Zebrafish as a model for systems biology

Figures & data

Figure 1 The reductionist vs. holistic approaches.

Figure 2 Three approaches used in systems biology.

Table 1. A general comparison of different features among vertebrate models.

	Zebrafish	Rodents model	Primates
Maintenance	+++	++	–
Spawning	+++	+	–
Development rate	+++	++	–
Genetic modification	+++	++	–
Gene conservation	+	++	+++
Anatomical similarities	+	++	+++
Cost efficiency	+++	+	–

Table 2. Some examples of mutation based disease models in zebrafish.

Human condition	Gene	Zebrafish mutant	Reference
Menkes	atp7a	Calamity	Madsen et al., 2008
Arrhythmia	zerg	BreakDance	Langheinrich et al., 2003
Osteogenesis imperfecta	colla i	Chihuahua	Fisher et al., 2003
Alzheimer’s disease	tau	Tau	Paquet et al., 2009
Anemia	alas2	sauternes	Brownlie et al., 1998
Heart/finTbx5 deficiency	tbx5	heartstrings	Garrity et al., 2002
Parkinson disease	pink1	pink1-/-	Xi et al., 2010
Epithelial cancer	separase	Cease&desist	Shepard et al., 2007
Polycystic kidney disease	m468,m153,m587	doublebubble	Drummond et al., 1998
Innate immunity system	rag1	rag1 mutant	Petrie et al., 2009

Figure 3 The different approaches for proteomics.

Table 3. Examples of using zebrafish in different toxicological analyses.

Toxicity type	Chemical agent	Reference
Cardio toxicity	Pyrene	Zhang et al., 2012
Nephrotoxicity	Acetaminophen; aristocholic acid	Peng et al., 2010; Ding & Chen, 2012
Neurotoxicity	Fipronil	Stehr et al., 2006
Muscletoxicity	Statins	Hanai et al., 2007
Ototoxicity	Cisplatin	Ton & Parng, 2005
Hepatotoxicity	Mercury	Ung et al., 2010

Figure 4 The systems biology approach for zebrafish.

Madsen , E. C. , Morcos , P. A. , Mendelsohn , B. A. and Gitlin , J. D. 2008 . In vivo correction of a Menkes disease model using antisense oligonucleotides . Proceedings of the National Academy of Sciences of the United States of America , 105 : 3909 – 3914 .

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Langheinrich , U. , Vacun , G. and Wagner , T. 2003 . Zebrafish embryos express an orthologue of HERG and are sensitive toward a range of QT-prolonging drugs inducing severe arrhythmia . Toxicology and Applied Pharmacology , 193 : 370 – 382 .

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Fisher , S. , Jagadeeswaran , P. and Halpern , M. E. 2003 . Radiographic analysis of zebrafish skeletal defects . Developmental Biology , 264 : 64 – 76 .

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Garrity , D. M. , Childs , S. and Fishman , M. C. 2002 . The heartstrings mutation in zebrafish causes heart/fin Tbx5 deficiency syndrome . Development , 129 : 4635 – 4645 .

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Xi , Y. , Ryan , J. , Noble , S. , Yu , M. , Yilbas , A. E. and Ekker , M. 2010 . Impaired dopaminergic neuron development and locomotor function in zebrafish with loss of pink1 function . European Journal of Neuroscience , 31 : 623 – 633 .

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Shepard , J. L. , Amatruda , J. F. , Finkelstein , D. , Ziai , J. , Finley , K. R. , Stern , H. M. , … and Zon , L. I. 2007 . A mutation in separase causes genome instability and increased susceptibility to epithelial cancer . Genes & Development , 21 : 55 – 59 .

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Petrie , H. L. , Hohn , C. and Hanson , L. 2009 . Characterization of rag1 mutant zebrafish leukocytes . BMC Immunology , 10 : 1 – 8 .

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Zhang , Y. , Wang , C. , Huang , L. , Chen , R. , Chen , Y. and Zuo , Z. 2012 . Low-level pyrene exposure causes cardiac toxicity in zebrafish (Danio rerio) embryos . Aquatic Toxicology , 114–115 : 119 – 124 .

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Peng , H. C. , Wang , Y. H. , Wen , C. C. , Wang , W. H. , Cheng , C. C. and Chen , Y. H. 2010 . Nephrotoxicity assessments of acetaminophen during zebrafish embryogenesis . Comparative Biochemistry and Physiology Part C: Toxicology and Pharmacology , 151 : 480 – 486 .

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Ding , Y. J. and Chen , Y. H. 2012 . Developmental nephrotoxicity of aristolochic acid in a zebrafish model . Toxicology and Applied Pharmacology , 261 : 59 – 65 .

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Stehr , C. M. , Linbo , T. L. , Incardona , J. P. and Scholz , N. L. 2006 . The developmental neurotoxicity of fipronil: Notochord degeneration and locomotor defects in zebrafish embryos and larvae . Toxicological Sciences , 92 : 270 – 278 .

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Hanai , J. I. , Cao , P. , Tanksale , P. , Imamura , S. , Koshimizu , E. , Zhao , J. , … and Lecker , S. H. 2007 . The muscle-specific ubiquitin ligase atrogin-1/MAFbx mediates statin-induced muscle toxicity . Journal of Clinical Investigation , 117 : 3940 – 3951 .

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Ton , C. and Parng , C. 2005 . The use of zebrafish for assessing ototoxic and otoprotective agents . Hearing Research , 208 : 79 – 88 .

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Ung , C. , Lam , S. , Hlaing , M. , Winata , C. , Korzh , S. , Mathavan , S. and Gong , Z. 2010 . Mercury-induced hepatotoxicity in zebrafish: In vivo mechanistic insights from transcriptome analysis, phenotype anchoring and targeted gene expression validation . BMC Genomics , 11 : 212

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