarnación Capilla
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Isabel Navarro
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
- * E-mail: (IN); (PJB)
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211
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Oltrabella F, Melgoza A, Nguyen B, Guo S. Role of the endocannabinoid system in vertebrates: Emphasis on the zebrafish model. Dev Growth Differ 2017; 59:194-210. [PMID: 28516445 DOI: 10.1111/dgd.12351] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 03/18/2017] [Accepted: 03/24/2017] [Indexed: 12/15/2022]
Abstract
The endocannabinoid system (eCBs), named after the plant Cannabis sativa, comprises cannabinoid receptors, endogenous ligands known as "endocannabinoids", and enzymes involved in the biosynthesis and degradation of these ligands, as well as putative transporters for these ligands. ECBs proteins and small molecules have been detected in early embryonic stages of many vertebrate models. As a result, cannabinoid receptors and endogenous as well as exogenous cannabinoids influence development and behavior in many vertebrate species. Understanding the precise mechanisms of action for the eCBs will provide an invaluable guide towards elucidation of vertebrate development and will also help delineate how developmental exposure to marijuana might impact health and cognitive/executive functioning in adulthood. Here we review the developmental roles of the eCBs in vertebrates, focusing our attention on the zebrafish model. Since little is known regarding the eCBs in zebrafish, we provide new data on the expression profiles of eCBs genes during development and in adult tissue types of this model organism. We also highlight exciting areas for future investigations, including the synaptic regulation of eCBs, its role in reward and addiction, and in nervous system development and plasticity.
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Affiliation(s)
- Francesca Oltrabella
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, 94158-2811, USA
| | - Adam Melgoza
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, 94158-2811, USA.,Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, California, 94158-2811, USA
| | - Brian Nguyen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, 94158-2811, USA.,Department of Nutritional Sciences and Toxicology, University of California, Berkeley, California, 94720-3104, USA
| | - Su Guo
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, 94158-2811, USA.,Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, California, 94158-2811, USA.,Institute for Human Genetics, University of California, San Francisco, California, 94158-2811, USA
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212
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Pham DH, Zhang C, Yin C. Using zebrafish to model liver diseases-Where do we stand? CURRENT PATHOBIOLOGY REPORTS 2017; 5:207-221. [PMID: 29098121 DOI: 10.1007/s40139-017-0141-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Purpose of Review The liver is the largest internal organ and performs both exocrine and endocrine function that is necessary for survival. Liver failure is among the leading causes of death and represents a major global health burden. Liver transplantation is the only effective treatment for end-stage liver diseases. Animal models advance our understanding of liver disease etiology and hold promise for the development of alternative therapies. Zebrafish has become an increasingly popular system for modeling liver diseases and complements the rodent models. Recent Findings The zebrafish liver contains main cell types that are found in mammalian liver and exhibits similar pathogenic responses to environmental insults and genetic mutations. Zebrafish have been used to model neonatal cholestasis, cholangiopathies, such as polycystic liver disease, alcoholic liver disease, and non-alcoholic fatty liver disease. It also provides a unique opportunity to study the plasticity of liver parenchymal cells during regeneration. Summary In this review, we summarize the recent work of building zebrafish models of liver diseases. We highlight how these studies have brought new knowledge of disease mechanisms. We also discuss the advantages and challenges of using zebrafish to model liver diseases.
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Affiliation(s)
- Duc-Hung Pham
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Changwen Zhang
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
| | - Chunyue Yin
- Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, 45229, USA
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213
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Fukui H, Chiba A, Miyazaki T, Takano H, Ishikawa H, Omori T, Mochiuzki N. Spatial Allocation and Specification of Cardiomyocytes during Zebrafish Embryogenesis. Korean Circ J 2017; 47:160-167. [PMID: 28382067 PMCID: PMC5378018 DOI: 10.4070/kcj.2016.0280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/05/2016] [Accepted: 10/13/2016] [Indexed: 12/21/2022] Open
Abstract
Incomplete development and severe malformation of the heart result in miscarriage of embryos because of its malfunction as a pump for circulation. During cardiogenesis, development of the heart is precisely coordinated by the genetically-primed program that is revealed by the sequential expression of transcription factors. It is important to investigate how spatial allocation of the heart containing cardiomyocytes and other mesoderm-derived cells is determined. In addition, the molecular mechanism underlying cardiomyocyte differentiation still remains elusive. The location of ectoderm-, mesoderm-, and endoderm-derived organs is determined by their initial allocation and subsequent mutual cell-cell interactions or paracrine-based regulation. In the present work, we provide an overview of cardiac development controlled by the germ layers and discuss the points that should be uncovered in future for understanding cardiogenesis.
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Affiliation(s)
- Hajime Fukui
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Ayano Chiba
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Takahiro Miyazaki
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Haruko Takano
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Hiroyuki Ishikawa
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
| | - Toyonori Omori
- Management office, National Center for Child Health and Development, Tokyo, Japan
| | - Naoki Mochiuzki
- Department of Cell Biology, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan.; AMED-CREST, National Cerebral and Cardiovascular Center Research Institute, Osaka, Japan
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Lee IJ, Yang YC, Hsu JW, Chang WT, Chuang YJ, Liau I. Zebrafish model of photochemical thrombosis for translational research and thrombolytic screening in vivo. JOURNAL OF BIOPHOTONICS 2017; 10:494-502. [PMID: 27174426 DOI: 10.1002/jbio.201500287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/22/2016] [Accepted: 04/22/2016] [Indexed: 06/05/2023]
Abstract
Acute thromboembolic diseases remain the major global cause of death or disability. Although an array of thrombolytic and antithrombotic drugs has been approved to treat or prevent thromboembolic diseases, many more drugs that target specific clotting mechanisms are under development. Here a novel zebrafish model of photochemical thrombosis is reported and its prospective application for the screening and preclinical testing of thrombolytic agents in vivo is demonstrated. Through photochemical excitation, a thrombus was induced to form at a selected section of the dorsal aorta of larval zebrafish, which had been injected with photosensitizers. Such photochemical thrombosis can be consistently controlled to occlude partially or completely the targeted blood vessel. Detailed mechanistic tests indicate that the zebrafish model of photochemical thrombosis exhibits essential features of classical coagulation and a thrombolytic pathway. For demonstration, tissue plasminogen activator (tPA), a clinically feasible thrombolytic agent, was shown to effectively dissolve photochemically induced blood clots. In light of the numerous unique advantages of zebrafish as a model organism, our approach is expected to benefit not only the development of novel thrombolytic and antithrombotic strategies but also the fundamental or translational research targeting hereditary thrombotic or coagulation disorders.
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Affiliation(s)
- I-Ju Lee
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yi-Cyun Yang
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Jia-Wen Hsu
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Tien Chang
- Department of Emergency Medicine and Cardiovascular Center, National Taiwan University Hospital and College of Medicine, Taipei, 100, Taiwan
| | - Yung-Jen Chuang
- Department of Medical Science and Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Ian Liau
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, Hsinchu, 300, Taiwan
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215
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Schenk H, Müller-Deile J, Kinast M, Schiffer M. Disease modeling in genetic kidney diseases: zebrafish. Cell Tissue Res 2017; 369:127-141. [PMID: 28331970 DOI: 10.1007/s00441-017-2593-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/22/2017] [Indexed: 01/07/2023]
Abstract
Growing numbers of translational genomics studies are based on the highly efficient and versatile zebrafish (Danio rerio) vertebrate model. The increasing types of zebrafish models have improved our understanding of inherited kidney diseases, since they not only display pathophysiological changes but also give us the opportunity to develop and test novel treatment options in a high-throughput manner. New paradigms in inherited kidney diseases have been developed on the basis of the distinct genome conservation of approximately 70 % between zebrafish and humans in terms of existing gene orthologs. Several options are available to determine the functional role of a specific gene or gene sets. Permanent genome editing can be induced via complete gene knockout by using the CRISPR/Cas-system, among others, or via transient modification by using various morpholino techniques. Cross-species rescues succeeding knockdown techniques are employed to determine the functional significance of a target gene or a specific mutation. This article summarizes the current techniques and discusses their perspectives.
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Affiliation(s)
- Heiko Schenk
- Department of Medicine/Nephrology, Hannover Medical School, Hannover, Germany
- Mount Desert Island Biological Laboratory, Salisbury Cove, Bar Harbor, Me., USA
| | - Janina Müller-Deile
- Department of Medicine/Nephrology, Hannover Medical School, Hannover, Germany
- Mount Desert Island Biological Laboratory, Salisbury Cove, Bar Harbor, Me., USA
| | - Mark Kinast
- Department of Medicine/Nephrology, Hannover Medical School, Hannover, Germany
- Mount Desert Island Biological Laboratory, Salisbury Cove, Bar Harbor, Me., USA
| | - Mario Schiffer
- Department of Medicine/Nephrology, Hannover Medical School, Hannover, Germany.
- Mount Desert Island Biological Laboratory, Salisbury Cove, Bar Harbor, Me., USA.
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216
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Modelling viral infections using zebrafish: Innate immune response and antiviral research. Antiviral Res 2017; 139:59-68. [DOI: 10.1016/j.antiviral.2016.12.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/21/2016] [Indexed: 12/20/2022]
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217
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Forn-Cuní G, Varela M, Pereiro P, Novoa B, Figueras A. Conserved gene regulation during acute inflammation between zebrafish and mammals. Sci Rep 2017; 7:41905. [PMID: 28157230 PMCID: PMC5291205 DOI: 10.1038/srep41905] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 01/03/2017] [Indexed: 11/09/2022] Open
Abstract
Zebrafish (Danio rerio), largely used as a model for studying developmental processes, has also emerged as a valuable system for modelling human inflammatory diseases. However, in a context where even mice have been questioned as a valid model for these analysis, a systematic study evaluating the reproducibility of human and mammalian inflammatory diseases in zebrafish is still lacking. In this report, we characterize the transcriptomic regulation to lipopolysaccharide in adult zebrafish kidney, liver, and muscle tissues using microarrays and demonstrate how the zebrafish genomic responses can effectively reproduce the mammalian inflammatory process induced by acute endotoxin stress. We provide evidence that immune signaling pathways and single gene expression is well conserved throughout evolution and that the zebrafish and mammal acute genomic responses after lipopolysaccharide stimulation are highly correlated despite the differential susceptibility between species to that compound. Therefore, we formally confirm that zebrafish inflammatory models are suited to study the basic mechanisms of inflammation in human inflammatory diseases, with great translational impact potential.
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Affiliation(s)
- G Forn-Cuní
- Inmunología y Genómica, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), c/Eduardo Cabello, 6, 36208, Vigo, Spain
| | - M Varela
- Inmunología y Genómica, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), c/Eduardo Cabello, 6, 36208, Vigo, Spain
| | - P Pereiro
- Inmunología y Genómica, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), c/Eduardo Cabello, 6, 36208, Vigo, Spain
| | - B Novoa
- Inmunología y Genómica, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), c/Eduardo Cabello, 6, 36208, Vigo, Spain
| | - A Figueras
- Inmunología y Genómica, Institute of Marine Research (IIM), Spanish National Research Council (CSIC), c/Eduardo Cabello, 6, 36208, Vigo, Spain
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218
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Rey S, Moiche V, Boltaña S, Teles M, MacKenzie S. Behavioural fever in zebrafish larvae. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 67:287-292. [PMID: 27670815 DOI: 10.1016/j.dci.2016.09.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/15/2016] [Accepted: 09/15/2016] [Indexed: 06/06/2023]
Abstract
Behavioural fever has been reported in different species of mobile ectotherms including the zebrafish, Danio rerio, in response to exogenous pyrogens. In this study we report, to our knowledge for the first time, upon the ontogenic onset of behavioural fever in zebrafish (Danio rerio) larvae. For this, zebrafish larvae (from first feeding to juveniles) were placed in a continuous thermal gradient providing the opportunity to select their preferred temperature. The novel thermal preference aquarium was based upon a continuous vertical column system and allows for non-invasive observation of larvae vertical distribution under isothermal (TR at 28 °C) and thermal gradient conditions (TCH: 28-32 °C). Larval thermal preference was assessed under both conditions with or without an immersion challenge, in order to detect the onset of the behavioural fever response. Our results defined the onset of the dsRNA induced behavioural fever at 18-20 days post fertilization (dpf). Significant differences were observed in dsRNA challenged larvae, which prefer higher temperatures (1-4 °C increase) throughout the experimental period as compared to non-challenged larvae. In parallel we measured the abundance of antiviral transcripts; viperin, gig2, irf7, trim25 and Mxb mRNAs in dsRNA challenged larvae under both thermal regimes: TR and TCh. Significant increases in the abundance of all measured transcripts were recorded under thermal choice conditions signifying that thermo-coupling and the resultant enhancement of the immune response to dsRNA challenge occurs from 18 dpf onwards in the zebrafish. The results are of importance as they identify a key developmental stage where the neuro-immune interface matures in the zebrafish likely providing increased resistance to viral infection.
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Affiliation(s)
- Sonia Rey
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Visila Moiche
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Sebastian Boltaña
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Mariana Teles
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain
| | - Simon MacKenzie
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, 08193 Bellaterra, Spain.
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Abstract
Animal models have been an invaluable means to advance biomedical research as they provide experimental avenues for cellular and molecular investigations of disease pathology. The zebrafish (Danio rerio) is a good alternative to mammalian models that can be used to apply powerful genetic experimental methods normally used in invertebrates to answer questions about vertebrate development and disease. In the case of the kidney, the zebrafish has proven itself to be an applicable and versatile experimental system, mainly due to the simplicity of its pronephros, which contains two nephrons that possess conserved structural and physiological aspects with mammalian nephrons. Numerous genes that were not previously related to kidney conditions have now been linked to renal diseases by applying genetic screening with the zebrafish. In fact, a large collection of mutations that affect nephron formation and function were generated through phenotype-based forward screens. Complementary reverse genetic approaches have also been insightful, with methods spanning the use of antisense morpholino oligonucleotides to genome editing approaches such as the CRISPR/Cas9 system, to selectively knock down or knock out genes of interest to see if they produce kidney phenotypes. Acute kidney injury (AKI) has also been easily modeled in the zebrafish by injecting nephrotoxins, directly inducing damage through surgical intervention, or by generating transgenic lines that express compounds in a tissue-specific manner that when exposed to certain drugs promote an apoptotic response within cells. In this chapter, we provide an overview of these various approaches as well as discuss many of the contributions that have been achieved through the use of zebrafish to model kidney disease.
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220
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Garg R, Ko GM, Smith CJ. QSAR molecular parameters calculated for US EPA ToxCast Phase 1 and 2 chemical compounds tested against embryonic zebrafish. TOXICOLOGY RESEARCH AND APPLICATION 2017. [DOI: 10.1177/2397847317707371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Freshwater and marine environments are exposed to small concentrations of many different chemicals produced by industrial, agricultural, pharmaceutical, cosmetic, food, and household applications. Due to concerns regarding potential adverse events from these exposures, regulatory agencies around the world have established aquatic toxicology testing protocols that measure untoward responses in a wide variety of freshwater and marine organisms. Following a literature review of databases on the toxicity of chemicals to fish, the embryonic zebrafish ( Danio rerio) database compiled by the Tanguay Laboratory at Oregon State University was determined to be well suited for quantitative structure–activity relationship (QSAR) analysis. This database possesses a number of favorable characteristics including large size (1060 unique US Environmental Protection Agency ToxCast phase 1 and 2 chemical compounds), relatively recent data collected using state-of-the-art methods, 18 simultaneously measured toxicological end points, transparent embryos that develop externally thereby facilitating toxicological evaluation, and the vast majority of the genetic code is expressed and active during early life stages. The molecular parameters calculated for each of the chemicals in the database include the logarithm of the octanol–water partition coefficient, molar volume, and molar refractivity. For each chemical, the availability of these molecular parameter values can facilitate future QSAR studies using any of the 18 different toxicological end points measured as the biological activity of interest.
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Affiliation(s)
- Rajni Garg
- Computational Science Research Center, San Diego State University, San Diego, CA, USA
| | - Gene M Ko
- Electromagnetic Systems Group, General Atomics, San Diego, CA, USA
| | - Carr J Smith
- Department of Nurse Anesthesia, Florida State University, Panama City, FL, USA
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221
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Animal Models in Glioblastoma: Use in Biology and Developing Therapeutic Strategies. ADVANCES IN BIOLOGY AND TREATMENT OF GLIOBLASTOMA 2017. [DOI: 10.1007/978-3-319-56820-1_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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222
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Abstract
Skeletal muscle performs an essential function in human physiology with defects in genes encoding a variety of cellular components resulting in various types of inherited muscle disorders. Muscular dystrophies (MDs) are a severe and heterogeneous type of human muscle disease, manifested by progressive muscle wasting and degeneration. The disease pathogenesis and therapeutic options for MDs have been investigated for decades using rodent models, and considerable knowledge has been accumulated on the cause and pathogenetic mechanisms of this group of human disorders. However, due to some differences between disease severity and progression, what is learned in mammalian models does not always transfer to humans, prompting the desire for additional and alternative models. More recently, zebrafish have emerged as a novel and robust animal model for the study of human muscle disease. Zebrafish MD models possess a number of distinct advantages for modeling human muscle disorders, including the availability and ease of generating mutations in homologous disease-causing genes, the ability to image living muscle tissue in an intact animal, and the suitability of zebrafish larvae for large-scale chemical screens. In this chapter, we review the current understanding of molecular and cellular mechanisms involved in MDs, the process of myogenesis in zebrafish, and the structural and functional characteristics of zebrafish larval muscles. We further discuss the insights gained from the key zebrafish MD models that have been so far generated, and we summarize the attempts that have been made to screen for small molecules inhibitors of the dystrophic phenotypes using these models. Overall, these studies demonstrate that zebrafish is a useful in vivo system for modeling aspects of human skeletal muscle disorders. Studies using these models have contributed both to the understanding of the pathogenesis of muscle wasting disorders and demonstrated their utility as highly relevant models to implement therapeutic screening regimens.
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Affiliation(s)
- M Li
- Monash University, Clayton, VIC, Australia
| | - K J Hromowyk
- The Ohio State University, Columbus, OH, United States
| | - S L Amacher
- The Ohio State University, Columbus, OH, United States
| | - P D Currie
- Monash University, Clayton, VIC, Australia
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223
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Punwani D, Zhang Y, Yu J, Cowan MJ, Rana S, Kwan A, Adhikari AN, Lizama CO, Mendelsohn BA, Fahl SP, Chellappan A, Srinivasan R, Brenner SE, Wiest DL, Puck JM. Multisystem Anomalies in Severe Combined Immunodeficiency with Mutant BCL11B. N Engl J Med 2016; 375:2165-2176. [PMID: 27959755 PMCID: PMC5215776 DOI: 10.1056/nejmoa1509164] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND Severe combined immunodeficiency (SCID) is characterized by arrested T-lymphocyte production and by B-lymphocyte dysfunction, which result in life-threatening infections. Early diagnosis of SCID through population-based screening of newborns can aid clinical management and help improve outcomes; it also permits the identification of previously unknown factors that are essential for lymphocyte development in humans. METHODS SCID was detected in a newborn before the onset of infections by means of screening of T-cell-receptor excision circles, a biomarker for thymic output. On confirmation of the condition, the affected infant was treated with allogeneic hematopoietic stem-cell transplantation. Exome sequencing in the patient and parents was followed by functional analysis of a prioritized candidate gene with the use of human hematopoietic stem cells and zebrafish embryos. RESULTS The infant had "leaky" SCID (i.e., a form of SCID in which a minimal degree of immune function is preserved), as well as craniofacial and dermal abnormalities and the absence of a corpus callosum; his immune deficit was fully corrected by hematopoietic stem-cell transplantation. Exome sequencing revealed a heterozygous de novo missense mutation, p.N441K, in BCL11B. The resulting BCL11B protein had dominant negative activity, which abrogated the ability of wild-type BCL11B to bind DNA, thereby arresting development of the T-cell lineage and disrupting hematopoietic stem-cell migration; this revealed a previously unknown function of BCL11B. The patient's abnormalities, when recapitulated in bcl11ba-deficient zebrafish, were reversed by ectopic expression of functionally intact human BCL11B but not mutant human BCL11B. CONCLUSIONS Newborn screening facilitated the identification and treatment of a previously unknown cause of human SCID. Coupling exome sequencing with an evaluation of candidate genes in human hematopoietic stem cells and in zebrafish revealed that a constitutional BCL11B mutation caused human multisystem anomalies with SCID and also revealed a prethymic role for BCL11B in hematopoietic progenitors. (Funded by the National Institutes of Health and others.).
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Affiliation(s)
- Divya Punwani
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Yong Zhang
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Jason Yu
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Morton J Cowan
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Sadhna Rana
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Antonia Kwan
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Aashish N Adhikari
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Carlos O Lizama
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Bryce A Mendelsohn
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Shawn P Fahl
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Ajithavalli Chellappan
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Rajgopal Srinivasan
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Steven E Brenner
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - David L Wiest
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
| | - Jennifer M Puck
- From the Department of Pediatrics, University of California, San Francisco (UCSF), School of Medicine and UCSF Benioff Children's Hospital (D.P., J.Y., M.J.C., A.K., B.A.M., J.M.P.), and the Cardiovascular Research Institute, UCSF (C.O.L.), San Francisco, and the Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley (A.N.A., S.E.B.) - all in California; the Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia (Y.Z., S.P.F., D.L.W.); and Innovation Labs, Tata Consultancy Services, Telangana, India (S.R., A.C., R.S.)
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Dubińska-Magiera M, Daczewska M, Lewicka A, Migocka-Patrzałek M, Niedbalska-Tarnowska J, Jagla K. Zebrafish: A Model for the Study of Toxicants Affecting Muscle Development and Function. Int J Mol Sci 2016; 17:E1941. [PMID: 27869769 PMCID: PMC5133936 DOI: 10.3390/ijms17111941] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/10/2016] [Accepted: 11/14/2016] [Indexed: 01/08/2023] Open
Abstract
The rapid progress in medicine, agriculture, and allied sciences has enabled the development of a large amount of potentially useful bioactive compounds, such as drugs and pesticides. However, there is another side of this phenomenon, which includes side effects and environmental pollution. To avoid or minimize the uncontrollable consequences of using the newly developed compounds, researchers seek a quick and effective means of their evaluation. In achieving this goal, the zebrafish (Danio rerio) has proven to be a highly useful tool, mostly because of its fast growth and development, as well as the ability to absorb the molecules diluted in water through its skin and gills. In this review, we focus on the reports concerning the application of zebrafish as a model for assessing the impact of toxicants on skeletal muscles, which share many structural and functional similarities among vertebrates, including zebrafish and humans.
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Affiliation(s)
- Magda Dubińska-Magiera
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, 21 Sienkiewicza Street, 50-335 Wroclaw, Poland.
| | - Małgorzata Daczewska
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, 21 Sienkiewicza Street, 50-335 Wroclaw, Poland.
| | - Anna Lewicka
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, 21 Sienkiewicza Street, 50-335 Wroclaw, Poland.
| | - Marta Migocka-Patrzałek
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, 21 Sienkiewicza Street, 50-335 Wroclaw, Poland.
| | - Joanna Niedbalska-Tarnowska
- Department of Animal Developmental Biology, Institute of Experimental Biology, University of Wroclaw, 21 Sienkiewicza Street, 50-335 Wroclaw, Poland.
| | - Krzysztof Jagla
- GReD-Genetics, Reproduction and Development Laboratory, INSERM U1103, CNRS UMR6293, University of Clermont-Auvergne, 28 Place Henri-Dunant, 63000 Clermont-Ferrand, France.
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225
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Felzien LK. Integration of a zebrafish research project into a molecular biology course to support critical thinking and course content goals. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:565-573. [PMID: 27229632 DOI: 10.1002/bmb.20983] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/27/2016] [Accepted: 04/03/2016] [Indexed: 05/24/2023]
Abstract
Engaging undergraduates in research is essential for teaching them to think like scientists, and it has become a desired component of classroom and laboratory instruction. Research projects that span an entire semester expose students to a variety of concepts and techniques and allow students to use experiments to learn scientific principles, understand why specific techniques are applicable, critically analyze varied data, and examine how experimentation leads to acquiring knowledge. To provide an experience with these features, a semester long research project was integrated into a combined lecture and laboratory course, Molecular Biology. The project utilized the zebrafish model to examine gene expression during embryonic development and required students to develop and test hypotheses about the timing of expression of previously uncharacterized genes. The main goals for the project were to provide opportunities for students to develop critical thinking skills required for conducting research and to support the content goals of the course. To determine whether these goals were met, student performance on the steps of the project and related pre-test and post-test questions was examined. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(6):565-573, 2016.
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Affiliation(s)
- Lisa K Felzien
- Biology Department, Rockhurst University, Kansas City, Missouri, 64110
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226
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Shim H, Kim JH, Kim CY, Hwang S, Kim H, Yang S, Lee JE, Lee I. Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource. Nucleic Acids Res 2016; 44:9611-9623. [PMID: 27903883 PMCID: PMC5175370 DOI: 10.1093/nar/gkw897] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 09/23/2016] [Accepted: 09/29/2016] [Indexed: 12/16/2022] Open
Abstract
Whole exome sequencing (WES) accelerates disease gene discovery using rare genetic variants, but further statistical and functional evidence is required to avoid false-discovery. To complement variant-driven disease gene discovery, here we present function-driven disease gene discovery in zebrafish (Danio rerio), a promising human disease model owing to its high anatomical and genomic similarity to humans. To facilitate zebrafish-based function-driven disease gene discovery, we developed a genome-scale co-functional network of zebrafish genes, DanioNet (www.inetbio.org/danionet), which was constructed by Bayesian integration of genomics big data. Rigorous statistical assessment confirmed the high prediction capacity of DanioNet for a wide variety of human diseases. To demonstrate the feasibility of the function-driven disease gene discovery using DanioNet, we predicted genes for ciliopathies and performed experimental validation for eight candidate genes. We also validated the existence of heterozygous rare variants in the candidate genes of individuals with ciliopathies yet not in controls derived from the UK10K consortium, suggesting that these variants are potentially involved in enhancing the risk of ciliopathies. These results showed that an integrated genomics big data for a model animal of diseases can expand our opportunity for harnessing WES data in disease gene discovery.
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Affiliation(s)
- Hongseok Shim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Ji Hyun Kim
- Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea
| | - Chan Yeong Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sohyun Hwang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hyojin Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sunmo Yang
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Ji Eun Lee
- Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul 06351, Korea .,Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
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227
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Chu Y, Zhang L, Zhu X, Zhang Y, Xia B, Hou L, Song R, Li T, Li C, Dong Q, Chen X. Investigation of hemostatic effect of Spleen-invigorating, Qi-replenishing and Blood-arresting Formula on simvastatin-induced zebrafish hemorrhage model. JOURNAL OF TRADITIONAL CHINESE MEDICAL SCIENCES 2016. [DOI: 10.1016/j.jtcms.2016.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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228
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Efficient genome engineering approaches for the short-lived African turquoise killifish. Nat Protoc 2016; 11:2010-2028. [DOI: 10.1038/nprot.2016.103] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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229
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Smidak R, Aradska J, Kirchberger S, Distel M, Sialana FJ, Wackerlig J, Mechtcheriakova D, Lubec G. A detailed proteomic profiling of plasma membrane from zebrafish brain. Proteomics Clin Appl 2016; 10:1264-1268. [PMID: 27459904 DOI: 10.1002/prca.201600081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 06/29/2016] [Accepted: 07/21/2016] [Indexed: 12/11/2022]
Abstract
Zebrafish (Danio rerio) is a well-established model organism in developmental biology and disease modeling. In recent years, an increasing amount of studies used zebrafish to analyze the genetic changes underlying various neurological disorders. The brain plasma membrane proteome represents the major subsets of signaling proteins and promising drug targets, but is often understudied due to traditional experimental difficulties including problems with solubility, detergent removal, or low abundance. Here, we report a comprehensive dataset of the proteins identified in the enriched plasma membrane of the zebrafish brain by applying sequential trypsin/chymotrypsin digestion with multidimensional LC-MS/MS. A total number of 97 017 peptide groups corresponding to 9201 proteins were identified. These were annotated in various molecular functions or neurological disorders. The dataset of the current study provides a useful data source for further utilizing zebrafish in basic and clinical neuroscience.
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Affiliation(s)
- Roman Smidak
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Jana Aradska
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | - Stefanie Kirchberger
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Innovative Cancer Models, Vienna, Austria
| | - Martin Distel
- Children's Cancer Research Institute, St. Anna Kinderkrebsforschung, Innovative Cancer Models, Vienna, Austria
| | | | - Judith Wackerlig
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Diana Mechtcheriakova
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Gert Lubec
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
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230
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Saraceni PR, Romero A, Figueras A, Novoa B. Establishment of Infection Models in Zebrafish Larvae (Danio rerio) to Study the Pathogenesis of Aeromonas hydrophila. Front Microbiol 2016; 7:1219. [PMID: 27540375 PMCID: PMC4972827 DOI: 10.3389/fmicb.2016.01219] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/21/2016] [Indexed: 12/12/2022] Open
Abstract
Aeromonas hydrophila is a Gram-negative opportunistic pathogen of fish and terrestrial animals. In humans, A. hydrophila mainly causes gastroenteritis, septicaemia, and tissue infections. The mechanisms of infection, the main virulence factors and the host immune response triggered by A. hydrophila have been studied in detail using murine models and adult fish. However, the great limitation of studying adult animals is that the animal must be sacrificed and its tissues/organs extracted, which prevents the study of the infectious processes in the whole living animal. Zebrafish larvae are being used for the analysis of several infectious diseases, but their use for studying the pathogenesis of A. hydrophila has never been explored. The great advantage of zebrafish larvae is their transparency during the first week after fertilization, which allows detailed descriptions of the infectious processes using in vivo imaging techniques such as differential interferential contrast (DIC) and fluorescence microscopy. Moreover, the availability of fluorescent pathogens and transgenic reporter zebrafish lines expressing fluorescent immune cells, immune marker genes or cytokines/chemokines allows the host-pathogen interactions to be characterized. The present study explores the suitability of zebrafish larvae to study the pathogenesis of A. hydrophila and the interaction mechanisms between the bacterium and the innate immune responses through an infection model using different routes for infection. We used an early-embryo infection model at 3 days post-fertilization (dpf) through the microinjection of A. hydrophila into the duct of Cuvier, caudal vein, notochord, or muscle and two bath infection models using 4 dpf healthy and injured larvae. The latter resembled the natural conditions under which A. hydrophila produces infectious diseases in animals. We compared the cellular processes after infection in each anatomical site by confocal fluorescence imaging and determined the implication of inflammatory immune genes by measuring gene expression by qPCR.
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Affiliation(s)
| | | | | | - Beatriz Novoa
- Immunology and Genomics, Institute of Marine Research (IIM) – Consejo Superior de Investigaciones Científicas (CSIC), VigoSpain
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231
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Oliveira ACN, Sárria MP, Moreira P, Fernandes J, Castro L, Lopes I, Côrte-Real M, Cavaco-Paulo A, Real Oliveira MECD, Gomes AC. Counter ions and constituents combination affect DODAX : MO nanocarriers toxicity in vitro and in vivo. Toxicol Res (Camb) 2016; 5:1244-1255. [PMID: 30090429 PMCID: PMC6062248 DOI: 10.1039/c6tx00074f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/22/2016] [Indexed: 12/31/2022] Open
Abstract
Liposomes have received extensive attention as nanocarriers for bioactive compounds due to their good biocompatibility, possibility of targeting and incorporation of hydrophilic and hydrophobic compounds. Although generally considered as safe, detailed knowledge of the effects induced in cells and tissues with which they interact is still underexplored. The aim of this study is to gain insight into the toxicity profile of dioctadecyldimethylammonium (DODAX) : monoolein(MO) liposomes (X is bromide or chloride), previously validated for gene therapy, by evaluating the effect of the counter ions Br- or Cl-, and of the cationic : neutral lipid molar fraction, both in vitro and in vivo. Effects on cellular metabolism and proliferation, plasma membrane integrity, oxidative stress, mitochondrial membrane potential dysfunction and ability to trigger apoptosis and necrosis were evaluated in a dose-/time-dependent manner in normal human skin fibroblasts. Also, newly fertilized zebrafish zygotes were exposed to liposomes, permitting a fast-track evaluation of the morphophysiological modifications. In vitro data showed that only very high doses of DODAX : MO induce apoptosis and necrosis, inhibit cell proliferation, and affect the metabolism and plasma membrane integrity of fibroblasts in a dose-/time-dependent manner. Furthermore, liposomes affected mitochondrial function, increasing ROS accumulation and disturbing mitochondrial membrane potential. DODAC-based liposomes were consistently more toxic when compared to DODAB-based formulations; furthermore, the inclusion of MO was found to reduce toxicity, in contrast to liposomes with cationic DODAX only, especially in DODAB : MO (1 : 2) nanocarriers. These results were corroborated, in a holistic approach, by cytotoxicity profiling in five additional human cell lines, and also with the zebrafish embryotoxicity testing, which constitutes a sensitive and informative tool and accurately extends cell-based assays.
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Affiliation(s)
- Ana Cristina Norberto Oliveira
- CBMA (Center of Molecular and Environmental Biology) , Department of Biology , University of Minho , Campus of Gualtar , 4710 057 Braga , Portugal . ; ; Tel: +351 253 601 511
- CFUM (Center of Physics) , Department of Physics , University of Minho , Campus of Gualtar , 4710-057 Braga , Portugal
| | - Marisa Passos Sárria
- INL - International Iberian Nanotechnology Laboratory , Av. Mestre José Veiga , 4715-330 Braga , Portugal
| | - Pedro Moreira
- CBMA (Center of Molecular and Environmental Biology) , Department of Biology , University of Minho , Campus of Gualtar , 4710 057 Braga , Portugal . ; ; Tel: +351 253 601 511
| | - Joana Fernandes
- CBMA (Center of Molecular and Environmental Biology) , Department of Biology , University of Minho , Campus of Gualtar , 4710 057 Braga , Portugal . ; ; Tel: +351 253 601 511
| | - Lisandra Castro
- CBMA (Center of Molecular and Environmental Biology) , Department of Biology , University of Minho , Campus of Gualtar , 4710 057 Braga , Portugal . ; ; Tel: +351 253 601 511
| | - Ivo Lopes
- CBMA (Center of Molecular and Environmental Biology) , Department of Biology , University of Minho , Campus of Gualtar , 4710 057 Braga , Portugal . ; ; Tel: +351 253 601 511
- CFUM (Center of Physics) , Department of Physics , University of Minho , Campus of Gualtar , 4710-057 Braga , Portugal
- Nanodelivery-I&D em Bionanotecnologia Lda. , Department of Biology , University of Minho , Campus of Gualtar , 4710-057 Braga , Portugal
| | - Manuela Côrte-Real
- CBMA (Center of Molecular and Environmental Biology) , Department of Biology , University of Minho , Campus of Gualtar , 4710 057 Braga , Portugal . ; ; Tel: +351 253 601 511
| | - Artur Cavaco-Paulo
- CEB , Department of Biological Engineering , University of Minho , Campus of Gualtar , 4710-057 Braga , Portugal
| | | | - Andreia Castro Gomes
- CBMA (Center of Molecular and Environmental Biology) , Department of Biology , University of Minho , Campus of Gualtar , 4710 057 Braga , Portugal . ; ; Tel: +351 253 601 511
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232
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Willis A, Mazon-Moya M, Mostowy S. Investigation of septin biology in vivo using zebrafish. Methods Cell Biol 2016; 136:221-41. [PMID: 27473912 DOI: 10.1016/bs.mcb.2016.03.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The zebrafish (Danio rerio) is an important animal model to study cell biology in vivo. Benefits of the zebrafish include a fully annotated reference genome, an easily manipulable genome (for example, by morpholino oligonucleotide or CRISPR-Cas9), and transparent embryos for noninvasive, real-time microscopy using fluorescent transgenic lines. Zebrafish have orthologues of most human septins, and studies using larvae were used to investigate the role of septins in vertebrate development. The zebrafish larva is also an established model to study the cell biology of infection and has recently been used to visualize septin assembly during bacterial infection in vivo. Here, we describe protocols for the study of septins in zebrafish, with emphasis on techniques used to investigate the role of septins in host defense against bacterial infection.
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Affiliation(s)
- A Willis
- Imperial College London, London, United Kingdom
| | | | - S Mostowy
- Imperial College London, London, United Kingdom
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233
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Mukherjee R, Patra M, Dutta D, Banik M, Basu T. Tetracycline-loaded calcium phosphate nanoparticle (Tet-CPNP): Rejuvenation of an obsolete antibiotic to further action. Biochim Biophys Acta Gen Subj 2016; 1860:1929-41. [PMID: 27288585 DOI: 10.1016/j.bbagen.2016.06.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/30/2016] [Accepted: 06/06/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Increasing resistance in bacteria towards antibiotics has made it imperative to research on their revitalization to combat infectious diseases. This study dealt with synthesis of a nano-form of the antibiotic tetracycline, its characterization and potency of killing different multi-drug resistant diarrhea-causing bacteria. METHODS Nano-formulation was done by loading tetracycline within biocompatible calcium phosphate nanoparticle. The synthesized tetracycline-loaded calcium phosphate nanoparticle (Tet-CPNP) was characterized by the techniques like TEM, DLS, EDS, FTIR, spectrofluorimetry and dialysis. Bactericidal activity of nano-particulate tetracycline was investigated by agar plating, spectrophotometry, phase contrast-fluorescence-atomic force microscopy and flow cytometry techniques. RESULTS The Tet-CPNPs were 8±5nm in size and nearly spherical in shape, efficiency of tetracycline loading in CPNP was about 20% and the release of antibiotic from Tet-CPNPs was sustainable during 7days. Minimum inhibitory concentration (MIC) of Tet-CPNP on multiple antibiotic (including tetracycline) resistant bacteria like Escherichia coli, Salmonella kentuckey and Shigella flexneri was in the range of 20-40μg/ml, whereas MIC of free tetracycline was in the range of 150-180μg/ml. NP-mediated cell filamentation and cell membrane disintegration caused cell killing. Moreover, death of Shigella-infected Zebra fish larvae was stalled by Tet-CPNP treatment. CPNP itself had no toxic effect on bacteria as well as on Zebra fish. CONCLUSION Our nano-formulation of tetracycline might reclaim a nearly obsolete antibiotic to further potential function. GENERAL SIGNIFICANCE Such a study on revival of an old, cheap, broad-spectrum antibiotic to further action is highly beneficial to developing countries with limited health care budgets.
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Affiliation(s)
- Riya Mukherjee
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, West Bengal, India
| | - Mousumi Patra
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, West Bengal, India
| | - Debanjan Dutta
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, West Bengal, India
| | - Milon Banik
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, West Bengal, India
| | - Tarakdas Basu
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani 741 235, West Bengal, India.
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234
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Li S, Peng Z, Dallman J, Baker J, Othman AM, Blackwelder PL, Leblanc RM. Crossing the blood-brain-barrier with transferrin conjugated carbon dots: A zebrafish model study. Colloids Surf B Biointerfaces 2016; 145:251-256. [PMID: 27187189 DOI: 10.1016/j.colsurfb.2016.05.007] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/02/2016] [Accepted: 05/04/2016] [Indexed: 12/22/2022]
Abstract
Drug delivery to the central nervous system (CNS) in biological systems remains a major medical challenge due to the tight junctions between endothelial cells known as the blood-brain-barrier (BBB). Here we use a zebrafish model to explore the possibility of using transferrin-conjugated carbon dots (C-Dots) to ferry compounds across the BBB. C-Dots have previously been reported to inhibit protein fibrillation, and they are also used to deliver drugs for disease treatment. In terms of the potential medical application of C-Dots for the treatment of CNS diseases, one of the most formidable challenges is how to deliver them inside the CNS. To achieve this in this study, human transferrin was covalently conjugated to C-Dots. The conjugates were then injected into the vasculature of zebrafish to examine the possibility of crossing the BBB in vivo via transferrin receptor-mediated endocytosis. The experimental observations suggest that the transferrin-C-Dots can enter the CNS while C-Dots alone cannot.
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Affiliation(s)
- Shanghao Li
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33146, United States
| | - Zhili Peng
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33146, United States
| | - Julia Dallman
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33146, United States
| | - James Baker
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33146, United States
| | - Abdelhameed M Othman
- Department of Chemistry, Faculty of Science in Yanbu, Taibah University, Yanbu, Saudi Arabia; Department of Environmental Biotechnology, Genetic Engineering and Biotechnology, University of Sadat City, Sadat City, Egypt
| | - Patrica L Blackwelder
- University of Miami Center for Advanced Microscopy and Marine Geosciences, 1301 Memorial Drive, University of Miami, Coral Gables, FL, 33146, United States; Nova Southeastern University Oceanographic Center, 8000 North Ocean Drive, Dania, FL, 33004, United States
| | - Roger M Leblanc
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33146, United States.
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235
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Anatomical features for the adequate choice of experimental animal models in biomedicine: I. Fishes. Ann Anat 2016; 205:75-84. [DOI: 10.1016/j.aanat.2016.02.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 12/01/2015] [Accepted: 02/01/2016] [Indexed: 11/21/2022]
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236
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CREB engages C/EBPδ to initiate leukemogenesis. Leukemia 2016; 30:1887-96. [PMID: 27118402 DOI: 10.1038/leu.2016.98] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/07/2016] [Accepted: 04/11/2016] [Indexed: 12/28/2022]
Abstract
cAMP response element binding protein (CREB) is frequently overexpressed in acute myeloid leukemia (AML) and acts as a proto-oncogene; however, it is still debated whether such overactivation alone is able to induce leukemia as its pathogenetic downstream signaling is still unclear. We generated a zebrafish model overexpressing CREB in the myeloid lineage, which showed an aberrant regulation of primitive hematopoiesis, and in 79% of adult CREB-zebrafish a block of myeloid differentiation, triggering to a monocytic leukemia akin the human counterpart. Gene expression analysis of CREB-zebrafish revealed a signature of 20 differentially expressed human homologous CREB targets in common with pediatric AML. Among them, we demonstrated that CREB overexpression increased CCAAT-enhancer-binding protein-δ (C/EBPδ) levels to cause myeloid differentiation arrest, and the silencing of CREB-C/EBPδ axis restored myeloid terminal differentiation. Then, C/EBPδ overexpression was found to identify a subset of pediatric AML affected by a block of myeloid differentiation at monocytic stage who presented a significant higher relapse risk and the enrichment of aggressive signatures. Finally, this study unveils the aberrant activation of CREB-C/EBPδ axis concurring to AML onset by disrupting the myeloid cell differentiation process. We provide a novel in vivo model to perform high-throughput drug screening for AML cure improvement.
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237
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Engerer P, Plucinska G, Thong R, Trovò L, Paquet D, Godinho L. Imaging Subcellular Structures in the Living Zebrafish Embryo. J Vis Exp 2016:e53456. [PMID: 27078038 DOI: 10.3791/53456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In vivo imaging provides unprecedented access to the dynamic behavior of cellular and subcellular structures in their natural context. Performing such imaging experiments in higher vertebrates such as mammals generally requires surgical access to the system under study. The optical accessibility of embryonic and larval zebrafish allows such invasive procedures to be circumvented and permits imaging in the intact organism. Indeed the zebrafish is now a well-established model to visualize dynamic cellular behaviors using in vivo microscopy in a wide range of developmental contexts from proliferation to migration and differentiation. A more recent development is the increasing use of zebrafish to study subcellular events including mitochondrial trafficking and centrosome dynamics. The relative ease with which these subcellular structures can be genetically labeled by fluorescent proteins and the use of light microscopy techniques to image them is transforming the zebrafish into an in vivo model of cell biology. Here we describe methods to generate genetic constructs that fluorescently label organelles, highlighting mitochondria and centrosomes as specific examples. We use the bipartite Gal4-UAS system in multiple configurations to restrict expression to specific cell-types and provide protocols to generate transiently expressing and stable transgenic fish. Finally, we provide guidelines for choosing light microscopy methods that are most suitable for imaging subcellular dynamics.
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Affiliation(s)
- Peter Engerer
- Institute of Neuronal Cell Biology, Technische Universität München;
| | - Gabriela Plucinska
- Institute of Neuronal Cell Biology, Technische Universität München; Cell Biology, Department of Biology, Faculty of Science, Utrecht University
| | - Rachel Thong
- Institute of Neuronal Cell Biology, Technische Universität München; Faculty of Biology, Ludwig-Maximilians-Universität-München
| | - Laura Trovò
- Institute of Neuronal Cell Biology, Technische Universität München
| | - Dominik Paquet
- Adolf-Butenandt-Institute, Biochemistry, Ludwig-Maximilians-Universität-München; German Center for Neurodegenerative Diseases; Laboratory of Brain Development and Repair, The Rockefeller University
| | - Leanne Godinho
- Institute of Neuronal Cell Biology, Technische Universität München;
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238
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Williams AM, Perkumas KM, Perry I, Wen JC, Keeling J, Tramber M, Liton PB, Stamer WD. Successful Implementation of a Program for Increasing Donor Eyes for Research: The Duke-Miracles In Sight Program. J Ocul Pharmacol Ther 2016; 32:145-9. [PMID: 26982653 PMCID: PMC4827310 DOI: 10.1089/jop.2015.0107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/04/2015] [Indexed: 02/03/2023] Open
Abstract
PURPOSE Although essential for development of ocular therapeutics, the quality and quantity of human donor eyes for research have been on the decline. To streamline procurement protocols, provide better medical documentation of tissue, and improve freshness and number of eyes, a pilot cooperative program was undertaken between the Duke University Eye Center and Miracles In Sight Eye Bank. METHODS For research eye donors who expire at Duke University Hospital, age restrictions to procurement were lifted, access to donors' electronic medical records was granted to researchers, and eye tissue was delivered directly to scientists. The number of eye pairs received per month and the time from death to arrival in the laboratory were documented, and independent-samples t-tests were used to compare the number of paired eyes and the death-to-laboratory time before and after implementation of the program. A cost analysis of the program was also conducted. RESULTS Implementation of the program decreased the time from death to arrival in the laboratory from an average of 22.1 ± 1.5 h (n = 22) to 11.6 ± 0.8 h (n = 75) for a pair of eyes (P < 0.0001). Moreover, the number of whole eye pairs increased from 1.57 ± 0.32 to 3.26 ± 0.27 donors per month (P = 0.0019). Cost analysis indicates that our program is financially viable and sustainable for the eye bank. CONCLUSIONS The Duke-Miracles In Sight Program implemented a number of operational changes that resulted in improved quantity and quality of ocular tissue to researchers. Such a model appears feasible for adoption between other eye centers and eye banks.
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Affiliation(s)
- Andrew M. Williams
- Michigan State University College of Human Medicine, Grand Rapids, Michigan
| | | | - Isaac Perry
- Miracles In Sight Eye Bank, Winston-Salem, North Carolina
| | - Joanne C. Wen
- Department of Ophthalmology, University of Washington, Seattle, Washington
| | - Janet Keeling
- Miracles In Sight Eye Bank, Winston-Salem, North Carolina
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Andrews N, Ramel MC, Kumar S, Alexandrov Y, Kelly DJ, Warren SC, Kerry L, Lockwood N, Frolov A, Frankel P, Bugeon L, McGinty J, Dallman MJ, French PMW. Visualising apoptosis in live zebrafish using fluorescence lifetime imaging with optical projection tomography to map FRET biosensor activity in space and time. JOURNAL OF BIOPHOTONICS 2016; 9:414-24. [PMID: 26753623 PMCID: PMC4858816 DOI: 10.1002/jbio.201500258] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/25/2015] [Accepted: 11/27/2015] [Indexed: 05/14/2023]
Abstract
Fluorescence lifetime imaging (FLIM) combined with optical projection tomography (OPT) has the potential to map Förster resonant energy transfer (FRET) readouts in space and time in intact transparent or near transparent live organisms such as zebrafish larvae, thereby providing a means to visualise cell signalling processes in their physiological context. Here the first application of FLIM OPT to read out biological function in live transgenic zebrafish larvae using a genetically expressed FRET biosensor is reported. Apoptosis, or programmed cell death, is mapped in 3-D by imaging the activity of a FRET biosensor that is cleaved by Caspase 3, which is a key effector of apoptosis. Although apoptosis is a naturally occurring process during development, it can also be triggered in a variety of ways, including through gamma irradiation. FLIM OPT is shown here to enable apoptosis to be monitored over time, in live zebrafish larvae via changes in Caspase 3 activation following gamma irradiation at 24 hours post fertilisation. Significant apoptosis was observed at 3.5 hours post irradiation, predominantly in the head region.
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Affiliation(s)
- Natalie Andrews
- Institute of Chemical Biology, Department of Chemistry, Imperial College London, SW7 2AZ, UK
- Department of Life Sciences, , Imperial College London, SW7 2AZ, UK
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | - Marie-Christine Ramel
- Department of Life Sciences, , Imperial College London, SW7 2AZ, UK
- Division of Medicine, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | - Yuriy Alexandrov
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | - Douglas J Kelly
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | - Sean C Warren
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | - Louise Kerry
- Department of Life Sciences, , Imperial College London, SW7 2AZ, UK
| | - Nicola Lockwood
- Division of Medicine, University College London, Gower Street, London, WC1E 6BT, UK
- COMPLEX, University College London, Gower Street, London, WC1E 6BT, UK
| | - Antonina Frolov
- Division of Medicine, University College London, Gower Street, London, WC1E 6BT, UK
| | - Paul Frankel
- Division of Medicine, University College London, Gower Street, London, WC1E 6BT, UK
| | - Laurence Bugeon
- Department of Life Sciences, , Imperial College London, SW7 2AZ, UK
| | - James McGinty
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK
| | | | - Paul M W French
- Photonics Group, Department of Physics, Prince Consort Road, Imperial College London, SW7 2AZ, UK.
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240
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Lee HB, Schwab TL, Koleilat A, Ata H, Daby CL, Cervera RL, McNulty MS, Bostwick HS, Clark KJ. Allele-Specific Quantitative PCR for Accurate, Rapid, and Cost-Effective Genotyping. Hum Gene Ther 2016; 27:425-35. [PMID: 26986823 PMCID: PMC4931339 DOI: 10.1089/hum.2016.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Customizable endonucleases such as transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9) enable rapid generation of mutant strains at genomic loci of interest in animal models and cell lines. With the accelerated pace of generating mutant alleles, genotyping has become a rate-limiting step to understanding the effects of genetic perturbation. Unless mutated alleles result in distinct morphological phenotypes, mutant strains need to be genotyped using standard methods in molecular biology. Classic restriction fragment length polymorphism (RFLP) or sequencing is labor-intensive and expensive. Although simpler than RFLP, current versions of allele-specific PCR may still require post-polymerase chain reaction (PCR) handling such as sequencing, or they are more expensive if allele-specific fluorescent probes are used. Commercial genotyping solutions can take weeks from assay design to result, and are often more expensive than assembling reactions in-house. Key components of commercial assay systems are often proprietary, which limits further customization. Therefore, we developed a one-step open-source genotyping method based on quantitative PCR. The allele-specific qPCR (ASQ) does not require post-PCR processing and can genotype germline mutants through either threshold cycle (Ct) or end-point fluorescence reading. ASQ utilizes allele-specific primers, a locus-specific reverse primer, universal fluorescent probes and quenchers, and hot start DNA polymerase. Individual laboratories can further optimize this open-source system as we completely disclose the sequences, reagents, and thermal cycling protocol. We have tested the ASQ protocol to genotype alleles in five different genes. ASQ showed a 98-100% concordance in genotype scoring with RFLP or Sanger sequencing outcomes. ASQ is time-saving because a single qPCR without post-PCR handling suffices to score genotypes. ASQ is cost-effective because universal fluorescent probes negate the necessity of designing expensive probes for each locus.
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Affiliation(s)
- Han B Lee
- 1 Neurobiology of Disease Graduate Program, Mayo Graduate School , Rochester, Minnesota
| | - Tanya L Schwab
- 2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota
| | - Alaa Koleilat
- 3 Clinical and Translational Science Graduate Program, Mayo Graduate School , Rochester, Minnesota
| | - Hirotaka Ata
- 3 Clinical and Translational Science Graduate Program, Mayo Graduate School , Rochester, Minnesota.,4 Medical Scientist Training Program, Mayo Graduate School , Rochester, Minnesota
| | - Camden L Daby
- 2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota
| | - Roberto Lopez Cervera
- 2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota
| | - Melissa S McNulty
- 2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota
| | - Hannah S Bostwick
- 2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota
| | - Karl J Clark
- 1 Neurobiology of Disease Graduate Program, Mayo Graduate School , Rochester, Minnesota.,2 Department of Biochemistry and Molecular Biology, Mayo Clinic , Rochester, Minnesota.,3 Clinical and Translational Science Graduate Program, Mayo Graduate School , Rochester, Minnesota
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241
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Hasumura T, Meguro S. Exercise quantity-dependent muscle hypertrophy in adult zebrafish (Danio rerio). J Comp Physiol B 2016; 186:603-14. [PMID: 26951149 DOI: 10.1007/s00360-016-0977-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 02/16/2016] [Accepted: 02/24/2016] [Indexed: 01/28/2023]
Abstract
Exercise is very important for maintaining and increasing skeletal muscle mass, and is particularly important to prevent and care for sarcopenia and muscle disuse atrophy. However, the dose-response relationship between exercise quantity, duration/day, and overall duration and muscle mass is poorly understood. Therefore, we investigated the effect of exercise duration on skeletal muscle to reveal the relationship between exercise quantity and muscle hypertrophy in zebrafish forced to exercise. Adult male zebrafish were exercised 6 h/day for 4 weeks, 6 h/day for 2 weeks, or 3 h/day for 2 weeks. Flow velocity was adjusted to maximum velocity during continual swimming (initial 43 cm/s). High-speed consecutive photographs revealed that zebrafish mainly drove the caudal part. Additionally, X-ray micro computed tomography measurements indicated muscle hypertrophy of the mid-caudal half compared with the mid-cranial half part. The cross-sectional analysis of the mid-caudal half muscle revealed that skeletal muscle (red, white, or total) mass increased with increasing exercise quantity, whereas that of white muscle and total muscle increased only under the maximum exercise load condition of 6 h/day for 4 weeks. Additionally, the muscle fiver size distributions of exercised fish were larger than those from non-exercised fish. We revealed that exercise quantity, duration/day, and overall duration were correlated with skeletal muscle hypertrophy. The forced exercise model enabled us to investigate the relationship between exercise quantity and skeletal muscle mass. These results open up the possibility for further investigations on the effects of exercise on skeletal muscle in adult zebrafish.
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Affiliation(s)
- Takahiro Hasumura
- Biological Science Research, Kao Corporation, 2606 Akabane, Ichikai-machi, Haga-gun, Tochigi, 321-3497, Japan
| | - Shinichi Meguro
- Biological Science Research, Kao Corporation, 2606 Akabane, Ichikai-machi, Haga-gun, Tochigi, 321-3497, Japan.
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242
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Non-mammalian Animal Models Offer New Perspectives on the Treatment of TBI. CURRENT PHYSICAL MEDICINE AND REHABILITATION REPORTS 2016. [DOI: 10.1007/s40141-016-0107-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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243
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Abstract
As the processes of embryogenesis become increasingly well understood, there is growing interest in the development that occurs at later, postembryonic stages. Postembryonic development holds tremendous potential for discoveries of both fundamental and translational importance. Zebrafish, which are small, rapidly and externally developing, and which boast a wealth of genetic resources, are an outstanding model of vertebrate postembryonic development. Nonetheless, there are specific challenges posed by working with zebrafish at these stages, and this chapter is meant to serve as a primer for those working with larval and juvenile zebrafish. Since accurate staging is critical for high-quality results and experimental reproducibility, we outline best practices for reporting postembryonic developmental progress. Emphasizing the importance of accurate staging, we present new data showing that rates of growth and size-stage relationships can differ even between wild-type strains. Finally, since rapid and uniform development is particularly critical when working at postembryonic stages, we briefly describe methods that we use to achieve high rates of growth and developmental uniformity through postembryonic stages in both wild-type and growth-compromised zebrafish.
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Affiliation(s)
- S K McMenamin
- University of Massachusetts, Lowell, MA, United States; University of Washington, Seattle, WA, United States
| | - M N Chandless
- University of Washington, Seattle, WA, United States
| | - D M Parichy
- University of Washington, Seattle, WA, United States
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244
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Abstract
Hemostasis is a coordinated system through which blood is prevented from exiting a closed circulatory system. We have taken advantage of the zebrafish, an emerging model for the study of blood coagulation, and describe three techniques for quantitative analysis of primary and secondary hemostasis. Collectively, these three techniques comprise a toolset to aid in our understanding of hemostasis and pathological clotting.
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Affiliation(s)
- M S Rost
- University of Michigan, Ann Arbor, MI, United States
| | | | - J A Shavit
- University of Michigan, Ann Arbor, MI, United States
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245
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Morales Fénero CI, Colombo Flores AA, Câmara NOS. Inflammatory diseases modelling in zebrafish. World J Exp Med 2016; 6:9-20. [PMID: 26929916 PMCID: PMC4759353 DOI: 10.5493/wjem.v6.i1.9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/20/2015] [Accepted: 12/18/2015] [Indexed: 02/06/2023] Open
Abstract
The ingest of diets with high content of fats and carbohydrates, low or no physical exercise and a stressful routine are part of the everyday lifestyle of most people in the western world. These conditions are triggers for different diseases with complex interactions between the host genetics, the metabolism, the immune system and the microbiota, including inflammatory bowel diseases (IBD), obesity and diabetes. The incidence of these disorders is growing worldwide; therefore, new strategies for its study are needed. Nowadays, the majority of researches are in use of murine models for understand the genetics, physiopathology and interaction between cells and signaling pathways to find therapeutic solutions to these diseases. The zebrafish, a little tropical water fish, shares 70% of our genes and conserves anatomic and physiological characteristics, as well as metabolical pathways, with mammals, and is rising as a new complementary model for the study of metabolic and inflammatory diseases. Its high fecundity, fast development, transparency, versatility and low cost of maintenance makes the zebrafish an interesting option for new researches. In this review, we offer a discussion of the existing genetic and induced zebrafish models of two important Western diseases that have a strong inflammatory component, the IBD and the obesity.
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246
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Dewari PS, Ajani F, Kushawah G, Kumar DS, Mishra RK. Reversible loss of reproductive fitness in zebrafish on chronic alcohol exposure. Alcohol 2016; 50:83-9. [PMID: 26781213 DOI: 10.1016/j.alcohol.2015.11.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 11/10/2015] [Indexed: 01/10/2023]
Abstract
Alcoholism is one of the most prevalent diseases in society and causes significant health and social problems. Alcohol consumption by pregnant women is reported to cause adverse effects on the physical and psychological growth of the fetus. However, the direct effect of chronic alcohol consumption on reproductive fitness has not been tested. In recent years, the zebrafish (Danio rerio) has emerged as a versatile model system to study the effects of alcohol on behavior and embryonic development. We utilized the zebrafish model system to address the effect of chronic alcohol exposure (0.5% alcohol in the holding tank for 9 weeks) on reproductive capacity. We found a dramatic decrease in fecundity, measured by counting the number of eggs laid, when at least one of the parents is subject to chronic alcohol exposure. Interestingly, a 9-week alcohol withdrawal program completely restored the reproductive capacity of the treated subjects. In agreement with observations on fecundity, the chronic alcohol exposure leads to increased anxiety, as measured by the novel-tank diving assay. Conversely, the withdrawal program diminished heightened anxiety in alcohol-exposed subjects. Our results highlight the adverse effects of chronic alcohol exposure on the reproductive capacity of both males and females, and underscore the utility of the zebrafish model system to understand the biology of chronic alcoholism.
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Affiliation(s)
- Pooran Singh Dewari
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India
| | - Funmilola Ajani
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India
| | - Gopal Kushawah
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India
| | - Damera Santhosh Kumar
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Council of Scientific and Industrial Research, Uppal Road, Hyderabad 500007, India.
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247
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Bensimon-Brito A, Cardeira J, Dionísio G, Huysseune A, Cancela ML, Witten PE. Revisiting in vivo staining with alizarin red S--a valuable approach to analyse zebrafish skeletal mineralization during development and regeneration. BMC DEVELOPMENTAL BIOLOGY 2016; 16:2. [PMID: 26787303 PMCID: PMC4719692 DOI: 10.1186/s12861-016-0102-4] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 01/08/2016] [Indexed: 12/30/2022]
Abstract
BACKGROUND The correct evaluation of mineralization is fundamental for the study of skeletal development, maintenance, and regeneration. Current methods to visualize mineralized tissue in zebrafish rely on: 1) fixed specimens; 2) radiographic and μCT techniques, that are ultimately limited in resolution; or 3) vital stains with fluorochromes that are indistinguishable from the signal of green fluorescent protein (GFP)-labelled cells. Alizarin compounds, either in the form of alizarin red S (ARS) or alizarin complexone (ALC), have long been used to stain the mineralized skeleton in fixed specimens from all vertebrate groups. Recent works have used ARS vital staining in zebrafish and medaka, yet not based on consistent protocols. There is a fundamental concern on whether ARS vital staining, achieved by adding ARS to the water, can affect bone formation in juvenile and adult zebrafish, as ARS has been shown to inhibit skeletal growth and mineralization in mammals. RESULTS Here we present a protocol for vital staining of mineralized structures in zebrafish with a low ARS concentration that does not affect bone mineralization, even after repetitive ARS staining events, as confirmed by careful imaging under fluorescent light. Early and late stages of bone development are equally unaffected by this vital staining protocol. From all tested concentrations, 0.01% ARS yielded correct detection of bone calcium deposits without inducing additional stress to fish. CONCLUSIONS The proposed ARS vital staining protocol can be combined with GFP fluorescence associated with skeletal tissues and thus represents a powerful tool for in vivo monitoring of mineralized structures. We provide examples from wild type and transgenic GFP-expressing zebrafish, for endoskeletal development and dermal fin ray regeneration.
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Affiliation(s)
- A Bensimon-Brito
- Centre of Marine Sciences - CCMar, University of Algarve, Campus de Gambelas, Faro, Portugal.
- Evolutionary Developmental Biology, Biology Department, Ghent University, Ghent, Belgium.
- Current address: CEDOC - Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisbon, Portugal.
| | - J Cardeira
- Centre of Marine Sciences - CCMar, University of Algarve, Campus de Gambelas, Faro, Portugal.
- ProRegeM PhD Programme, Department of Biomedical Sciences and Medicine, University of Algarve, Campus de Gambelas, Faro, Portugal.
| | - G Dionísio
- Centre of Marine Sciences - CCMar, University of Algarve, Campus de Gambelas, Faro, Portugal.
- Guia Marine Laboratory, Oceanography Centre, Faculty of Sciences of University of Lisbon, Cascais, Portugal.
| | - A Huysseune
- Evolutionary Developmental Biology, Biology Department, Ghent University, Ghent, Belgium.
| | - M L Cancela
- Centre of Marine Sciences - CCMar, University of Algarve, Campus de Gambelas, Faro, Portugal.
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus de Gambelas, Faro, Portugal.
| | - P E Witten
- Evolutionary Developmental Biology, Biology Department, Ghent University, Ghent, Belgium.
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248
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Lawrence C, Best J, Cockington J, Henry EC, Hurley S, James A, Lapointe C, Maloney K, Sanders E. The Complete and Updated "Rotifer Polyculture Method" for Rearing First Feeding Zebrafish. J Vis Exp 2016:e53629. [PMID: 26863035 DOI: 10.3791/53629] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The zebrafish (Danio rerio) is a model organism of increasing importance in many fields of science. One of the most demanding technical aspects of culture of this species in the laboratory is rearing first-feeding larvae to the juvenile stage with high rates of growth and survival. The central management challenge of this developmental period revolves around delivering highly nutritious feed items to the fish on a nearly continuous basis without compromising water quality. Because larval zebrafish are well-adapted to feed on small zooplankton in the water column, live prey items such as brachionid rotifers, Artemia, and Paramecium are widely recognized as the feeds of choice, at least until the fish reach the juvenile stage and are able to efficiently feed on processed diets. This protocol describes a method whereby newly hatched zebrafish larvae are cultured together with live saltwater rotifers (Brachionus plicatilis) in the same system. This polyculture approach provides fish with an "on-demand", nutrient-rich live food source without producing chemical waste at levels that would otherwise limit performance. Importantly, because the system harnesses both the natural high productivity of the rotifers and the behavioral preferences of the fish, the labor involved with maintenance is low. The following protocol details an updated, step-by-step procedure that incorporates rotifer production (scalable to any desired level) for use in a polyculture of zebrafish larvae and rotifers that promotes maximal performance during the first 5 days of exogenous feeding.
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Affiliation(s)
| | - Jason Best
- Aquatic Resources Program, Boston Children's Hospital
| | | | | | - Shane Hurley
- Aquatic Resources Program, Boston Children's Hospital
| | - Althea James
- Aquatic Resources Program, Boston Children's Hospital
| | | | - Kara Maloney
- Aquatic Resources Program, Boston Children's Hospital
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Varshney GK, Zhang S, Pei W, Adomako-Ankomah A, Fohtung J, Schaffer K, Carrington B, Maskeri A, Slevin C, Wolfsberg T, Ledin J, Sood R, Burgess SM. CRISPRz: a database of zebrafish validated sgRNAs. Nucleic Acids Res 2016; 44:D822-6. [PMID: 26438539 PMCID: PMC4702947 DOI: 10.1093/nar/gkv998] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 09/22/2015] [Indexed: 12/26/2022] Open
Abstract
CRISPRz (http://research.nhgri.nih.gov/CRISPRz/) is a database of CRISPR/Cas9 target sequences that have been experimentally validated in zebrafish. Programmable RNA-guided CRISPR/Cas9 has recently emerged as a simple and efficient genome editing method in various cell types and organisms, including zebrafish. Because the technique is so easy and efficient in zebrafish, the most valuable asset is no longer a mutated fish (which has distribution challenges), but rather a CRISPR/Cas9 target sequence to the gene confirmed to have high mutagenic efficiency. With a highly active CRISPR target, a mutant fish can be quickly replicated in any genetic background anywhere in the world. However, sgRNA's vary widely in their activity and models for predicting target activity are imperfect. Thus, it is very useful to collect in one place validated CRISPR target sequences with their relative mutagenic activities. A researcher could then select a target of interest in the database with an expected activity. Here, we report the development of CRISPRz, a database of validated zebrafish CRISPR target sites collected from published sources, as well as from our own in-house large-scale mutagenesis project. CRISPRz can be searched using multiple inputs such as ZFIN IDs, accession number, UniGene ID, or gene symbols from zebrafish, human and mouse.
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Affiliation(s)
- Gaurav K Varshney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Suiyuan Zhang
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wuhong Pei
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ashrifia Adomako-Ankomah
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jacob Fohtung
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine Schaffer
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anoo Maskeri
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Claire Slevin
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tyra Wolfsberg
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Johan Ledin
- Department of Organismal Biology, Science for Life Laboratory, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Baiting for Cancer: Using the Zebrafish as a Model in Liver and Pancreatic Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:391-410. [DOI: 10.1007/978-3-319-30654-4_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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