BioMediTech Research Infrastructure

Zebrafish Facility

Our facility serves all scientists using zebrafish as a research model system. The facility is composed of a laboratory room, a microscope room for fluorescence microscopy and imaging, two large fish rooms with separate systems, and two quarantine rooms with stand-alone units for infection experiments.

Introduction

Zebrafish (Danio rerio) are small freshwater fish popular in home aquaria. In the last decades interest in using zebrafish models in biomedical research has increased greatly. Zebrafish provide a vertebrate model in which many advantages of lower invertebrate model organisms are combined to the advantages of mammalian research models:

  • Embryonic development ex utero
  • Transparency of embryos
  • Rapid embryonic development
  • Fast progeny production
  • Genetically traceable
  • Easy genetic manipulation
  • Suitability for large scale genetic screens and small molecule screens
  • Anatomical and physiological similarities with mammals
  • Various established human disease models

Animal Welfare

Keeping and raising of zebrafish stocks is performed under permission of the State Provincial Office of Western Finland (permission ESAVI/10079/04.10.06/2015). Care of animals is done in accordance with the EU-directive 2010/ 63/EU on the protection of animals used for scientific purposes and the Finnish Act on the Protection of Animals Used for Scientific or Educational Purposes (497/2013) and the Government Decree on the Protection of Animals Used for Scientific or Educational Purposes (564/2013). All experiments with zebrafish that are older than 7 days post fertilization are done under permissions granted by the National Animal Experiment Board.

Facility

Our facility serves all scientists using zebrafish as a research model system. The facility is capable of housing up to 50 000 adult zebrafish. It is composed of a laboratory room, a microscope room for fluorescence microscopy and imaging, two large fish rooms with separate systems, and two quarantine rooms with stand-alone units for infection experiments. The zebrafish housing system was designed and installed by Aquatic Habitats. The facility is equipped with a reverse osmosis water purification system, and a Pentair control box which automatically monitors pH, conductivity, temperature, water level and water exchange in the fish water. The system is capable of maintaining consistent pH and conductivity by dosing salt and sodium bicarbonate solutions automatically as necessary. The system water recirculates through several filtration units, including mechanical, biological and chemical filters, as well as an ultraviolet sterilizer.

Equipment

The facility is equipped with:

  • 3 WPI Pneumatic Picopump microinjectors and Narishige micromanipulators
  • Nikon SMZ645 stereomicroscope
  • Nikon SMZ800 stereomicroscope
  • Zeiss Lumar V1.1 fluorescence stereomicroscope
  • Sutter P-97 capillary needle puller
  • 650 A Aquatic washing system

Prices

Internal price list (University of Tampere):

SERVICE PRICE
Maintenance costs 1,5 liter tank 3 €/month
Maintenance costs 3 liter tank 5 €/month
Maintenance costs 10 liter tank 15 €/month
Adult fish (wt) 1,5 €/piece
Adult fish (mt/tg) 5 €/piece
Crosses/tank (wt) 10 €
Crosses/tank (mt/tg) 20 €
Annual fee for the use of the fish laboratory/group 5000 €

If the use of the services exceeds the annual fee, excessive use will be charged according to the list of fees.

Other academic users: Internal price list + VAT

Commercial users: Please inquire!

Zebrafish laboratory reserves the right to price adjustments.

Contacts

Zebrafish facility:
Zflab(at)uta.fi
Tel: +358 50 318 3864

Director:
Mataleena Parikka, D.D.S., Ph.D., docent
mataleena.parikka(at)uta.fi
Tel: +358 40 735 5052
Room: ARVO D432

Facility Manager:
Leena Mäkinen
leena.makinen(at)uta.fi
Tel: +358 40 190 9728
Room: ARVO F324

Publications

2017

Al-Samadi A, Awad S, Tuomainen K, Zhao Y, Salem A, Parikka M, Salo T.
Crosstalk between tongue carcinoma cells, extracellular vesicles, and immune cells in in vitro and in vivo models.
Oncotarget. 2017; 8:60123-60134.

Myllymäki H, Niskanen M, Oksanen KE, Sherwood E, Ahava M, Parikka M, Rämet M.
Identification of novel antigen candidates for a tuberculosis vaccine in the adult zebrafish (Danio rerio).
PLoS One. 2017 Jul 25;12(7):e0181942.

Bootorabi F, Manouchehri H, Changizi R, Barker H, Palazzo E, Saltari A, Parikka M, Pincelli C, Aspatwar A.
Zebrafish as a Model Organism for the Development of Drugs for Skin Cancer.
Int J Mol Sci. 2017 Jul 18;18(7).

Aspatwar A, Hammarén M, Koskinen S, Luukinen B, Barker H, Carta F, Supuran CT, Parikka M, Parkkila S.
β-CA-specific inhibitor dithiocarbamate Fc14-584B: a novel antimycobacterial agent with potential to treat drug-resistant tuberculosis.
J Enzyme Inhib Med Chem. 2017 Dec;32(1):832-840.

2016

Myllymäki H, Bäuerlein CA, Rämet M
The Zebrafish Breathes New Life into the Study of Tuberculosis.
Front Immunol ;2016. PMID: 27242801

Oksanen KE, Myllymäki H, Ahava MJ, Mäkinen L, Parikka M, Rämet M
DNA vaccination boosts Bacillus Calmette-Guérin protection against mycobacterial infection in zebrafish.
Dev Comp Immunol ;54(1)89-96, 2016. PMID: 26363085

2015

Aspatwar A, Tolvanen ME, Ojanen MJ, Barker HR, Saralahti AK, Bäuerlein CA, Ortutay C, Pan P, Kuuslahti M, Parikka M, Rämet M, Parkkila S
Inactivation of ca10a and ca10b Genes Leads to Abnormal Embryonic Development and Alters Movement Pattern in Zebrafish
PLoS One. 2015 Jul 28;10(7):e0134263. doi: 10.1371/journal.pone.0134263. eCollection 2015

Saralahti A, Rämet M
Zebrafish and Streptococcal Infections
Scand J Immunol. 2015 Sep;82(3):174-83. doi: 10.1111/sji.12320

Myllymäki H, Niskanen M, Oksanen KE, Rämet M
Animal models in tuberculosis research – where is the beef?
Expert Opin Drug Discov. 2015;10(8):871-83. doi: 10.1517/17460441.2015.1049529. Epub 2015 Jun 13

Ojanen MJ, Turpeinen H, Cordova ZM, Hammarén MM, Harjula SK, Parikka M, Rämet M, Pesu M
The proprotein convertase subtilisin/kexin furinA regulates zebrafish host response against Mycobacterium marinum
Infect Immun. 2015 Apr;83(4):1431-42. doi: 10.1128/IAI.03135-14. Epub 2015 Jan 26

2014

Hammarén MM, Oksanen KE, Nisula HM, Luukinen BV, Pesu M, Rämet M, Parikka M
Adequate Th2-type response associates with restricted bacterial growth in latent mycobacterial infection of zebrafish
PLoS Pathog. 2014 Jun 26;10(6):e1004190. doi: 10.1371/journal.ppat.1004190. eCollection 2014 Jun

Saralahti A, Piippo H, Parikka M, Henriques-Normark B, Rämet M, Rounioja S
Adult zebrafish model for pneumococcal pathogenesis
Dev Comp Immunol. 2014, 42(2):345-53

2013

Oksanen KE, Halfpenny NJ, Sherwood E, Harjula SK, Hammarén MM, Ahava MJ, Pajula ET, Lahtinen MJ, Parikka M & Rämet M
An adult zebrafish model for preclinical tuberculosis vaccine development
Vaccine,31:5202-9

Taskinen B, Zmurko J, Ojanen M, Kukkurainen S, Parthiban M, Määttä JAE, Leppiniemi J, Jänis J, Parikka M, Turpeinen H, Rämet M, Pesu M, Johnson MS, Kulomaa MS, Airenne TT & Hytönen VP
Zebavidin – An avidin-like protein from zebrafish
PLoS ONE,8(10): e77207

Turpeinen H, Oksanen A, Kivinen V, Oksanen A, Kukkurainen S, Uusimäki A, Rämet M, Parikka M, Hytönen V, Nykter M & Pesu M
Proprotein Convertase Subtilisin/Kexin Type 7 (PCSK7) is essential for the zebrafish development and bioavailability of Transforming Growth Factor Beta 1a (TGFβ1a)
Journal of Biological Chemistry,288:36610-23

Aspatwar A, Tolvanen M, Jokitalo E, Parikka M, Ortutay C, Harjula SK, Rämet M, Vihinen M & Parkkila S
Altered cerebellum development and motor dysfunction in CARP VIII morphant zebrafish embryos
Hum Mol Genet. 2013 Feb 1;22(3):417-32

2012

Teittinen K, Parikka M, Latvala A, Junttila S, Laiho A, Korkeamäki H, Gröngroos T, Kurppa K, Turpeinen H, Pesu M, Gyenesei A, Rämet M & Lohi O
Knockdown of SAP30L disrupts early heart development and function in zebrafish
Journal of Cellular Biochemistry, 2012, 113:3843-3852

Lohi O, Parikka M & Rämet M
The zebrafish as a model for paediatric diseases
Acta Paediatrica. Epub Aug 24, 2012, doi: 10.1111/j.1651-2227.2012.02835.x

Parikka M, Vuoksio M, Harjula SK, Halfpenny N, Oksanen K, Lahtinen MJ, Pajula E, Iivanainen A, Pesu M & Rämet M
Mycobacterium marinum causes a latent infection that can be reactivated by gamma irradiation in adult zebrafish
PLoS Pathogens, 2012, 8:e1002944

Patterson H, Saralahti A, Parikka M, Dramsi S, Trieu-Cuot P, Poyart C, Rounioja S & Rämet M
Adult zebrafish model of bacterial meningitis in Streptococcus agalactiae infection
Developmental and Comparative Immunology, Epub Aug 4, 2012

Teittinen K, Grönroos T, Parikka M, Rämet M & Lohi O
The zebrafish as a tool in leukemia research
Leukemia Research, 2012, 36:1082-1088

Rounioja S, Saralahti A, Rantala L, Parikka M, Henriques-Normark B, Silvennoinen O, Rämet M
Defense of zebrafish embryos against Streptococcus pneumoniae infection is dependent on the phagocytic activity of leukocytes
Developmental and Comparative Immunology, 2012, 36(2):342-348

2011

Ulvila J, Vanha-aho LM, Kleino A, Vähä-Mäkilä M, Vuoksio M, Eskelinen S, Hultmark D, Kocks C, Hallman M, Parikka M & Rämet M
Cofilin regulator 14-3-3-zeta is an evolutionarily conserved protein required for phagocytosis and microbial resistance
Journal of Leukocyte Biology, 2011,89(5):649-659

2010

Hyvärinen J, Parikka M, Sormunen R, Rämet M, Tryggvason K, Kivirikko KI, Myllyharju J & Koivunen P
Deficiency of a transmembrane prolyl 4-hydroxylase in the zebrafish leads to basement membrane defects and compromized kidney function
Journal of Biological Chemistry, 2010, 285(53):42023-42032

Valanne S, Myllymäki H, Kallio J, Schmid M, Kleino A, Murumägi A, Airaksinen L, Kotipelto T, Kaustio M, Ulvila J, Esfahani S, Engström Y, Silvennoinen O, Hultmark D, Parikka M & Rämet M
Genome-wide RNAi in Drosophila cells identifies G protein-coupled receptor kinase 2 as an evolutionary conserved regulator of the NF-kB signaling
Journal of Immunology, 2010, 184:6188-6198

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