We thank P. Verrijzer, J. Johansen H., Okhura for antibodies and A. Debec, the Bloomington and Vienna stock centers for flies. Thanks to C. Jackson for suggestions and stimulating discussions.

1. Drosophila testes collection
NOTE: Young males (0-15 h post-eclosion) are necessary for examining diploid germ cells (i.e., spermatogonia and spermatocytes).
<ol>
	<li>Select young flies as much as possible to minimize interference from developing spermatids.</li>
	<li>Anesthetize flies by brief exposure to carbon dioxide and transfer to a fly pad14,15.</li>
	<li>Under a dissecting microscope (10x magnification), use forceps to re...

<ol>
	<li>Cenci, G., Bonaccorsi, S., Pisano, C., Verni, F., Gatti, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromatin+and+microtubule+organization+during+premeiotic,+meiotic+and+early+postmeiotic+stages+of+Drosophila+melanogaster+spermatogenesis.">Chromatin and microtubule organization during premeiotic, meiotic and early postmeiotic stages of Drosophila melanogaster spermatogenesis.</a> Journal of Cell Science. 107, 3521-3534 (1994).</li><li>Bonaccorsi, S., Giansanti, M. G., Gatti, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spindle+assembly+in+Drosophila+neuroblasts+and+ganglion+mother+cells.">Spindle assembly in Drosophila neuroblasts and ganglion mother cells.</a> Nature Cell Biology. 2 (1), 54-56 (2000).</li><li>Fabbretti, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Confocal+Analysis+of+Nuclear+Lamina+Behavior+during+Male+Meiosis+and+Spermatogenesis+in+Drosophila+melanogaster.">Confocal Analysis of Nuclear Lamina Behavior during Male Meiosis and Spermatogenesis in Drosophila melanogaster.</a> PLoS One. 11 (3), 0151231 (2016).</li><li>Fuller, M. T., Bate, M., Martinas-Arias, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> The Development of Drosophila melanogaster. 1, 71-148 (1993).</li><li>Hiller, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Testis-specific+TAF+homologs+collaborate+to+control+a+tissue-specific+transcription+program.">Testis-specific TAF homologs collaborate to control a tissue-specific transcription program.</a> Development. 131 (21), 5297-5308 (2004).</li><li>Chen, X., Hiller, M., Sancak, Y., Fuller, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue-specific+TAFs+counteract+Polycomb+to+turn+on+terminal+differentiation.">Tissue-specific TAFs counteract Polycomb to turn on terminal differentiation.</a> Science. 310 (5749), 869-872 (2005).</li><li>White-Cooper, H., Davidson, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Unique+aspects+of+transcription+regulation+in+male+germ+cells.">Unique aspects of transcription regulation in male germ cells.</a> Cold Spring Harbor Perspectives in Biology. 3 (7), (2011).</li><li>Luo, Y., Ahmad, E., Liu, S. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MAD1:+Kinetochore+Receptors+and+Catalytic+Mechanisms.">MAD1: Kinetochore Receptors and Catalytic Mechanisms.</a> Frontiers in Cell and Developmental Biology. 6, 51 (2018).</li><li>Chen, R. H., Shevchenko, A., Mann, M., Murray, A. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spindle+checkpoint+protein+Xmad1+recruits+Xmad2+to+unattached+kinetochores.">Spindle checkpoint protein Xmad1 recruits Xmad2 to unattached kinetochores.</a> Journal of Cell Biology. 143 (2), 283-295 (1998).</li><li>Campbell, M. S., Chan, G. K., Yen, T. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mitotic+checkpoint+proteins+HsMAD1+and+HsMAD2+are+associated+with+nuclear+pore+complexes+in+interphase.">Mitotic checkpoint proteins HsMAD1 and HsMAD2 are associated with nuclear pore complexes in interphase.</a> Journal of Cell Science. 114, 953-963 (2001).</li><li>Katsani, K. R., Karess, R. E., Dostatni, N., Doye, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=In+vivo+dynamics+of+Drosophila+nuclear+envelope+components.">In vivo dynamics of Drosophila nuclear envelope components.</a> Molecular Biology of the Cell. 19 (9), 3652-3666 (2008).</li><li>Raich, N., Mahmoudi, S., Emre, D., Karess, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mad1+influences+interphase+nucleoplasm+organization+and+chromatin+regulation+in+Drosophila.">Mad1 influences interphase nucleoplasm organization and chromatin regulation in Drosophila.</a> Open Biology. 8 (10), (2018).</li><li>Chang, Y. J., Pi, H., Hsieh, C. C., Fuller, M. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Smurf-mediated+differential+proteolysis+generates+dynamic+BMP+signaling+in+germline+stem+cells+during+Drosophila+testis+development.">Smurf-mediated differential proteolysis generates dynamic BMP signaling in germline stem cells during Drosophila testis development.</a> Developmental Biology. 383 (1), 106-120 (2013).</li><li>Stocker, H., Gallant, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Getting+started:+an+overview+on+raising+and+handling+Drosophila.">Getting started: an overview on raising and handling Drosophila.</a> Methods in Molecular Biology. 420, 27-44 (2008).</li><li>Zamore, P. D., Ma, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+Drosophila+melanogaster+testes.">Isolation of Drosophila melanogaster testes.</a> Journal of Visualized Experiments. (51), e2641 (2011).</li><li>Gigliotti, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nup154,+a+new+Drosophila+gene+essential+for+male+and+female+gametogenesis+is+related+to+the+nup155+vertebrate+nucleoporin+gene.">Nup154, a new Drosophila gene essential for male and female gametogenesis is related to the nup155 vertebrate nucleoporin gene.</a> Journal of Cell Biology. 142 (5), 1195-1207 (1998).</li><li>Chen, H., Chen, X., Zheng, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+nuclear+lamina+regulates+germline+stem+cell+niche+organization+via+modulation+of+EGFR+signaling.">The nuclear lamina regulates germline stem cell niche organization via modulation of EGFR signaling.</a> Cell Stem Cell. 13 (1), 73-86 (2013).</li><li>Fawcett, D. W., Chemes, H. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Changes+in+distribution+of+nuclear+pores+during+differentiation+of+the+male+germ+cells.">Changes in distribution of nuclear pores during differentiation of the male germ cells.</a> Tissue Cell. 11 (1), 147-162 (1979).</li><li>Bolte, S., Cordelieres, F. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+guided+tour+into+subcellular+colocalization+analysis+in+light+microscopy.">A guided tour into subcellular colocalization analysis in light microscopy.</a> Journal of Microscopy. 224, 213-232 (2006).</li><li>White-Cooper, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue,+cell+type+and+stage-specific+ectopic+gene+expression+and+RNAi+induction+in+the+Drosophila+testis.">Tissue, cell type and stage-specific ectopic gene expression and RNAi induction in the Drosophila testis.</a> Spermatogenesis. 2 (1), 11-22 (2012).</li><li>Bonaccorsi, S., Giansanti, M. G., Cenci, G., Gatti, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Immunostaining of Drosophila testes. 2011 (10), 1273-1275 (2011).</li><li>Bonaccorsi, S., Giansanti, M. G., Cenci, G., Gatti, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Paraformaldehyde fixation of Drosophila testes. 2012 (1), 102-104 (2012).</li><li>White-Cooper, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Spermatogenesis:+analysis+of+meiosis+and+morphogenesis.">Spermatogenesis: analysis of meiosis and morphogenesis.</a> Methods in Molecular Biology. 247, 45-75 (2004).</li><li>Kibanov, M. V., Kotov, A. A., Olenina, L. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multicolor+fluorescence+imaging+of+whole-mount+Drosophila+testes+for+studying+spermatogenesis.">Multicolor fluorescence imaging of whole-mount Drosophila testes for studying spermatogenesis.</a> Analytical Biochemistry. 436 (1), 55-64 (2013).</li><li>Theofel, I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=tBRD-1+and+tBRD-2+regulate+expression+of+genes+necessary+for+spermatid+differentiation.">tBRD-1 and tBRD-2 regulate expression of genes necessary for spermatid differentiation.</a> Biology Open. 6 (4), 439-448 (2017).</li><li>Trost, M., Blattner, A. C., Leo, S., Lehner, C. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drosophila+dany+is+essential+for+transcriptional+control+and+nuclear+architecture+in+spermatocytes.">Drosophila dany is essential for transcriptional control and nuclear architecture in spermatocytes.</a> Development. 143 (14), 2664-2676 (2016).</li></ol>

This protocol provides a method for successful immunolabeling of whole-mount adult Drosophila testes. As reported in other procedures young males must be used (we even shortened the age to less than 20 hours after eclosion) to minimize the presence of developing sperm, which risks obstructing the spermatocytes. The dissection should be rapid and the antibody dilution must be adjusted to optimize the signal-to-noise ratio21,22,23...

Drosophila testes are a valuable model for the study of nuclear architecture. In mitotic spermatogonial cells, the nuclear volume is largely occupied by chromatin. These cells undergo four rounds of division, producing a cyst of 16 primary spermatocytes. Over the next several days, the spermatocytes pass through 6 developmental stages (S1-S6), greatly increasing in volume, approximatively 20-fold1,2. They also change their nuclear morphology. The outline of the nucleus, revealed by the lamin Dm0, becomes irregular and shows deep invaginations1,3. This is accompanied by extensive gene expression changes and modifications in chromatin organization1,4,5,6,7. The interphase chromosomes are well-defined in stage S4-S5, forming three distinct masses corresponding to the 2 major bivalent autosomes and the X-Y pair docked with the nucleolus.
Mad1 was originally isolated as a key component of the mitotic checkpoint (reviewed in8). In interphase, it is described as located primarily at the nuclear envelope but also in the nucleoplasm9,10,11. In Drosophila testis, we reported that Mad1 is prominent in the nucleoplasm, intimately associated with the two major autosomal chromatin masses and to a lesser extent with the XY chromatin. We defined this chromatin-associated structure as MINT (Mad1-containing IntraNuclear Territory)12. Four other proteins were associated with MINTs in spermatocytes: the nucleoporin Mtor/Tpr, the SUMO peptidase Ulp1, the mitotic checkpoint protein Mad2 and a subunit of a Polycomb-like complex Raf212.
To complete the description of MINTs, we needed to use antibodies and were confronted with the technical problems generally encountered with immunostaining in testis: a poor permeability resulting in a significant non-uniformity of staining in the depth of the testis, particularly in the large spermatocytes. Squashed preparations increased antibody access but led to compressed images, restricting the 3D analyses, and preventing measurement of quantitative fluorescence, including colocalization. The problem of antibody penetration could also be addressed by permeabilizing agents such as 0.3% Na deoxycholate13, but this procedure did not in our hands yield reproducible results. Because we performed many co-labeling experiments, we looked to improve the permeabilization protocol. The combination of 1% NP40 plus heptane resulted in more reproducibility, particularly in studying the large spermatocytes.
This protocol performs fixation and immunostaining of testes in suspension, improving the sample quality as well as enhancing reproducibility, and rendering it suitable for confocal microscopy. We used the protocol to better define the spatial relationships of certain nuclear envelope proteins with the nucleoplasmic structures of large spermatocytes. This method will permit better investigations of the changes that accompany spermatocyte development, for example the dynamic structural changes of the nucleus including chromatin, nucleoplasm and the nuclear pores.

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	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:277px;">Drosophila srains</td>
			<td style="width:129px;"></td>
			<td style="width:93px;"></td>
			<td style="width:505px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:277px;">ketelGFP y; ketelGFP/y+CyO</td>
			<td style="width:129px;"></td>
			<td style="width:93px;"></td>
			<td>Gift from A. Debec (Institut Jacques Monod, UMR 7592, Paris, France)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:277px;">Mad1-GFP</td>
			<td style="width:129px;"></td>
			<td style="width:93px;"></td>
			<td>J Cell Sci. 2011 May 15;124(Pt 10):1664-71.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:277px;">Mtor RNAi&#160;</td>
			<td style="width:129px;">VDRC</td>
			<td style="width:93px;">ID 110218</td>
			<td>Vienna Drosophila RNAi Center</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:277px;">Materials</td>
			<td style="width:129px;"></td>
			<td style="width:93px;"></td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;width:277px;">DAPI&#160;</td>
			<td style="width:129px;">Thermo</td>
			<td>D1306</td>
			<td>Stock solution must be prepared in H2O</td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Dumont # 5 Fine Forseps&#160;</td>
			<td style="width:129px;">Fine Science Tools</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">MBP Wide Bore Pipette Tips</td>
			<td style="width:129px;">Fisherbrand</td>
			<td>11917744</td>
			<td>Wide aperture tip</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Thermo Scientific&#160;0.2 mL Individual Tube</td>
			<td style="width:129px;">Thermo</td>
			<td>AB-0620</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">2 ml micro centrifuge tubes&#160;</td>
			<td style="width:129px;">Sigma</td>
			<td>T3531-200EA&#160;</td>
			<td>Siliconized 2ml tube</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Citifluor AF1</td>
			<td style="width:129px;">Citifluor</td>
			<td>AF1</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Dakopen&#160;</td>
			<td style="width:129px;">Sigma</td>
			<td style="width:93px;">Z377821-1EA&#160;</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Normal Goat Serum (NGS)</td>
			<td style="width:129px;">Sigma</td>
			<td>NS02L-1ML</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Paraformaldehyde 4%</td>
			<td style="width:129px;">Sigma</td>
			<td style="width:93px;">P6148-500G&#160;</td>
			<td>Paraformaldehyde (4%) dissolved in PBS 1X&#160;; aliquot by 600 ml&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">PBS 1X</td>
			<td style="width:129px;">Thermo</td>
			<td>14190094</td>
			<td>DPBS, no calcium, no magnesium</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">0.1% (0.2 or 0.3%) PBS-T&#160;</td>
			<td style="width:129px;"></td>
			<td></td>
			<td>PBS 1X&#160; containing 0.1% (0.2 % or 0.3%) Triton X-100</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Triton X-100, for molecular biology,&#160;</td>
			<td style="width:129px;">Sigma</td>
			<td>T8787</td>
			<td></td>
		</tr>
		<tr height="22">
			<td height="22" style="height:22px;">Antibodies</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">GFP booster</td>
			<td style="width:129px;">Chromotek</td>
			<td>gba488</td>
			<td>1/200</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Mouse anti-Mtor</td>
			<td style="width:129px;"></td>
			<td style="width:93px;"></td>
			<td style="width:505px;">1/40 gift from J. Johansen, Iowa State University</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Rat anti-Nup62</td>
			<td style="width:129px;"></td>
			<td style="width:93px;"></td>
			<td style="width:505px;">1/200 gift from H. Ohkura (University of Edinburgh, UK</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Guinea-pig anti-Ulp1</td>
			<td style="width:129px;"></td>
			<td style="width:93px;"></td>
			<td>1/200 gift from C. P. Verrijzer, Erasmus University, Rotterdam</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:277px;">Rabbit anti-Raf2</td>
			<td style="width:129px;"></td>
			<td style="width:93px;"></td>
			<td>1/200 gift from C. P. Verrijzer, Erasmus University, Rotterdam</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DyLight conjugated series&#160;</td>
			<td style="width:129px;">Thermo</td>
			<td style="width:93px;"></td>
			<td>1/500 Donkey anti-(guinea-pig, mouse,&#160; rabbit or rat) as second antibodies</td>
		</tr>
	</tbody>
</table>

immunostaining of whole-mount drosophila testes for 3d confocal analysis of large spermatocytes

Drosophila testes are a powerful model system for studying biological processes including stem cell biology, nuclear architecture, meiosis and sperm development. However, immunolabeling of the whole Drosophila testis is often associated with significant non-uniformity of staining due to antibody penetration. Squashed preparations only partially overcome the problem since it decreases the 3D quality of the analyses. Herein, we describe a whole-mount protocol using NP40 and heptane during fixation together with immunolabeling in liquid media. It preserves the volume suitable for confocal microscopy together with reproducible and reliable labeling. We show different examples of 3D reconstitution of spermatocyte nuclei from confocal sections. The intra- and inter-testes reproducibility allows 3D quantification and comparison of fluorescence between single cells from different genotypes. We used different components of the intranuclear MINT structure (Mad1-containing Intra Nuclear Territory) as well as two components associated with the nuclear pore complex to illustrate this protocol and its applications on the largest cells of the testis, the S4-S5 spermatocytes.

The main obstacle to obtaining adequate staining of Drosophila testes is the limited penetrability of antibodies, which has been partially resolved by using squashed preparations but at the cost of inducing a restriction of the 3D analyses (for example 3D representation or measure of colocalization). The procedure permits uniform labeling and preserves the volume of all the cells of the testis. Here we have focused the illustration of the method on the 3D representation of S4-S5 spermatocytes, as they are the largest cel...

Watch this Scientific Journal Video about Immunostaining of Whole-Mount Drosophila Testes for 3D Confocal Analysis of Large Spermatocytes at JoVE.com

Immunostaining of Whole-Mount Drosophila Testes for 3D Confocal Analysis of Large Spermatocytes

We present here an improved protocol for the whole-mount preparation and immunostaining of Drosophila testes, suitable for confocal microscopy and also allowing reproducible and reliable labeling. We illustrate this protocol by 3D representation and quantification of colocalization experiments on the large S4-S5 spermatocytes.

Immunostaining of Whole-Mount Drosophila Testes for 3D Confocal Analysis of Large Spermatocytes

Drosophila testes are a powerful model system for studying biological processes including stem cell biology, nuclear architecture, meiosis and sperm ...

Whole-mount staining of Drosophila tissues, such as testis samples, is often problematic due to limited antibody penetration. Our fixation protocol using NP40 and heptane permits a uniform and reproducible labeling. By maintaining tissue shape while permitting deep antibody penetration, this procedure facilitates the reproducible, quantifiable acquisition of immunostaining in three dimensions, both singly and in colocalization studies.For diploid germ cell evaluation, zero to 15 hours post-eclosion, anesthetize the flies by a brief exposure to carbon dioxide, and transfer the flies to a fly pad. Place the pad under a dissecting microscope at a 10X magnification, and use forceps to remove the heads from five to 10 male flies. Transfer the decapitated fly bodies to 100 microliters of Ringer's buffer on a silicone-coated glass slide on a black background support, and use the 40X magnification and a pair of number five forceps to grasp a fly between the thorax and the abdomen.Then pull the abdomen away from the thorax and rapidly isolate the testes and adjacent tissues from the fly carcass. Once all of the testes have been collected, clean the samples of any remaining tissue and use a 200 microliter pipette tip to remove the excess buffer from around the dissected testes. Then place a drop of 4%paraformaldehyde onto the testes and quickly transfer the tissues to a tube containing two milliliters of freshly prepared 4%paraformaldehyde solution supplemented with 20%NP40 and heptane.For thorough fixation of the testes samples, shake the tube vertically for 30 seconds before incubating the testes on a rotary mixer at room temperature for 30 minutes. At the end of the incubation, transfer the tube to a tube rack and allow the testes to settle at the bottom of the tube. Remove all of the heptane and fixative solution and quickly rinse the testes three times with PBS.After the last wash, transfer the testes to a new 200 microliter tube and use a 200 microliter pipette equipped with a 10 microliter pipette tip to remove any excess buffer. Then add 200 microliters of fresh PBS-To the tube and place the testes on ice. For antibody labeling of the testes samples, replace the PBS with 200 microliters of 0.3%PBS-T for a 30-minute incubation at room temperature.After permeabilization, block any non-specific binding with 0.3%PBS-T plus 5%normal goat serum for one hour at room temperature before adding 200 microliters of the primary antibody of interest diluted in 0.3%PBS-T plus 5%normal goat serum for an overnight incubation at four degrees Celsius or room temperature with rocking. The next morning, wash the samples with three 15-minute washes with fresh 0.3%PBS-T and rocking at room temperature per wash and allow the testes to settle to the bottom of the tube by gravity. Add 200 microliters of an appropriate secondary antibody to the tube for a four-hour incubation with rocking at room temperature protected from light before washing the samples in fresh 0.3%PBS-T per wash, as demonstrated.After the 0.3%PBS-T wash, wash the samples one time in 0.2%PBS-T and one time in 0.1%PBS-T for 30 minutes per wash on the rocker, followed by a final 30-minute wash in PBS alone. After the PBS wash, label the samples with 180 microliters of a one microgram per milliliter DAPI solution in PBS for 15 minutes at room temperature protected from light, followed by three 5-minute washes in fresh PBS per wash. After the last wash, use a hydrophobic barrier pen to draw a circle on a clean slide, and use a 0.1%PBS-T primed pipette tip to transfer the testes to the slide.Aspirate any excess PBS and add 100 microliters of Citifluor AF1. Gently place a glass cover slip over the tissue, taking care to avoid trapping air bubbles, and use clear nail polish to seal the cover slip to the slide before observing the slides by confocal fluorescence microscopy. After acquiring confocal images of the samples, import the images into an appropriate image analysis software program.Then use manual segmentation to define the nucleus within each cell and determine the Pearson's correlation coefficients inside the entire volume between two fluorophores. This protocol permits the acquisition of confocal images of a sufficient quality to be treated for 3D reconstitution. For example, in these four adjacent serial sections of a stage S5 spermatocyte, a low level of Mad1 is observed at the nuclear envelope and a high-level accumulation of Mad1 can be visualized in conjunction with DAPI staining within the nucleus.in this 3D reconstituted image, the low level presence of Mad1 at the nuclear surface and high-level accumulation of Mad1 within the nucleus can be observed together with the DNA. In these 3D reconstitutions, large S5 spermatocytes stained with Nucleoporin 62 and Mad1 or Importin-beta and DAPI can be observed. In both reconstructions, the nuclear pore-associated components appear to be non-uniformly distributed over the nuclear rim as dots of irregular size.While conserving the 3D volume of the cells, this protocol also facilitates a uniform penetration of antibodies of interest into the depth of every cell, allowing quantitative analyses, such as colocalization. Because the protocol permits a reliable measurement of colocalizations from independent testes, it can also be used to compare staining in different fly genotypes. The amount of NP40 used is critical for sufficient permeabilization.If the procedure is followed closely, reproducible labeling and 3D nuclear structure preservation can be achieved. Although whole-mount staining of tissues within Drosophila can be tricky, this protocol can be easily adapted for other samples.

immunostaining-whole-mount-drosophila-testes-for-3d-confocal-analysis

Research

JoVE Journal

Biology

4.0K Views.  Université de Paris, F 75006, Paris, France. Whole-mount staining of Drosophila tissues, such as testis samples, is often problematic due to limited antibody penetration. Our fixation protocol using NP40 and heptane permits a uniform and reproducible labeling. By maintaining tissue shape while permitting deep antibody penetration, this procedure facilitates the reproducible, quantifiable acquisition of immunostaining in three dimensions, both singly and in colocalization studies.For diploid germ cell evaluation, zero to 15 hours ...

Video: Immunostaining of Whole-Mount Drosophila Testes for 3D Confocal Analysis of Large Spermatocytes

We present here an improved protocol for the whole-mount preparation and immunostaining of Drosophila testes, suitable for confocal microscopy and also allowing reproducible and reliable labeling. We illustrate this protocol by 3D representation and quantification of colocalization experiments on the large S4-S5...

immunostaining of whole-mount retinas with the clarity tissue clearing method

Immunostaining of Whole-Mount Retinas with the CLARITY Tissue Clearing Method

Here we present a protocol to adapt the CLARITY method of the brain tissues for whole-mount retinas to improve the quality of standard immunohistochemical staining and high-resolution imaging of retinal neurons and their subcellular...

cytological analysis of spermatogenesis: live and fixed preparations of drosophila testes

Cytological Analysis of Spermatogenesis: Live and Fixed Preparations of Drosophila Testes

Methods for isolating and preparing Drosophila testes samples (live and fixed) for imaging by phase-contrast and fluorescence microscopy are described...

Cytological Analysis of Spermatogenesis: Live and Fixed Preparations of Drosophila Testes

preparation of drosophila larval and pupal testes for analysis of cell division in live, intact tissue

Preparation of Drosophila Larval and Pupal Testes for Analysis of Cell Division in Live, Intact Tissue

The goal of this protocol is to analyze cell division in intact tissue by live and fixed cell microscopy using Drosophila meiotic spermatocytes. The protocol demonstrates how to isolate whole, intact testes from Drosophila larvae and early pupae, and how to process and mount them for...

Preparation of Drosophila Larval and Pupal Testes for Analysis of Cell Division in Live, Intact Tissue

immunostaining for dna modifications: computational analysis of confocal images

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

Newly discovered oxidized forms of 5-methylcytosine (oxi-mCs), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) may represent distinct DNA modifications with unique functional roles. Here a semi-quantitative workflow for visualization of oxi-mCs' spatial distribution, signal intensity profiling and colocalization is described.

whole-mount immunostaining and automatic counting of mouse retinal ganglion cells

Author Spotlight: Efficient Retinal Ganglion Cell Counting in Mouse Models of Glaucoma for Treatment Evaluation

This protocol describes the procedure for isolating the whole-mount mouse retina and performing immunostaining to label all retinal ganglion cells (RGCs). The process is followed by imaging and automatically counting RGCs using AI-based software, providing a simple, fast, and accurate method for quantifying RGCs in the entire mouse...

Whole-Mount Immunostaining and Automatic Counting of Mouse Retinal Ganglion Cells

immunostaining phospho-epitopes in ciliated organs of whole mount zebrafish embryos

Immunostaining Phospho-epitopes in Ciliated Organs of Whole Mount Zebrafish Embryos

Techniques are described to immunostain phospho-epitopes in whole zebrafish embryos and then conduct two-color fluorescent confocal localization in cellular structures as small as primary cilia. The techniques for fixing and imaging can define the location and kinetics of the appearance or activation of specific...

enrichment of pachytene spermatocytes and spermatids from mouse testes using standard laboratory equipment

Enrichment of Pachytene Spermatocytes and Spermatids from Mouse Testes Using Standard Laboratory Equipment

Presented here is a protocol for enriching pachytene spermatocytes, round spermatids, and elongating spermatids from adult mouse testes using a discontinuous bovine serum albumin density gradient with standard laboratory...

visualization of 3d white adipose tissue structure using whole-mount staining

Visualization of 3D White Adipose Tissue Structure Using Whole-mount Staining

The focus of the present study is to demonstrate the whole-mount immunostaining and visualization technique as an ideal method for 3D imaging of adipose tissue architecture and cellular...

isolation of drosophila melanogaster testes

Isolation of Drosophila melanogaster Testes

Drosophila melanogaster testes can be rapidly and efficiently isolated from adult males using dissecting needles. With practice, one can readily isolate in one or two days an amount of testes sufficient for the analysis of DNA or RNA by high throughput sequencing or more traditional molecular biology methods or of protein for antibody- or enzyme-based...

Isolation of Drosophila melanogaster Testes

visualization and analysis of pharyngeal arch arteries using whole-mount immunohistochemistry and 3d reconstruction

Visualization and Analysis of Pharyngeal Arch Arteries using Whole-mount Immunohistochemistry and 3D Reconstruction

Here, we describe a protocol to visualize and analyze the pharyngeal arch arteries 3, 4, and 6 of mouse embryos using whole-mount immunofluorescence, tissue clearing, confocal microscopy, and 3D...

batch immunostaining for large-scale protein detection in the whole monkey brain

Batch Immunostaining for Large-Scale Protein Detection in the Whole Monkey Brain

Large-scale immunodetection of target proteins across the entire primate brain is possible by employing novel tissue embedding and sectioning methods combined with the use of creative apparatus for batch staining of multiple free-floating sections at a given...

whole-mount immunofluorescence staining, confocal imaging and 3d reconstruction of the sinoatrial and atrioventricular node in the mouse

Whole-Mount Immunofluorescence Staining, Confocal Imaging and 3D Reconstruction of the Sinoatrial and Atrioventricular Node in the Mouse

We provide a step-by-step protocol for whole-mount immunofluorescence staining of the sinoatrial node (SAN) and atrioventricular node (AVN) in murine...

a simple one-step dissection protocol for whole-mount preparation of adult drosophila brains

A Simple One-step Dissection Protocol for Whole-mount Preparation of Adult Drosophila Brains

The adult Drosophila brain is a valuable system for studying neuronal circuitry, higher brain functions, and complex disorders. An efficient method to dissect whole brain tissue from the small fly head will facilitate brain-based studies. Here we describe a simple, one-step dissection protocol of adult brains with well-preserved...

A Simple One-step Dissection Protocol for Whole-mount Preparation of Adult Drosophila Brains

whole mount immunolabeling of olfactory receptor neurons in the drosophila antenna

Whole Mount Immunolabeling of Olfactory Receptor Neurons in the Drosophila Antenna

Herein we describe the process of whole mount immunostaining of Drosophila antennae, which enables us to better understand the molecular mechanisms involved in the diversification of olfactory receptor neurons...

Whole Mount Immunolabeling of Olfactory Receptor Neurons in the Drosophila Antenna

whole mount rna fluorescent in situ hybridization of drosophila embryos

Whole Mount RNA Fluorescent in situ Hybridization of Drosophila Embryos

Here we describe a whole-mount fluorescent in situ hybridization (FISH) protocol for determining the expression and localization properties of RNAs expressed during embryogenesis in the fruit fly, Drosophila...

Whole Mount RNA Fluorescent in situ Hybridization of Drosophila Embryos

whole mount preparation of the adult drosophila ventral nerve cord for giant fiber dye injection

Whole Mount Preparation of the Adult Drosophila Ventral Nerve Cord for Giant Fiber Dye Injection

An in vivo dissection of the adult Drosophila ventral nerve cord (VNC) is demonstrated. This particular dissection method causes little damage to the VNC allowing the subsequent labeling of the giant fiber neurons with fluorescent dye for high resolution...

Whole Mount Preparation of the Adult Drosophila Ventral Nerve Cord for Giant Fiber Dye Injection

confocal laser scanning microscopy-based quantitative analysis of aspergillus fumigatus conidia distribution in whole-mount optically cleared mouse lung

Confocal Laser Scanning Microscopy-Based Quantitative Analysis of Aspergillus fumigatus Conidia Distribution in Whole-Mount Optically Cleared Mouse Lung

We describe the method for quantitative analysis of the distribution of Aspergillus fumigatus conidia (3 &#181;m in size) in the airways of mice. The method also can be used for the analysis of microparticles and nanoparticle agglomerate distribution in the airways in various pathological condition...

Confocal Laser Scanning Microscopy-Based Quantitative Analysis of Aspergillus fumigatus Conidia Distribution in Whole-Mount Optically Cleared Mouse Lung

dissection of the transversus abdominis muscle for whole-mount neuromuscular junction analysis

Dissection of the Transversus Abdominis Muscle for Whole-mount Neuromuscular Junction Analysis

In this video we demonstrate a protocol for dissection of the transversus abdominis muscle of the mouse and use immunofluorescence and microscopy to visualize neuromuscular...

Dissection of the Transversus Abdominis Muscle for Whole-mount Neuromuscular Junction Analysis

visualization of the embryonic nervous system in whole-mount drosophila embryos

Visualization of the Embryonic Nervous System in Whole-mount Drosophila Embryos

We describe the procedure to prepare staged Drosophila embryos for the visualization of the embryonic nervous system during...

Visualization of the Embryonic Nervous System in Whole-mount Drosophila Embryos

Double Whole Mount in situ Hybridization of Early Chick Embryos

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying  gene expression in brain, neural tube, somite and heart primordia formation. This video demonstrates the different steps in 2-color whole mount in situ hybridization; First, the embryo is dissected from the egg and fixed in paraformaldehyde. Second, the embryo is processed for prehybridization. The embryo is then hybridized with two different probes, one coupled to DIG, and one coupled to FITC.  Following overnight hybridization, the embryo is incubated with DIG coupled antibody. Color reaction for DIG substrate is performed, and the region of interest appears blue. The embryo is then incubated with FITC coupled antibody. The embryo is processed for color reaction with FITC, and the region of interest appears red. Finally, the embryo is fixed and processed for phtograph and sectioning. A troubleshooting guide is also presented.

This video demonstrates 2-color whole mount in situ hybridization, a method by which the spatial and temporal expression pattern of 2 different genes can be visualized in young chick embryos. This method was originally introduced by David Wilkinson, Domingos Henrique, Phil Ingham and David Ish -Horowicz.

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ...

Method for Whole Mount Antibody Staining in Chick

The chick embryo is a valuable tool in the study of early embryonic development. Its transparency, accessibility and ease of manipulation, make it an ideal tool for studying antibody expression in developing brain, neural tube and somite. This video demonstrates the different steps in whole-mount antibody staining using HRP conjugated secondary antibodies; First, the embryo is dissected from the egg and fixed in paraformaldehyde. Second, endogenous peroxidase is inactivated; The embryo is then exposed to primary antibody. After several washes, the embryo is incubated with secondary antibody conjugated to HRP. Peroxidase activity is revealed using reaction with diaminobenzidine substrate. Finally, the embryo is fixed and processed for photography and sectioning. The advantage of this method over the use of fluorescent antibodies is that embryos can be processed for wax sectioning, thus enabling the study of antigen sites in cross section. This method was originally introduced by Jane Dodd and Tom Jessell 1.

This video demonstrates whole mount immunohistochemistry, a method by which the spatial and temporal expression pattern of an antigen can be visualized in young chick embryos. This method was originally introduced by Jane Dodd and Tom Jessell.

Zebrafish Whole Mount High-Resolution Double Fluorescent In Situ Hybridization

Whole mount in situ hybridization is one of the most widely used techniques in developmental biology. Here, we present a high-resolution double fluorescent in situ hybridization protocol for analyzing the precise expression pattern of a single gene and for determining the overlap of the expression domains of two genes. The protocol is a modified version of the standard in situ hybridization using alkaline phosphatase and substrates such as NBT/BCIP and Fast Red 1,2. This protocol utilizes standard digoxygenin and fluorescein labeled probes along with tyramide signal amplification (TSA) 3. The commercially available TSA kits allow flexible experimental design as fluorescence emission from green to far-red can be used in combination with various nuclear stains, such as propidium iodide, or fluorescence immunohistochemistry for proteins. TSA produces a reactive fluorescent substrate that quickly covalently binds to moieties, typically tyrosine residues, in the immediate vicinity of the labeled antisense riboprobe. The resulting staining patterns are high resolution in that subcellular localization of the mRNA can be observed using laser scanning confocal microscopy 3,4. One can observe nascent transcripts at the chromosomal loci, distinguish nuclear and cytoplasmic staining and visualize other patterns such as cortical localization of mRNA. Studies in Drosophila indicate that roughly 70% of mRNAs exhibit specific patterns of subcellular localization that frequently correlate with the function of the encoded protein 5. When combined with computer-aided reconstruction of 3D confocal datasets, our protocol allows the detailed analysis of mRNA distribution with sub-cellular resolution in whole vertebrate embryos.

Zebrafish Whole Mount High-Resolution Double Fluorescent In Situ Hybridization

Whole mount in situ hybridization is one of the most widely used techniques in developmental biology. Here, we present a high-resolution double fluorescent in situ hybridization protocol for analyzing the precise expression pattern of a single gene and for determining the overlap of the expression domains of two genes. We include a propidium iodide nuclear counter-stain to highlight tissue organization.

Whole mount in situ hybridization is one of the most widely used techniques in developmental biology.  Here, we present a high-resolution double ...

Immunohistochemistry (IHC) is one of the most widely used laboratory techniques for the detection of target proteins in situ. Questions concerning the expression pattern of a target protein across the entire brain are relatively easy to answer when using IHC in small brains, such as those of rodents. However, answering the same questions in large and convoluted brains, such as those of primates presents a number of challenges. Here we present a systematic approach for immunodetection of target proteins in an adult monkey brain. This approach relies on the tissue embedding and sectioning methodology of NeuroScience Associates (NSA) as well as tools developed specifically for batch-staining of free-floating sections. It results in uniform staining of a set of sections which, at a particular interval, represents the entire brain. The resulting stained sections can be subjected to a wide variety of analytical procedures in order to measure protein levels, the population of neurons expressing a certain protein.

Large-scale immunodetection of target proteins across the entire primate brain is possible by employing novel tissue embedding and sectioning methods combined with the use of creative apparatus for batch staining of multiple free-floating sections at a given time.

Immunohistochemistry (IHC) is one of the most widely used laboratory techniques for the detection of target proteins in situ. Questions concerning the ...

The testes of Drosophila melanogaster provide an important model for the study of stem cell maintenance and differentiation, meiosis, and soma-germline interactions. Testes are typically isolated from adult males 0-3 days after eclosion from the pupal case. The testes of wild-type flies are easily distinguished from other tissues because they are yellow, but the testes of white mutant flies, a common genetic background for laboratory experiments are similar in both shape and color to the fly gut. Performing dissection on a glass microscope slide with a black background makes identifying the testes considerably easier. Testes are removed from the flies using dissecting needles. Compared to protocols that use forceps for testes dissection, our method is far quicker, allowing a well-practiced individual to dissect testes from 200-300 wild-type flies per hour, yielding 400-600 testes. Testes from white flies or from mutants that reduce testes size are harder to dissect and typically yield 200-400 testes per hour.

Drosophila melanogaster testes can be rapidly and efficiently isolated from adult males using dissecting needles. With practice, one can readily isolate in one or two days an amount of testes sufficient for the analysis of DNA or RNA by high throughput sequencing or more traditional molecular biology methods or of protein for antibody- or enzyme-based assays.

The testes of Drosophila melanogaster provide an important model for the study of stem cell maintenance and differentiation, meiosis, and soma-germline ...

Whole Mount in Situ Hybridization of E8.5 to E11.5 Mouse Embryos

Whole mount in situ hybridization is a very informative approach for defining gene expression patterns in embryos. The in situ hybridization procedures are lengthy and technically demanding with multiple important steps that collectively contribute to the quality of the final result. This protocol describes in detail several key quality control steps for optimizing probe labeling and performance. Overall, our protocol provides a detailed description of the critical steps necessary to reproducibly obtain high quality results. First, we describe the generation of digoxygenin (DIG) labeled RNA probes via in vitro transcription of DNA templates generated by PCR. We describe three critical quality control assays to determine the amount, integrity and specific activity of the DIG-labeled probes. These steps are important for generating a probe of sufficient sensitivity to detect endogenous mRNAs in a whole mouse embryo. In addition, we describe methods for the fixation and storage of E8.5-E11.5 day old mouse embryos for in situ hybridization. Then, we describe detailed methods for limited proteinase K digestion of the rehydrated embryos followed by the details of the hybridization conditions, post-hybridization washes and RNase treatment to remove non-specific probe hybridization. An AP-conjugated antibody is used to visualize the labeled probe and reveal the expression pattern of the endogenous transcript. Representative results are shown from successful experiments and typical suboptimal experiments.

Whole Mount in Situ Hybridization of E8.5 to E11.5 Mouse Embryos

This whole mount in situ hybridization protocol discusses critical steps that ensure reproducible high quality results for gene expression studies in E8.5-E11.5 day old mouse embryos.

Whole mount in situ hybridization is a very informative approach for defining gene expression patterns in embryos. The in situ hybridization procedures ...

Assessing the expression pattern of a gene, as well as the subcellular localization properties of its transcribed RNA, are key features for understanding its biological function during development. RNA in situ hybridization (RNA-ISH) is a powerful method used for visualizing RNA distribution properties, be it at the organismal, cellular or subcellular levels 1. RNA-ISH is based on the hybridization of a labeled nucleic acid probe (e.g. antisense RNA, oligonucleotides) complementary to the sequence of an mRNA or a non-coding RNA target of interest 2. As the procedure requires primary sequence information alone to generate sequence-specific probes, it can be universally applied to a broad range of organisms and tissue specimens 3. Indeed, a number of large-scale ISH studies have been implemented to document gene expression and RNA localization dynamics in various model organisms, which has led to the establishment of important community resources 4-11. While a variety of probe labeling and detection strategies have been developed over the years, the combined usage of fluorescently-labeled detection reagents and enzymatic signal amplification steps offer significant enhancements in the sensitivity and resolution of the procedure 12. Here, we describe an optimized fluorescent in situ hybridization method (FISH) employing tyramide signal amplification (TSA) to visualize RNA expression and localization dynamics in staged Drosophila embryos. The procedure is carried out in 96-well PCR plate format, which greatly facilitates the simultaneous processing of large numbers of samples.

Here we describe a whole-mount fluorescent in situ hybridization (FISH) protocol for determining the expression and localization properties of RNAs expressed during embryogenesis in the fruit fly, Drosophila melanogaster.

Assessing  the expression pattern of a gene, as well as the subcellular localization  properties of its transcribed RNA, are key features for ...

Drosophila melanogaster is a powerful model system that has been widely used to elucidate a variety of biological processes. For example, studies of both the female and male germ lines of Drosophila have contributed greatly to the current understanding of meiosis as well as stem cell biology. Excellent protocols are available in the literature for the isolation and imaging of Drosophila ovaries&#160;and testes3-12. Herein, methods for the dissection and preparation of Drosophila testes for microscopic analysis are described with an accompanying video demonstration. A protocol for isolating testes from the abdomen of adult males and preparing slides of live tissue for analysis by phase-contrast microscopy as well as a protocol for fixing and immunostaining testes for analysis by fluorescence microscopy are presented. These techniques can be applied in the characterization of Drosophila mutants that exhibit defects in spermatogenesis as well as in the visualization of subcellular localizations of proteins.

Methods for isolating and preparing Drosophila testes samples (live and fixed) for imaging by phase-contrast and fluorescence microscopy are described herein.&#160;

Drosophila melanogaster is a powerful model system that has been widely used to elucidate a variety of biological processes. For example, studies of both ...

Analysis of Apoptosis in Zebrafish Embryos by Whole-mount Immunofluorescence to Detect Activated Caspase 3

Whole-mount immunofluorescence to detect activated Caspase 3 (Casp3 assay) is useful to identify cells undergoing either intrinsic or extrinsic apoptosis in zebrafish embryos. The whole-mount analysis provides spatial information in regard to tissue specificity of apoptosing cells, although sectioning and/or colabeling is ultimately required to pinpoint the exact cell types undergoing apoptosis. The whole-mount Casp3 assay is optimized for analysis of fixed embryos between the 4-cell stage and 32 hr-post-fertilization and is useful for a number of applications, including analysis of zebrafish mutants and morphants, overexpression of mutant and wild-type mRNAs, and exposure to chemicals. Compared to acridine orange staining, which can identify apoptotic cells in live embryos in a matter of hours, Casp3 and TUNEL assays take considerably longer to complete (2-4 days). However, because of the dynamic nature of apoptotic cell formation and clearance, analysis of fixed embryos ensures accurate comparison of apoptotic cells across multiple samples at specific time points. We have also found the Casp3 assay to be superior to analysis of apoptotic cells by the whole-mount TUNEL assay in regard to cost and reliability. Overall, the Casp3 assay represents a robust, highly reproducible assay in which to analyze apoptotic cells in early zebrafish embryos.

Certain genetic perturbations or exposure to toxins can disrupt normal developmental processes leading to death of specific cell types. The analysis of activated Caspase 3 by whole-mount immunofluorescence in zebrafish embryos reveals stage- and tissue-specific localization of cells specifically undergoing apoptosis.

Whole-mount immunofluorescence to detect activated Caspase 3 (Casp3 assay) is useful to identify cells undergoing either intrinsic or extrinsic apoptosis ...

Flat Mount Preparation for Observation and Analysis of Zebrafish Embryo Specimens Stained by Whole Mount In situ Hybridization

The zebrafish embryo is now commonly used for basic and biomedical research to investigate the genetic control of developmental processes and to model congenital abnormalities. During the first day of life, the zebrafish embryo progresses through many developmental stages including fertilization, cleavage, gastrulation, segmentation, and the organogenesis of structures such as the kidney, heart, and central nervous system. The anatomy of a young zebrafish embryo presents several challenges for the visualization and analysis of the tissues involved in many of these events because the embryo develops in association with a round yolk mass. Thus, for accurate analysis and imaging of experimental phenotypes in fixed embryonic specimens between the tailbud and 20 somite stage (10 and 19 hours post fertilization (hpf), respectively), such as those stained using whole mount in situ hybridization (WISH), it is often desirable to remove the embryo from the yolk ball and to position it flat on a glass slide. However, performing a flat mount procedure can be tedious. Therefore, successful and efficient flat mount preparation is greatly facilitated through the visual demonstration of the dissection technique, and also helped by using reagents that assist in optimal tissue handling. Here, we provide our WISH protocol for one or two-color detection of gene expression in the zebrafish embryo, and demonstrate how the flat mounting procedure can be performed on this example of a stained fixed specimen. This flat mounting protocol is broadly applicable to the study of many embryonic structures that emerge during early zebrafish development, and can be implemented in conjunction with other staining methods performed on fixed embryo samples.

Flat Mount Preparation for Observation and Analysis of Zebrafish Embryo Specimens Stained by Whole Mount In situ Hybridization

The zebrafish embryo is an excellent model for developmental biology research. During embryogenesis, zebrafish develop with a yolk mass, which presents three-dimensional challenges for sample observation and analysis. This protocol describes how to create two-dimensional flat mount preparations of whole mount in situ (WISH) stained zebrafish embryo specimens.

The zebrafish embryo is now commonly used for basic and biomedical research to investigate the genetic control of developmental processes and to model ...