Table I.
Techniques Available to Study the Zebrafish Retina and Their Sources/Examples of Use
| Protocol | Goal | Sources/Examples of Use |
|---|---|---|
| Histological analysis | ||
| Electron microscopy | Evaluation of phenotype on a subcellular level | Allwardt et al. (2001), Doerre and Malicki (2002), Kimmel et al. (1981) |
| Light microscopy | Evaluation of phenotype on a cellular level | Malicki et al. (1996), Schmitt and Dowling (1994) |
| Molecular marker analysis | ||
| Antibody staining (whole mount) | Determination of expression pattern on protein level | Schmitt and Dowling (1996) |
| Antibody staining (sections) | Determination of expression pattern on protein level | Pujic and Malicki (2001), Wei and Malicki (2002) |
| In situ hybridization—double labeling | Parallel determination of two expression patterns on transcript level | Hauptmann and Gerster (1994), Jowett (2001), Jowett and Lettice (1994), Strahle et al. (1994) |
| In situ hybridization—frozen sections | Determination of expression pattern on transcript level | Barthel and Raymond (1993), Hisatomi et al. (1996) |
| In situ hybridization—whole mount | Determination of expression pattern on transcript level | Oxtoby and Jowett (1993), Thisse et al. (2004) |
| Gene function analysis | ||
| Implantation | Test of function for a factor (most often diffusible) via the implantation of a bead saturated with this substance | Hyatt et al. (1996), Martinez-Morales et al. (2005) |
| Morpholino knockdown | Test of gene function based on antisense inhibition of its activity | Eisen and Smith (2008), Nasevicius and Ekker (2000), Tsujikawa and Malicki (2004a) |
| Overexpression (DNA injections) | Test of gene function based on enhancement of its activity through DNA injections | Koster and Fraser (2001), Mumm et al. (2006) |
| Overexpression (light-mediated RNA/DNA uncaging) | Identification of gene function through enhancement of its activity in selected tissues at specific developmental stages | Ando et al. (2001), Ando and Okamoto (2003) |
| Overexpression (RNA injections) | Test of gene function based on enhancement of its activity through RNA injections | Macdonald et al. (1995), reviewed in Malicki et al. (2002) |
| Overexpression (UAS–GAL4 system) | Test of gene function in selected tissues using stable transgenic lines | Del Bene et al. (2008), Scheer and Campos-Ortega (1999) |
| TILLING (targeting induced local lesions in genomes) | Identification of chemically induced mutant alleles in a specific genetic locus | Colbert et al. (2001), Wienholds et al. (2002) |
| Zinc finger nucleases | Identification of mutant alleles in a specific locus | Doyon et al. (2008), Meng et al. (2008) |
| Embryological techniques | ||
| Cell labeling (caged fluorophore) | Fate determination for a specific group of cells | Take-uchi et al. (2003) |
| Cell labeling (iontophoretic) | Determination of morphogenetic movements or cell lineage relationships | Li et al. (2000b), Varga et al. (1999), Woo and Fraser (1995) |
| Cell labeling (lipophilic tracers) | Analysis of ganglion cell development (for example, retino tectal projection) | Baier et al. (1996), Malicki and Driever (1999) Mangrum et al. (2002) |
| Cell labeling (fluorescent protein transgenes) | Determination of cell fate and fine differentiation features in living animals | Hatta et al. (2006), Mumm et al. (2006), Neumann and Nuesslein-Volhard (2000) |
| Mitotic activity detection (BrdU) | Identification of mitotically active cell populations; birth dating | Hu and Easter (1999), Larison and Bremiller (1990), Del Bene et al. (2008) |
| Mitotic activity detection (tritiated thymidine) | Identification of mitotically active cell populations; birth dating | Nawrocki (1985) |
| Tissue ablation | Functional test for a field of cells via their removal by surgical means | Masai et al. (2000) |
| Transplantation (whole eye) | Test whether a defect (in axonal navigation, for example) originates within or outside the eye | Fricke et al. (2001) |
| Transplantation (fragment of tissue) | Functional test for a field of cells via their transplantation to an ectopic position by surgical means | Masai et al. (2000) |
| Transplantation (blastomere) | Test of cell autonomy of a mutant phenotype by generating a genetically mosaic embryo | Ho and Kane (1990), Jensen et al. (2001), Malicki and Driever (1999), Jing and Malicki (2009) |
| Behavioral tests | ||
| Optokinetic response | Test of vision based on eye movements; allows for evaluation of visual acuity | Brockerhoff et al. (1995), Clark (1981), Neuhauss et al. (1999) |
| Optomotor response | Test of vision based on swimming behavior | Clark (1981), Neuhauss et al. (1999) |
| Startle response | Simple test of vision based on swimming behavior | Easter and Nicola (1996) |
| Electrophysiological tests | ||
| ERG | Test of retinal function based on the detection of electrical activity of retinal neurons and glia | Avanesov et al. (2005), Brockerhoff et al. (1995) |
| Biochemical approaches | ||
| Co-immunoprecipitation from embryo extracts | Identification of direct and indirect protein binding partners | Insinna et al. (2008), Krock and Perkins (2008) |
| Tandem affinity purification from embryo extracts | Identification of direct and indirect protein binding partners | Omori et al. (2008) |
| Chemical screens | ||
| Screens of small-molecule libraries | Identification of chemicals that affect a developmental process | Kitambi et al. (2008) |
| Genetic screens | ||
| Behavioral | Detection of mutant phenotypes by behavioral tests | Muto et al. (2005), Neuhauss et al. (1999) |
| Histological | Detection of mutant phenotypes via histological analysis of sections | Mohideen et al. (2003) |
| Marker/tracer labeling | Detection of mutant phenotypes via staining with antibodies, RNA probes, or lipophilic tracers | Baier et al. (1996), Guo et al. (1999) |
| Morphological | Detection of mutant phenotypes by morphological criteria | Malicki et al. (1996) |
| Transgene guided | Detection of mutant phenotypes in transgenic lines expressing fluorescent proteins in specific cell populations | Xiao et al. (2005) |
In this table, we primarily cite experiments performed on the retina. Only where references to work on the eye are not available, we refer to studies of other organs. Most forward genetic approaches such as mutagenesis, mapping, and positional cloning methods do not contain visual system-specific features and thus are not listed in this table. These approaches are discussed in depth in other sections of this volume. Entries are listed alphabetically within each section of the table.