Zebrafish (Danio rerio) are widely used in neuroscience research, where their utility as a model organism is rapidly expanding. Low cost, ease of experimental manipulations, and sufficient behavioral complexity make zebrafish a valuable tool for high-throughput studies in biomedicine. To complement the available repositories for zebrafish genetic information, there is a growing need for the collection of zebrafish neurobehavioral and neurological phenotypes. For this, we are establishing the Zebrafish Neurophenome Database (ZND; www.tulane.edu/∼znpindex/search) as a new dynamic online open-access data repository for behavioral and related physiological data. ZND, currently focusing on adult zebrafish, combines zebrafish neurophenotypic data with a simple, easily searchable user interface, which allow scientists to view and compare results obtained by other laboratories using various treatments in different testing paradigms. As a developing community effort, ZND is expected to foster innovative research using zebrafish by federating the growing body of zebrafish neurophenotypic data.
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References
1.
GerlaiR, LeeV, BlaserR. Effects of acute and chronic ethanol exposure on the behavior of adult zebrafish (Danio rerio)Pharmacol Biochem Behav, 2006; 85:752–761.
2.
ZonLI. Zebrafish: A new model for human disease. Genome Res, 1999; 9:99–100.
MaximinoC, da SilvaAW, GouveiaAJr., HerculanoAM. Pharmacological analysis of zebrafish (Danio rerio) scototaxis. Prog Neuropsychopharmacol Biol Psychiat, 2011; 35:624–631.
5.
AhmedO, SeguinD, GerlaiR. An automated predator avoidance task in zebrafish. Behav Brain Res, 2011; 216:166–171.
6.
SackermanJ, DoneganJJ, CunninghamCS, NguyenNN, LawlessK, LongAet al.Zebrafish behavior in movel environments: Effects of acute exposure to anxiolytic compounds and choice of Danio rerio line. Int J Comp Psychol., 2010; 23:43–61.
7.
PiatoAL, CapiottiKM, TamborskiAR, OsesJP, BarcellosLJ, BogoMRet al.Unpredictable chronic stress model in zebrafish (Danio rerio): Behavioral and physiological responses. Prog Neuropsychopharmacol Biol Psychiatry, 2011; 35:561–567.
8.
MiklosiA, AndrewRJ. The zebrafish as a model for behavioral studies. Zebrafish, 2006; 3:227–234.
9.
LockwoodB, BjerkeS, KobayashiK, GuoS. Acute effects of alcohol on larval zebrafish: A genetic system for large-scale screening. Pharmacol Biochem Behav, 2004; 77:647–654.
10.
TiedekenJA, RamsdellJS. Embryonic exposure to domoic acid increases the susceptibility of zebrafish larvae to the chemical convulsant pentylenetetrazole. Environ Health Perspect, 2007; 115:1547–1552.
JinM, ZhangX, WangL, HuangC, ZhangY, ZhaoM. Developmental toxicity of bifenthrin in embryo-larval stages of zebrafish. Aquat Toxicol, 2009; 95:347–354.
13.
LieschkeGJ, CurriePD. Animal models of human disease: Zebrafish swim into view. Nat Rev Genet, 2007; 8:353–367.
14.
BrittijnSA, DuivesteijnSJ, BelmamouneM, BertensLF, BitterW, de BruijnJDet al.Zebrafish development and regeneration: New tools for biomedical research. Int J Dev Biol, 2009; 53:835–850.
15.
EkkerSC, StempleDL, ClarkM, ChienCB, RasoolyRS, JavoisLC. Zebrafish genome project: Bringing new biology to the vertebrate genome field. Zebrafish, 2007; 4:239–251.
16.
JekoschK. The zebrafish genome project: Sequence analysis and annotation. Methods Cell Biol, 2004; 77:225–239.
17.
WoodsIG, KellyPD, ChuF, Ngo-HazelettP, YanYL, HuangHet al.A comparative map of the zebrafish genome. Genome Res, 2000; 10:1903–1914.
18.
CachatJM, CanavelloPR, EleganteMF, BartelsBK, ElkhayatSI, HartPCet al.Modeling stress and anxiety in zebrafish. Zebrafish Models in Neurobehavioral Research. KalueffAV, CachatJ. 73–88. Humana Press: New York, 2010.
19.
EganRJ, BergnerCL, HartPC, CachatJM, CanavelloPR, EleganteMFet al.Understanding behavioral and physiological phenotypes of stress and anxiety in zebrafish. Behav Brain Res, 2009; 205:38–44.
20.
LevinED, LimpuangthipJ, RachakondaT, PetersonM. Timing of nicotine effects on learning in zebrafish. Psychopharmacology (Berl), 2006; 184:547–552.
21.
MaximinoC, de BritoTM, da Silva BatistaAW, HerculanoAM, MoratoS, GouveiaAJr.Measuring anxiety in zebrafish: A critical review. Behav Brain Res, 2010; 214:157–171.
22.
SeibtKJ, Oliveira RdaL, ZimmermannFF, CapiottiKM, BogoMR, GhisleniGet al.Antipsychotic drugs prevent the motor hyperactivity induced by psychotomimetic MK-801 in zebrafish (Danio rerio)Behav Brain Res, 2010; 214:417–422.
23.
ToTT, HahnerS, NicaG, RohrKB, HammerschmidtM, WinklerCet al.Pituitary-interrenal interaction in zebrafish interrenal organ development. Mol Endocrinol, 2007; 21:472–485.
24.
von KroghK. Environmental enrichment and its effects on telencephalic neurogenesis and behaviour in isolated adult zebrafish, Danio rerio. Oslo: University of Oslo, 2007.
25.
XiY, RyanJ, NobleS, YuM, YilbasAE, EkkerM. Impaired dopaminergic neuron development and locomotor function in zebrafish with loss of pink1 function. Eur J Neurosci., 2010; 31:623–633.
26.
StewartA, GaikwadS, HartP, KyzarE, RothA, KalueffAV. Experimental models for anxiolytic drug discovery in the era of omes and omics. Expert Opin Drug Discov, 2011; 6:755–769.
27.
LeinES, HawrylyczMJ, AoN, AyresM, BensingerA, BernardAet al.Genome-wide atlas of gene expression in the adult mouse brain. Nature, 2007; 445:168–176.
28.
LiuP, VikisH, LuY, WangD, YouM. Large-scale in silico mapping of complex quantitative traits in inbred mice. PLoS One, 2007; 2:e651.
29.
GrupeA, GermerS, UsukaJ, AudD, BelknapJK, KleinRFet al.In silico mapping of complex disease-related traits in mice. Science, 2001; 292:1915–1918.
30.
DitzenC, VaradarajuluJ, CzibereL, GonikM, TargoszBS, HambschBet al.Proteomic-based genotyping in a mouse model of trait anxiety exposes disease-relevant pathways. Mol Psychiat, 2010; 15:702–711.
31.
StoneN, PangilinanF, MolloyAM, ShaneB, ScottJM, UelandPMet al.Bioinformatic and genetic association analysis of microRNA target sites in one-carbon metabolism genes. PLoS One, 2011; 6:e21851.
32.
GerlaiR. Phenomics: Fiction or the future?Trends Neurosci, 2002; 25:506–509.
33.
BhaveSV, HornbakerC, PhangTL, SabaL, LapadatR, KechrisKet al.The PhenoGen informatics website: Tools for analyses of complex traits. BMC Genet, 2007; 8:59.
34.
Colorado-Denver Uo. PhenoGen Informatics: Denver, Colorado USA, 2011.
35.
D'EustachioP. Reactome knowledgebase of human biological pathways and processes. Methods Mol Biol, 2011; 694:49–61.
36.
CroftD, O'KellyG, WuG, HawR, GillespieM, MatthewsLet al.Reactome: A database of reactions, pathways, and biological processes. Nucleic Acids Res, 2011; 39:691–697.
37.
ShawDR. Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype. Curr Protoc Bioinformatics, 2009; Chapter 1,Unit1:7.
38.
Jackson Laboratory. Mouse Genome Informatics: Bar Harbor, ME, 2011. www.informatics.jax.org/. 2011 December 1.
39.
ThorissonGA, SmithAV, KrishnanL, SteinLD. The International HapMap Project Web site. Genome Res, 2005; 15:1592–1593.
40.
GibbsRA, BelmontJW, HardenbolP, WillisTD, YuF, YangH, Ch'angLYet al.The International HapMap Consortium. The International HapMap Project. Nature, 2003; 426:789–796.
41.
HamoshA, ScottAF, AmbergerJS, BocchiniCA, McKusickVA. Online Mendelian Inheritance in Man (OMIM), a knowledge base of human genes and genetic disorders. Nucleic Acids Res, 2005; 33:D514–517.
NicholasFW. Online Mendelian Inheritance in Animals (OMIA): A comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals. Nucleic Acids Res, 2003; 31:275–277.
HahnU, WermterJ, BlasczykR, HornPA. Text mining: Powering the database revolution. Nature, 2007; 448:130.
48.
GolleryM. Your database is obsolete: The promise of contextual bioinformatics. Bioinformation, 2007; 1:356.
49.
HoffmanPL, BennettB, SabaLM, BhaveSV, Carosone-LinkPJ, HornbakerCKet al.Using the Phenogen website for 'in silico' analysis of morphine-induced analgesia: Identifying candidate genes. Addict Biol, 2011; 16:393–404.
50.
ElkinsKM. An in silico DNA cloning experiment for the biochemistry laboratory. Biochem Mol Biol Educ, 2011; 39:211–215.
51.
TakanoM, TeradaTP, SasaiM. Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor. Proc Natl Acad Sci USA, 2010; 107:7769–7774.
52.
ChanCH, MitchisonHM, PearceDA. Transcript and in silico analysis of CLN3 in juvenile neuronal ceroid lipofuscinosis and associated mouse models. Hum Mol Genet, 2008; 17:3332–3339.
53.
NaumovaEN, GorskiJ, NaumovYN. Simulation studies for a multistage dynamic process of immune memory response to influenza: Experiment in silico. Ann Zool Fennici, 2008; 45:369–384.
54.
O'ConnorKA, RothBL. Screening the receptorome for plant-based psychoactive compounds. Life Sci, 2005; 78:506–511.
55.
KokelD, PetersonRT. Chemobehavioural phenomics and behaviour-based psychiatric drug discovery in the zebrafish. Brief Funct Genomic Proteomic, 2008; 7:483–490.
56.
KariG, RodeckU, DickerAP. Zebrafish: An emerging model system for human disease and drug discovery. Clin Pharmacol Ther, 2007; 82:70–80.
57.
TomasiewiczHG, FlahertyDB, SoriaJP, WoodJG. Transgenic zebrafish model of neurodegeneration. J Neurosci Res, 2002; 70:734–745.
58.
LinkerA, StewartA, GaikwadS, CachatJ, EleganteM, KalueffAVet al.Assessing the maximal predictive validity for neuropharmacological anxiety screening assays using zebrafish. Zebrafish Neurobehavioral Protocols. KalueffAV, CachatJ. Humana Press: New York, 2010.
59.
BennettB, SabaLM, HornbakerCK, KechrisKJ, HoffmanP, TabakoffB. Genetical genomic analysis of complex phenotypes using the PhenoGen website. Behav Genet, 2011; 41:625–628.
60.
HoffmanPL, BennettB, SabaLM, BhaveSV, Carosone-LinkPJ, HornbakerCKet al.Using the Phenogen website for 'in silico' analysis of morphine-induced analgesia: Identifying candidate genes. Addict Biol, 2011; 16:393–404.
61.
GardnerD, TogaAW, AscoliGA, BeattyJT, BrinkleyJF, DaleAMet al.Towards effective and rewarding data sharing. Neuroinformatics, 2003; 1:289–295.
62.
ChervitzSA, DeutschEW, FieldD, ParkinsonH, QuackenbushJ, Rocca-SerraPet al.Data standards for Omics data: The basis of data sharing and reuse. Methods Mol Biol, 2011; 719:31–69.
ArzbergerP, SchroederP, BeaulieuA, BowkerG, CaseyK, LaaksonenLet al.Science and government. An international framework to promote access to data. Science, 2004; 303:1777–1778.
65.
SpragueJ, BayraktarogluL, BradfordY, ConlinT, DunnN, FashenaDet al.The Zebrafish Information Network: The zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res, 2008; 36:D768–772.
66.
SpragueJ, ClementsD, ConlinT, EdwardsP, FrazerK, SchaperKet al.The Zebrafish Information Network (ZFIN): The zebrafish model organism database. Nucleic Acids Res, 2003; 31:241–243.
67.
WesterfieldM, DoerryE, KirkpatrickAE, DouglasSA. Zebrafish informatics and the ZFIN database. Methods Cell Biol, 1999; 60:339–355.
68.
SpragueJ, DoerryE, DouglasS, WesterfieldM. The Zebrafish Information Network (ZFIN): A resource for genetic, genomic and developmental research. Nucleic Acids Res, 2001; 29:87–90.
69.
KalueffAV, OkamotoH, ZukowskaZ, GodwinJ, RobinsonBR, HerculanoA, MaximinoCet al.Statement of support of ZNP database. http://kaluefflab.com/znpstatement.html. 2011 December 1.
70.
VeronaM. VFront: Provincia di Cagliari, Italy, 2007. www.vfront.org. 2011 December 1.
71.
ZapolskyI, KyzarE, GreenJ, GaikwadS, PhamM, ChaninSet al.Utilizing the Zebrafish Neurophenome Project (ZNP) Database for analyses of complex neurophenotypes in zebrafish models. Zebrafish Protocols for Neurobehavioral Research. KalueffA, StewartA. Humana Press: New York, 2011.
72.
RussellWMS, BurchRL. The Principles of Humane Experimental Technique. London: Metheun, 1959.
73.
FlecknellP. Replacement, reduction and refinement. ALTEX, 2002; 19:73–78.
ShudaJ, Kearns-SixsmithD. Outreach: Empowering students and teachers to fish outside the box. Zebrafish, 2009; 6:133–138.
77.
BilottaJ, SaszikS, DeLorenzoAS, HardestyHR. Establishing and maintaining a low-cost zebrafish breeding and behavioral research facility. Behav Res Methods Instrum Comput, 1999; 31:178–184.
78.
McKeownKA, DownesGB, HutsonLD. Modular laboratory exercises to analyze the development of zebrafish motor behavior. Zebrafish, 2009; 6:179–185.
79.
HutsonLD, LiangJO. Making an impact: Zebrafish in education. Zebrafish, 2009; 6:119–120.
80.
NortonW, Bally-CuifL. Adult zebrafish as a model organism for behavioural genetics. BMC Neurosci, 2010; 11:90.
81.
ContiLH, MaciverCR, FerkanyJW, AbreuME. Footshock-induced freezing behavior in rats as a model for assessing anxiolytics. Psychopharmacology (Berl), 1990; 102:492–497.
82.
FanselowMS. Conditioned and unconditional components of post-shock freezing. Pavlov J Biol Sci, 1980; 15:177–182.
83.
GouldTD, O'DonnellKC, PicchiniAM, ManjiHK. Strain differences in lithium attenuation of d-amphetamine-induced hyperlocomotion: A mouse model for the genetics of clinical response to lithium. Neuropsychopharmacology, 2007; 32:1321–1333.
84.
IrifuneM, SatoT, NishikawaT, MasuyamaT, NomotoM, FukudaTet al.Hyperlocomotion during recovery from isoflurane anesthesia is associated with increased dopamine turnover in the nucleus accumbens and striatum in mice. Anesthesiology, 1997; 86:464–475.
85.
DarlandT, DowlingJE. Behavioral screening for cocaine sensitivity in mutagenized zebrafish. Proc Natl Acad Sci USA, 2001; 98:11691–11696.
86.
WilliamsLR, WongK, StewartA, SuciuC, GaikwadS, WuNet al.Behavioral and physiological effects of RDX on adult zebrafish. Comp Biochem Physiol C Toxicol Pharmacol, 2012; 155:33–38.
87.
LampreaMR, CardenasFP, SetemJ, MoratoS. Thigmotactic responses in an open-field. Braz J Med Biol Res, 2008; 41:135–140.
88.
CholerisE, ThomasAW, KavaliersM, PratoFS. A detailed ethological analysis of the mouse open field test: Effects of diazepam, chlordiazepoxide and an extremely low frequency pulsed magnetic field. Neurosci Biobehav Rev, 2001; 25:235–260.
89.
BlaserRE, ChadwickL, McGinnisGC. Behavioral measures of anxiety in zebrafish (Danio rerio)Behav Brain Res, 2010; 208:56–62.
90.
GrossmanL, UtterbackE, StewartA, GaikwadS, ChungKM, SuciuCet al.Characterization of behavioral and endocrine effects of LSD on zebrafish. Behav Brain Res, 2010; 214:277–284.
91.
BelzungC, GriebelG. Measuring normal and pathological anxiety-like behaviour in mice: A review. Behav Brain Res, 2001; 125:141–149.
92.
BelzungC, MisslinR, VogelE. Anxiogenic effects of a benzodiazepine receptor partial inverse agonist, RO 19-4603, in a light/dark choice situation. Pharmacol Biochem Behav, 1990; 36:593–596.
93.
MaximinoC, Marques de BritoT, DiasCA, GouveiaAJr., MoratoS. Scototaxis as anxiety-like behavior in fish. Nat Protoc, 2010; 5:209–216.
94.
MaximinoC, de BritoTM, ColmanettiR, PontesAA, de CastroHM, de LacerdaRIet al.Parametric analyses of anxiety in zebrafish scototaxis. Behav Brain Res, 2010; 210:1–7.
95.
EilamD, GolaniI. Home base behavior of rats (Rattus norvegicus) exploring a novel environment. Behav Brain Res, 1989; 34:199–211.
96.
StewartA, CachatJ, WongK, GaikwadS, GilderT, DiLeoJet al.Homebase behavior of zebrafish in novelty-based paradigms. Behav Processes, 2010; 85:198–203.
97.
RoweWB, SpreekmeesterE, MeaneyMJ, QuirionR, RochfordJ. Reactivity to novelty in cognitively-impaired and cognitively-unimpaired aged rats and young rats. Neuroscience, 1998; 83:669–680.
98.
WongK, EleganteM, BartelsB, ElkhayatS, TienD, RoySet al.Analyzing habituation responses to novelty in zebrafish (Danio rerio)Behav Brain Res, 2010; 208:450–457.
99.
Van LooPL, Van de WeerdHA, Van ZutphenLF, BaumansV. Preference for social contact versus environmental enrichment in male laboratory mice. Lab Anim, 2004; 38:178–188.
100.
WinslowJT. Mouse social recognition and preference. Curr Protoc Neurosci, 2003; Chapter 8,Unit 8:16.
101.
SaverinoC, GerlaiR. The social zebrafish: Behavioral responses to conspecific, heterospecific, and computer animated fish. Behav Brain Res, 2008; 191:77–87.
102.
EngeszerRE, RyanMJ, ParichyDM. Learned social preference in zebrafish. Curr Biol, 2004; 14:881–884.
