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Measuring Behavioral Individuality in the Acoustic Startle Behavior in Zebrafish

Featured protocol,  Authors: Carlos Pantoja*
Carlos PantojaAffiliation: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
Bio-protocol author page: a4294
Adam Hoagland*
Adam HoaglandAffiliation: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
Bio-protocol author page: a4295
Elizabeth Carroll
Elizabeth CarrollAffiliation: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
Bio-protocol author page: a4296
David Schoppik
David SchoppikAffiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, USA
Present address: Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute New York University Langone School of Medicine, New York, USA
Bio-protocol author page: a4297
 and Ehud Y. Isacoff
Ehud Y. IsacoffAffiliation 1: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
Affiliation 2: Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, USA
Affiliation 3: Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, USA
For correspondence: ehud@berkeley.edu
Bio-protocol author page: a4298
 (*contributed equally to this work) date: 4/5/2017, 128 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2200.

Brief version appeared in Neuron, Aug 2016
The objective of this protocol is to provide a detailed description for the construction and use of a behavioral apparatus, the zBox, for high-throughput behavioral measurements in larval zebrafish (Danio rerio). The zBox is used to measure behavior in multiple individuals simultaneously. Individual fish are housed in wells of multi-well plates and receive acoustic/vibration stimuli with simultaneous recording of behavior. Automated analysis of behavioral movies is performed with MATLAB scripts. This protocol was adapted from two of our previously published papers (Levitz et al., 2013; Pantoja et al., 2016). The zBox provides an easy to setup flexible platform for behavioral experiments in zebrafish larvae.

Measuring Behavioral Individuality in the Acoustic Startle Behavior in Zebrafish

Authors: Carlos Pantoja*
Carlos PantojaAffiliation: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
Bio-protocol author page: a4294
Adam Hoagland*
Adam HoaglandAffiliation: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
Bio-protocol author page: a4295
Elizabeth Carroll
Elizabeth CarrollAffiliation: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
Bio-protocol author page: a4296
David Schoppik
David SchoppikAffiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, USA
Present address: Departments of Otolaryngology, Neuroscience & Physiology, and the Neuroscience Institute New York University Langone School of Medicine, New York, USA
Bio-protocol author page: a4297
 and Ehud Y. Isacoff
Ehud Y. IsacoffAffiliation 1: Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
Affiliation 2: Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, USA
Affiliation 3: Physical Bioscience Division, Lawrence Berkeley National Laboratory, Berkeley, USA
For correspondence: ehud@berkeley.edu
Bio-protocol author page: a4298
 (*contributed equally to this work) date: 4/5/2017, 128 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2200.

[Abstract] The objective of this protocol is to provide a detailed description for the construction and use of a behavioral apparatus, the zBox, for high-throughput behavioral measurements in larval zebrafish (Danio rerio). The zBox is used to measure behavior in multiple individuals simultaneously. Individual ...

Transplantation of Mesenchymal Cells Including the Blastema in Regenerating Zebrafish Fin

Authors: Eri Shibata
Eri ShibataAffiliation: School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
Bio-protocol author page: a4049
Kazunori Ando
Kazunori AndoAffiliation: School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
Bio-protocol author page: a4050
 and Atsushi Kawakami
Atsushi KawakamiAffiliation: School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
For correspondence: atkawaka@bio.titech.ac.jp
Bio-protocol author page: a4051
date: 1/20/2017, 497 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2109.

[Abstract] Regeneration of fish fins and urodele limbs occurs via formation of the blastema, which is a mass of mesenchymal cells formed at the amputated site and is essential for regeneration. The blastema transplantation, a novel technique developed in our previous studies (Shibata et al., 2016; Yoshinari et ...

Various Modes of Spinal Cord Injury to Study Regeneration in Adult Zebrafish

Authors: Subhra Prakash Hui
Subhra Prakash HuiAffiliation 1: Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
Affiliation 2: Victor Chang Cardiac Research Institute, Lowy Packer Building, Darlinghurst, Australia
Bio-protocol author page: a3817
 and Sukla Ghosh
Sukla GhoshAffiliation: Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
For correspondence: suklagh2010@gmail.com
Bio-protocol author page: a3818
date: 12/5/2016, 885 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.2043.

[Abstract] Spinal cord injury (SCI) in mammals leads to failure of both sensory and motor functions, due to lack of axonal regrowth below the level of injury as well as inability to replace lost neural cells and to stimulate neurogenesis. In contrast, fish and amphibians are capable of regenerating a variety of ...

Allogeneic Transplantation of Testicular Hyperplasia in rag1 Mutant Zebrafish

Authors: Toshihiro Kawasaki
Toshihiro Kawasaki Affiliation: Genetic Strains Research Center, National Institute of Genetics, and Department of Genetics, School of Life Science, the Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
Bio-protocol author page: a3674
 and Noriyoshi Sakai
Noriyoshi SakaiAffiliation: Genetic Strains Research Center, National Institute of Genetics, and Department of Genetics, School of Life Science, the Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan
For correspondence: nosakai@nig.ac.jp
Bio-protocol author page: a3675
date: 11/5/2016, 589 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1992.

[Abstract] Allogeneic organ transplantation is a powerful tool for clinical and basic research studies. However, the graft is often rejected by the host organism. Here, we describe a protocol that uses immunodeficient rag1 mutant zebrafish. These zebrafish escaped rejection, which made it possible to successfully ...

Detection of Reactive Oxygen Species Using MitoSOX and CellROX in Zebrafish

Authors: Alberto Rissone
Alberto RissoneAffiliation 1: Translational and Functional Genomics Branch, National Human Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, USA
Affiliation 2: Disorders of Immunity Section, Genetics and Molecular Biology Branch, NHGRI, NIH, Bethesda, MD, USA
For correspondence: alberto.rissone@nih.gov
Bio-protocol author page: a3533
 and Fabio Candotti
Fabio CandottiAffiliation 1: Disorders of Immunity Section, Genetics and Molecular Biology Branch, NHGRI, NIH, Bethesda, MD, USA
Affiliation 2: Division of Immunology and Allergy, University Hospital of Lausanne, Lausanne, Switzerland
For correspondence: Fabio.Candotti@chuv.ch
Bio-protocol author page: a3534
date: 10/5/2016, 1523 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1941.

[Abstract] The production of free radicals is the result of normal cellular metabolism. Free radicals are involved in innumerable different cellular and biological functions such as signaling, proliferation, cell death, aging, inflammation, etc. Under physiological conditions, the levels of reactive oxygen species ...

Thirty-Second Net Stressor Task in Adult Zebrafish

Authors: Steven Tran
Steven TranAffiliation: Department of Cell and Systems Biology, University of Toronto Mississauga, Mississauga, Canada
For correspondence: stevenhuy.tran@mail.utoronto.ca
Bio-protocol author page: a2034
 and Robert Gerlai
Robert GerlaiAffiliation: Department of Psychology, University of Toronto Mississauga, Mississauga, Canada
For correspondence: robert_gerlai@yahoo.com
Bio-protocol author page: a2035
date: 3/5/2015, 1857 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1413.

[Abstract] Zebrafish have become a popular animal model for behavioral neuroscience (Gerlai, 2014). Recent studies have demonstrated that brief experimental handling prior to euthanizing animals can subsequently alter biological measures quantified post-mortem (e.g. cortisol levels) (Ramsay et al., 2009; Tran ...

Fluorescence Microscopy for Cilia in Cultured Cells and Zebrafish Embryos

Authors: Jingli Cao
Jingli CaoAffiliation: State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai, China
Bio-protocol author page: a1497
Xueliang Zhu
Xueliang Zhu Affiliation: State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai, China
Bio-protocol author page: a1498
 and Xiumin Yan
Xiumin YanAffiliation: State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai, China
For correspondence: yanx@sibcb.ac.cn
Bio-protocol author page: a1499
date: 7/20/2014, 4553 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.1188.

[Abstract] Cilia are microtubule-based hair-like projections found in organisms, ranging from protozoa to mammals. This protocol provides methods for immunofluorescence staining of cilia in cultured cells and zebrafish embryos....

Motility Assay for Zebrafish Embryos

Authors: Michelle F. Goody
Michelle F. Goody Affiliation: Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, USA
Bio-protocol author page: a619
 and Clarissa A. Henry
Clarissa A. HenryAffiliation: School of Biology and Ecology, University of Maine, Orono, USA
For correspondence: clarissa.henry@umit.maine.edu
Bio-protocol author page: a620
date: 6/5/2013, 4177 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.787.

[Abstract] Analyzing the swimming ability of 2 days post fertilization zebrafish embryos can be a useful technique to study neuromuscular function. Here is a protocol for determining the time it takes for zebrafish embryos to swim a predetermined distance....

Phalloidin Staining and Immunohistochemistry of Zebrafish Embryos

Authors: Michelle F. Goody
Michelle F. Goody Affiliation: Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, USA
Bio-protocol author page: a619
 and Clarissa A. Henry
Clarissa A. HenryAffiliation: School of Biology and Ecology, University of Maine, Orono, USA
For correspondence: clarissa.henry@umit.maine.edu
Bio-protocol author page: a620
date: 6/5/2013, 10080 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.786.

[Abstract] Fluorescent conjugated Phalloidin is a stain that allows for visualization of F-actin. In immunohistochemistry, primary antibodies and fluorescent conjugated secondary antibodies can be used to visualize subcellular localization and relative amounts of proteins of interest. Here is a protocol for Phalloidin ...

[Bio101] Cell Cycle Analysis and GFP Expression of Zebrafish Embryos by FACS (Originally by Narie Storer)

Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
date: 2/20/2012, 9355 views, 2 Q&A
DOI: https://doi.org/10.21769/BioProtoc.185.

[Abstract] Cell cycle analysis in combination of GFP expression has been well used to study the cell cycle distribution of GFP labeled cells. This protocol is a method to analyze the cell cycles of GFP marked cells from zebrafish embryos.
...
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[Bio101] Dig RNA Probe Synthesis and Purification

Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
date: 1/20/2012, 15915 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.173.

[Abstract] In situ hybridization is an effective method to examine the expression level and location of gene of interest on tissues or cells. The method provided in this protocol is a detailed description of synthesizing antisense probe for in situ hybridization....

[Bio101] pH3 Antibody Staining Protocol: For Zebrafish

Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
date: 1/20/2012, 13442 views, 2 Q&A
DOI: https://doi.org/10.21769/BioProtoc.175.

[Abstract] Phosphorylation of histone H3 is tightly correlated with chromosome condensation during both mitosis and meiosis. Staining for phosphor histone H3 is a good indicator for the proliferation of the interested cells. This protocol provides a method to stain p-Histone H3 in zebrafish embryos.
...

[Bio101] Genotyping for Single Zebrafish (Fin Clip) or Zebrafish Embryo

Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
date: 2/5/2012, 12883 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.182.

[Abstract] Zebrafish is increasingly used a genetic model organism in biomedical studies. This protocol provides a detailed procedure about the identification of the genotype of an adult zebrafish or a zebrafish embryo.
...

[Bio101] Preparation of Torula Yeast RNA for Hybe Solutions (Originally by Caroline Burns)

Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
date: 2/5/2012, 10930 views, 5 Q&A
DOI: https://doi.org/10.21769/BioProtoc.180.

[Abstract] In situ hybridization in zebrafish embryos frequently suffers from high background signal. Torular yeast RNA is often added to reduce the non-specific binding that leads to the high background signal. Without appropriate preparation, torular yeast RNA can also add background to the staining. This method ...

[Bio101] Zebrafish Embryo DNA Preparation

Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
date: 2/20/2012, 10464 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.184.

[Abstract] This protocol explains how to extract DNA from a single zebrafish embryo....

Phalloidin Staining and Immunohistochemistry of Zebrafish Embryos

Authors: Michelle F. Goody
Michelle F. Goody Affiliation: Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, USA
Bio-protocol author page: a619
 and Clarissa A. Henry
Clarissa A. HenryAffiliation: School of Biology and Ecology, University of Maine, Orono, USA
For correspondence: clarissa.henry@umit.maine.edu
Bio-protocol author page: a620
date: 6/5/2013, 10080 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.786.

[Abstract] Fluorescent conjugated Phalloidin is a stain that allows for visualization of F-actin. In immunohistochemistry, primary antibodies and fluorescent conjugated secondary antibodies can be used to visualize subcellular localization and relative amounts of proteins of interest. Here is a protocol for Phalloidin ...

[Bio101] Injecting Zebrafish Embryos

Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
date: 1/20/2011, 9417 views, 1 Q&A
DOI: https://doi.org/10.21769/BioProtoc.22.

[Abstract] Zebrafish is convenient for transient genetic manipulations such as morpholino-mediated gene knockdown, DNA/mRNA-based genetic overexpression. These genetic approaches do not involve the challenge of making transgenic animals, and their effect can last up to a week. This protocol describes the detailed ...

[Bio101] Cell Cycle Analysis and GFP Expression of Zebrafish Embryos by FACS (Originally by Narie Storer)

Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
date: 2/20/2012, 9355 views, 2 Q&A
DOI: https://doi.org/10.21769/BioProtoc.185.

[Abstract] Cell cycle analysis in combination of GFP expression has been well used to study the cell cycle distribution of GFP labeled cells. This protocol is a method to analyze the cell cycles of GFP marked cells from zebrafish embryos.
...

[Bio101] Genotyping Transgenic Zebrafish Using Genomic DNA Extracted from Clutch of Embryos (Originally by J. Lefebvre)

Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvania, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
date: 2/5/2012, 7886 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.181.

[Abstract] Transgenic zebrafish are very useful genetic tools to study various biological processes. Identification the right transgene founder and the subsequent transgenic animals are always tedious and time consuming. This protocol provides a relatively rapid and easy method to identify the founder parent using ...

[Bio101] Double In Situ Hybridization (the Fish Method)

Author: Lili Jing
Lili JingAffiliation: Department of Cell and Molecular Biology, University of Pennsylvani, Philadelphia, USA
For correspondence: lilijingcn@gmail.com
Bio-protocol author page: a38
date: 2/5/2012, 7796 views, 0 Q&A
DOI: https://doi.org/10.21769/BioProtoc.178.

[Abstract] Double in situ hybridization I very useful to examine the relationship between the expression of two genes. But it is tricky because of the cross reaction of two different antibodies. This protocol is a valid method to do double color in situ hybridization in zebrafish embryos.
...
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