Table II.
Selected Molecular Markers Available to Study the Zebrafish Retina
| Name | Type | Expression pattern | Referencesa/Sources |
|---|---|---|---|
| Optic lobe, optic stalk markers | |||
| pax2a (pax 2) | RNA probe & Ab (poly) | Nasal retina, optic stalk (≤24 hpf); ON (2 dpf) | Kikuchi et al. (1997), Macdonald et al. (1997), Covance PRB-276P |
| rx1 (zrx1) | RNA probe | Anterior neural keel, optic primordia (≤11 hpf) | Chuang et al. (1999), Pujic and Malicki (2001) |
| rx2 (zrx2) | RNA probe | Anterior neural keel, optic primordia (≤11 hpf) | Chuang et al. (1999), Pujic and Malicki (2001) |
| rx3 (zrx3) | RNA probe | Anterior neural plate (≤9 hpf); optic primordia (≤12 hpf) | Chuang et al. (1999), Pujic and Malicki (2001) |
| six3a (six3) | RNA probe | Neural keel, optic primordia (≤11 hpf) | Pujic and Malicki (2001), Seo et al. (1998) |
| six3b (six6) | RNA probe | Anterior neural keel, optic primordia (≤11 hpf) | Pujic and Malicki (2001), Seo et al. (1998) |
| vax2 | RNA probe | Optic stalk (≤15 hpf); optic stalk, ventral retina (≤18 hpf) | Takeuchi et al. (2003) |
| Ganglion cell markers | |||
| alcamb (neurolin) | RNA probe, Ab (mono & poly) | Ganglion cells (28 hpf, RNA; ≤32 hpf protein) | Fashena and Westerfield (1999), Laessing et al. (1994), Laessing and Stuermer (1996), Zn-5/Zn-8 DSHB and ZIRC |
| cxcr4b | RNA probe | Ganglion cells (30 hpf) | Pujic et al. (2006) |
| gc34 | RNA probe | Ganglion cells (≤36 hpf) | Pujic et al. (2006) |
| L3 | RNA probe | Ganglion cells (30 hpf) | Brennan et al. (1997) |
| Tg (ath5:GFP) | Transgene | Ganglion cells (25 hpf) | Masai et al. (2003, 2005) |
| Tg (brn3c: gap43-GFP) | Transgene | Ganglion cells (42 hpf) | Xiao et al. (2005) |
| Amacrine cell markers | |||
| Ap2α | RNA probe | Amacrine cells (1.5–2 dpf) | Pujic et al. (2006) |
| Ap2β | RNA prove | Amacrine cells (≤36 hpf) | Pujic et al. (2006) |
| Choline acetyltransferase | Ab (poly) | Subset in INL and GCL, IPL (≤5 dpf) | Avanesov et al. (2005), Millipore, cat# AB144P |
| GABA | Ab (poly) | Subset in INL and GCL, IPL (2.5 dpf); ON (2 dpf) | Sandell et al. (1994), Millipore, cat# AB131; Sigma, cat# A2052 |
| GAD67 | Ab (poly) | Subset in INL and few in GCL, IPL (≤7 dpf) | Connaughton et al. (1999), Kay et al. (2001), Millipore, cat# AB9706 |
| Hu C/D | Ab (mono) | INL and GCL (≤3 dpf) | Kay et al. (2001), Link et al. (2000), Invitrogen, cat# A21271 |
| Neuropeptide Y | Ab (poly) | Subset in INL, IPL (≤4 dpf) | Avanesov et al. (2005), ImmunoStar, cat# 22940 |
| Parvalbumin | Ab (mono) | Subset in INL and GCL, IPL (≤3 dpf) | Malicki et al. (2003), Millipore, cat# MAB1572 |
| pax6a (pax6.1) | RNA probe Ab (poly) |
Neuroepithelium (12–34 hpf); INL and GCL (2 dpf); INL (5 dpf) | Hitchcock et al. (1996), Macdonald and Wilson (1997) |
| Serotonin | Ab (poly) | Subset in INL (≤5 dpf) | Avanesov et al. (2005), Sigma, cat# S5545 |
| Somatostatin | Ab (poly) | Subset in INL (≤5 dpf) | Malicki Lab, unpublished data; ImmunoStar, cat# 20067 |
| Substance P | Ab (mono) | Subset in INL (≤5 dpf) | Malicki Lab, unpublished data; AbCam, cat# AB6338 |
| Tyrosine hydroxylase | Ab (mono) | Subset in INL (3–3.5 dpf) | Biehlmaier et al. (2003), Pujic and Malicki (2001), ImmunoStar, cat# 22941; Millipore, cat# MAB318 |
| Bipolar cell markers | |||
| vsx1 | RNA probe | Neuroepithelium (31 hpf); outer INL (50 hpf) | Passini et al. (1997) |
| vsx2 | RNA probe | Neuroepithelium (24 hpf); primarily or exclusively in the bipolar cells (50 hpf) | Passini et al. (1997) |
| Protein kinase C-β1 | Ab (poly) | IPL, OPL (2.5 dpf); bipolar cell somata (4 dpf) | Biehlmaier et al. (2003), Kay et al. (2001), Santa Cruz, cat# sc-209 |
| Tg(nyx::Gal4VP16; UAS::MYFP) | Transgene | ON bipolar cells (2.5 dpf) | Schroeter et al. (2006) |
| Horizontal cell markers | |||
| Cx 52.6 | Ab (poly) | Horizontal cells (≤7 dpf?) | Shields et al. (2007) |
| Cx 55.5 | Ab (poly) | Horizontal cells (≤7 dpf?) | Shields et al. (2007) |
| Horizin | RNA probe | Horizontal cells, weak staining in GCL and inner INL (≤60 hpf) | Pujic et al. (2006) |
| Photoreceptor markers | |||
| Blue opsin | Ab (poly) | Blue cones (≤3 dpf) | Doerre and Malicki (2001), Vihtelic et al. (1999) |
| Blue opsinc | RNA probe | Blue cones (52 hpf) | Chinen et al. (2003), Raymond et al. (1995), Vihtelic et al. (1999) |
| Green opsin | Ab (poly) | Green cones (≤3 dpf) | Doerre and Malicki (2001), Vihtelic et al. (1999) |
| Green opsins (four genes) | RNA probes | Green cones (40–45 hpf) | Chinen et al. (2003), Takechi and Kawamura (2005), Vihtelic et al. (1999) |
| NDRG1 | RNA probe | Photoreceptors (36–48 hpf) | Pujic et al. (2006) |
| Red opsin | Ab (poly) | Red cones (≤3 dpf) | Doerre and Malicki (2001), Vihtelic et al. (1999) |
| Red opsins (two genes) | RNA probes | Red cones (40–45 hpf) | Chinen et al. (2003), Raymond et al. (1995), Takechi and Kawamura (2005) |
| Rod opsin | Ab (poly) | Rods (≤3 dpf) | Doerre and Malicki (2001), Vihtelic et al. (1999) |
| Rod opsinc | RNA probe | Rods (50 hpf) | Chinen et al. (2003), Raymond et al. (1995) |
| Tg (opn1sw1: EGFP) | Transgene | UV cones (≤56 hpf) | Takechi et al. (2003) |
| Tg (xops: GFP) | Transgene | Rods | Fadool (2003) |
| UV opsin | RNA probe | UV cones (56 hpf) | Hisatomi et al. (1996), Takechi et al. (2003) |
| UV opsin | Ab (poly) | UV cones (≤3 dpf) | Doerre and Malicki (2001), Vihtelic et al. (1999) |
| Zpr1 (FRet 43) | Ab (mono) | Double cones in larvae (48 hpf); double cones &bipolar cell subpopulation in the adult | Larison and Bremiller (1990), ZIRC |
| Zpr3 (FRet 11) | Ab (mono) | Rods (50 hpf) | Schmitt and Dowling (1996), ZIRC |
| Zs-4 | Ab (mono) | Rod inner segments (adult), onset unknown | Vihtelic and Hyde (2000), ZIRC |
| Müller glia markers | |||
| cahz (carbonic anhydrase) | RNA probe Ab (poly) | Müller glia (≤4 dpf) | Peterson et al. (1997, 2001) |
| GFAP | Ab (poly) | Müller glia (5 dpf) | Malicki Lab, unpublished data; DAKO, cat# Z0334 |
| Glutamine synthetase | Ab (poly) | Müller glia (60 hpf) | Peterson et al. (2001) |
| Tg (gfap: GFP) | Transgene | Müller glia (48 hpf) | Bernardos and Raymond (2006) |
| Plexiform layer markers | |||
| Phalloidin | Fungal toxin | IPL, OPL, ON (≤60 hpf) | Malicki et al. (2003), Invitrogen, cat# A-12379 |
| Snap-25 | Ab (poly) | OPL, IPL (≤2.5 dpf) | Biehlmaier et al. (2003), StressGen, cat# VAP-SV002 |
| SV2 | Ab (mono) | IPL, OPL (≤2.5 dpf) | Biehlmaier et al. (2003), DSHB |
| Syntaxin-3 | Ab (poly) | OPL (2.5 dpf); faint IPL (5 dpf) | Biehlmaier et al. (2003), Alamone Labs, cat# ANR-005 |
Approximate time of the expression onset is indicated in parenthesis. Sources of commercially available reagents are listed, including catalog numbers where appropriate. Names of markers are listed alphabetically within each section.
DSHB = Developmental Studies Hybridoma Bank (http://dshb.biology.uiowa.edu); ZIRC = Zebrafish International Resource Center (http://zfin.org/zirc/home/guide.php). dpf = days post fertilization; hpf = hours post fertilization; GCL = ganglion cell layer; INL = inner nuclear layer; IPL = inner plexiform layer; OPL = outer plexiform layer; ON = optic nerve.
a
When references to work performed on zebrafish are not available, experiments on related fish species are cited.
b
Zn-5 and Zn-8 antibodies both recognize neurolin (Kawahara et al., 2002).
c
Transcript expression onset was estimated by using goldfish probes (Raymond et al., 1995).