We would like to thank Thomas Lecuit (sqh-Utrophin::GFP line), the Bloomington Stock Center, and the Developmental Studies Hybridoma Bank for reagents. We further thank all members of the Tootle Lab for helpful discussions and critiques of the manuscript. Funding from the National Science Foundation MCB-1158527, and start-up funds from the Anatomy and Cell Biology Department, University of Iowa supported this work. National Institutes of Health Predoctoral Training Grant in Pharmacological Sciences T32GM067795 supported AJS. Data storage support was provided by the ICTS, which is funded through the CTSA supported by the National Center for Research Resources and the National Center for Advancing Translational Sciences, National Institutes of Health, through Grant UL1RR024979.

1. Preparing Drosophila Prior to Stage Isolation
<ol>
	<li>Make wet yeast paste by combining 50 g of active dry yeast with 90 ml&#160;of distilled water. Mix with a spatula to combine. Let the mixture stand for ~30 min before assessing consistency. The consistency should be just thick enough to adhere to the side of a fly vial but not run down the side. To achieve the desired consistency it may be necessary to add up to 10 ml&#160;of additional water or a small amount of dry yeast. Store in a covered container at 4 &#176;C. The stored yeast can be used for ~1-2 weeks.</li>
	<li>Collect &#60;24 hr&#160;old adult flies (both males and females) of the desired genotypes and put them into a vial with fly food plus wet yeast paste smeared on the side of the vial. The temperature at which the flies are maintained will vary depending upon the experiment. For routine experiments, flies are maintained at room temperature. Whereas experiments in which a gene is being overexpressed using the UAS/GAL4 system15 may require maintaining the flies at 25 &#176;C or higher, as appropriate.</li>
	<li>Provide the flies with a fresh smear of yeast paste daily for 2 days. NOTE: As follicle development is tightly regulated by the nutritional status of the female fly, it is essential to provide the fly with the nutrient rich yeast paste for at least 36 hr&#160;prior to dissection.</li>
</ol>
2. Isolating Mid-to-late Staged Drosophila Follicles
<ol>
	<li>Allow the media to come to room temperature (~30 min). If the staged follicles are going to be used for in vitro development assays, freshly prepare IVEM media (Grace&#39;s insect media, 10% heat inactivated fetal bovine serum, and 1x penicillin/streptomycin). If the staged follicles are going to be used for mRNA or protein isolation use either Grace&#39;s insect or IVEM media. IMPORTANT: Media temperature is critical. If the media is cold it will alter both the actin and microtubule cytoskeletons and block development.</li>
	<li>Anesthetize the flies in the yeasted vial by injecting CO2 gas and place 3-5 female flies onto a fly pad under CO2. IMPORTANT: Do not leave more females than can be dissected in a 10 min time period on the fly pad as extended exposure to CO2 can cause sterility and death.</li>
	<li>Fill one well of a 9-spot plate with media and place it on top of a dark surface (a piece of black plexiglass works well). Focus the dissecting scope on the bottom of the well.</li>
	<li>Using #5 Dumont forceps pick up a single female with one hand (this is best done using the dominant hand). It is often easiest to pick up the female by the wings, legs, or thorax to abdomen transition. Submerge the female in the media filled well. Adjust the focus of the microscope as necessary.</li>
	<li>Using a second pair of forceps held in the nondominant hand, grab the female at the anterior end of the abdomen so that the posterior end is positioned towards the dominant hand (Figure 2A). Make sure to keep the fly submerged in the media.</li>
	<li>With the dominant hand, use the forceps to grab the cuticle at the 2nd most posterior pigmented segment and rip it away from the rest of the abdomen (Figures 2B-C).</li>
	<li>Using the forceps in the dominant hand, gently squeeze the anterior end of the abdomen until the ovaries emerge (Figures 2D-E). If necessary, place the forceps in between the two ovaries and pull them out of the carcass.</li>
	<li>Either move the ovaries to a new well with fresh media (Figure 2F) or remove the carcass to a Kimwipe or paper towel. This is particularly important if follicles are being isolated for in vitro development.</li>
	<li>Repeat until 3-5 pairs of ovaries have been isolated. NOTE: Each ovary is composed of ~16 ovarioles or chains of sequentially maturing follicles. Each ovariole is contained within a muscle sheath.</li>
	<li>Using pin vises and the needles supplied with them, gently pull apart the ovary by running the needles between the ovarioles (Figure 2G). This will sometimes release the individual follicles as well.</li>
	<li>Individual ovarioles and the easily distinguishable morphological stages of follicle development should now be visible (Figure 2G, teased apart ovary). Refer to Figures 1 and&#160;2H for morphological differences that can be used to distinguish the different stages. To isolate follicles that are within intact ovarioles and still contained within a muscle sheath, use a needle to cut across the ovariole at the anterior of the preceding follicle and at the posterior of the follicle immediately following the follicle of interest. This will break the muscle sheath and the follicle of interest away can now be cut away from the neighboring follicles without damaging it.</li>
	<li>As individual stages are separated, move the follicles of interest, using a glass pipette, to a new well with fresh media. This is particularly important when isolating follicles for in vitro development. NOTE: It is important to squeeze the pipette bulb before entering the media to prevent the air bubbles from redistributing the follicles of interest throughout the well. Additionally, if the follicles are sticking to the glass pipette, the pipette can be precoated with 3% bovine serum albumin (BSA) by pipetting the BSA solution up and down several times and rinsing with dissecting media.</li>
	<li>Once enough follicles have been isolated, proceed with subsequent experiments.</li>
</ol>
3. In vitro Development of S10B Follicles
<ol>
	<li>Isolate S10B follicles using the stage isolation protocol (step 2) in IVEM media. Make sure that the follicles are rapidly moved away from debris. As these follicles will continue to mature, it is important that S10Bs are collected for 30-60 min and then placed into the maturation media of choice. NOTE: S10B need to be carefully distinguished from S10A follicles (Figure 1C compared to 1B), as S10A follicles will not mature in the IVEM culture media. In both S10A and S10B follicles, half of the length is composed of nurse cells and the other half is the oocyte, but in S10B the length of the follicle is equal to that of the S14 follicles.</li>
	<li>Using a glass pipette, move ~30 S10B follicles into a well of a 24-well tissue culture plate. NOTE: Make sure to verify that all of the follicles being transferred are S10B and have not matured to S11.</li>
	<li>Prepare 1 &#956;l&#160;of maturation media per well, i.e. IVEM media plus pharmacological reagents.</li>
	<li>Using a pulled glass pipette*, remove as much media from the well (step 3.2) as possible, and quickly add maturation media of choice. NOTE: It is essential to use a pulled glass pipette as staged follicles can be easily taken up with either glass pipettes or pipette tips with a Pipetman. 
	*To make pulled pipettes: 1) heat the thin portion of long, glass pipettes in the flame of a Bunsen burner just until the glass begins to soften; 2) immediately move the pipette out of the flame and pull horizontally to draw the pipette into a finer tube; 3) break to generate a fine point. CAUTION: Use eye protection as fragments of glass may fly off.</li>
	<li>Repeat steps 3.1-3.4 for as many wells as the experiment requires.</li>
	<li>Allow follicles to develop for &#62;10 hr&#160;and score the developmental progression under a dissecting scope. NOTE: Experiments are usually scored the next day to allow sufficient time for the follicles to develop. S10B is ~5 hr, S11 is ~30 min, S12 is ~2 hr, and S13 is ~1 hr in duration at 25 &#176;C1 and development at room temperature will take slightly longer. Similar experiments to that described for S10B follicles can be performed using S11-S13 follicles.</li>
</ol>
4. Stage Isolation for Live Imaging
<ol>
	<li>Isolate late stage follicles (S10B-14) expressing the fluorescent marker of choice using the stage isolation protocol (step 2) in IVEM media, quickly moving follicles away from debris.</li>
	<li>Move follicles of interest into new media and then transfer by glass pipette to a coverslip bottom Petri plate. Take care to add media so that it bubbles up in the coverslip bottom area but does not spill over.</li>
	<li>For longer time-lapse movies, it is sometimes necessary to maintain humidity within the Petri plate by adding a rolled up Kimwipe, moistened with water, to the inside edge of the Petri plate. Place the lid on top.</li>
	<li>Image on an inverted microscope. Detailed resolution will require confocal microscopy. It is necessary to balance frequency of imaging, strength of illumination, and length of imaging; this will need to be independently worked out for each labeling tool and developmental process.</li>
</ol>
5. Stage Isolation for mRNA Preparation
<ol>
	<li>Isolate individual stage follicles using the stage isolation protocol (step 2) with either Grace&#39;s or IVEM media.</li>
	<li>Using a glass pipette, move the individual stages of interest into new wells with media; it is possible to collect multiple stages at once.</li>
	<li>Keep collection times under 1 hr. Move the follicles, using a glass pipette, to 1.5 ml&#160;microfuge tubes.</li>
	<li>Spin the tube briefly in a mini-microcentrifuge to pellet all of the follicles. Using a pulled glass pipette (see step 3.4) carefully remove all of the media. NOTE: If using a full size microcentrifuge, spin down the follicles at low speed.</li>
	<li>Add 100 &#956;l&#160;of Trizol and grind by hand for ~20 sec using a plastic pestle. Spin down at full-speed in a microcentrifuge and move Trizol to a new 1.5 ml&#160;microfuge tube being careful not to disturb any pelleted debris. Store at -80 &#176;C.</li>
	<li>Repeat steps 5.1-5.5 until enough follicles have been obtained for the experiment. Routinely, ~75 S10B, ~75 S12, and ~100 S14 follicles yield ~10 &#956;g of RNA.</li>
	<li>Thaw the samples on ice. Combine samples, as appropriate, into one microfuge tube and bring the Trizol volume up to 800 &#956;l. Proceed with RNA isolation as directed by the manufacturer. IMPORTANT: Remember to DNase treat the isolated RNA with RNase free DNase.</li>
</ol>
6. Stage Isolation for Western Blotting
<ol>
	<li>Preheat a heat block to 100 &#176;C.</li>
	<li>Isolate individual stage follicles using the stage isolation protocol (step 2) with either Grace&#39;s or IVEM media. NOTE: It is necessary to empirically determine how many of a particular stage follicle are needed to observe each specific protein. For highly expressed proteins 1-3 S10B follicles/well is enough to see a strong signal on a western blot. However, it is important to make a representative sample, taking follicles from multiple females. Thus, 15-20 follicles of a particular stage are usually collected.</li>
	<li>Move follicles, using a glass pipette, to a 1.5 ml&#160;microfuge tube. Spin briefly in a mini-microcentrifuge to pellet the follicles (see step 5.4). Carefully remove all of the media using a pulled glass pipette (see step 3.4) and add 50 &#956;l&#160;of 1x&#160;PBS and 50 &#956;l&#160;of 2x&#160;Laemmli buffer.</li>
	<li>Grind by hand for ~20 sec with a plastic pestle. NOTE: Plastic pestles can be reused for grinding western samples by washing and autoclaving them.</li>
	<li>Boil the samples for 10 min in the heat block.</li>
	<li>Chill briefly on ice and spin at full-speed for 15 sec in a microcentrifuge. Either immediately load onto a SDS-PAGE gel or store at -20 &#176;C. NOTE: If the samples are stored, remember to reboil the samples before loading onto the gel.</li>
	<li>Perform western blot analysis following standard protocols.</li>
</ol>

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	<li>Spradling, A. C., Bate, M., Martinez-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. , 1-70 (1993).</li><li>Guild, G. M., Connelly, P. S., Shaw, M. K., Tilney, L. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Actin+filament+cables+in+Drosophila+nurse+cells+are+composed+of+modules+that+slide+passively+past+one+another+during+dumping.">Actin filament cables in Drosophila nurse cells are composed of modules that slide passively past one another during dumping.</a> J. Cell Biol. 138, 783-797 (1997).</li><li>Horne-Badovinac, S., Bilder, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mass+transit:+epithelial+morphogenesis+in+the+Drosophila+egg+chamber.">Mass transit: epithelial morphogenesis in the Drosophila egg chamber.</a> Dev. Dyn. 232, 559-574 (2005).</li><li>McCall, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Eggs+over+easy:+cell+death+in+the+Drosophila+ovary.">Eggs over easy: cell death in the Drosophila ovary.</a> Dev. Biol. 274, 3-14 (2004).</li><li>Berg, C. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Drosophila+shell+game:+patterning+genes+and+morphological+change.">The Drosophila shell game: patterning genes and morphological change.</a> Trends Genet. 21, 346-355 (2005).</li><li>Taylor, C. R., Levenson, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantification+of+immunohistochemistry--issues+concerning+methods,+utility+and+semiquantitative+assessment+II.">Quantification of immunohistochemistry--issues concerning methods, utility and semiquantitative assessment II.</a> Histopathology. 49, 411-424 (2006).</li><li>Tootle, T. L., Spradling, A. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drosophila+Pxt:+a+cyclooxygenase-like+facilitator+of+follicle+maturation.">Drosophila Pxt: a cyclooxygenase-like facilitator of follicle maturation.</a> Development. 135, 839-847 (2008).</li><li>Weil, T. T., Parton, R. M., Davis, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Preparing+individual+Drosophila+egg+chambers+for+live+imaging.">Preparing individual Drosophila egg chambers for live imaging.</a> J. Vis. Exp. , (2012).</li><li>Groen, C. M., Spracklen, A. J., Fagan, T. N., Tootle, T. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drosophila+Fascin+is+a+novel+downstream+target+of+prostaglandin+signaling+during+actin+remodeling.">Drosophila Fascin is a novel downstream target of prostaglandin signaling during actin remodeling.</a> Mol. Biol. Cell. 23, 4567-4578 (2012).</li><li>Dorman, J. B., James, K. E., Fraser, S. E., Kiehart, D. P., Berg, C. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=bullwinkle+is+required+for+epithelial+morphogenesis+during+Drosophila+oogenesis.">bullwinkle is required for epithelial morphogenesis during Drosophila oogenesis.</a> Dev. Biol. 267, 320-341 (2004).</li><li>Prasad, M., Montell, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cellular+and+molecular+mechanisms+of+border+cell+migration+analyzed+using+time-lapse+live-cell+imaging.">Cellular and molecular mechanisms of border cell migration analyzed using time-lapse live-cell imaging.</a> Dev. Cell. 12, 997-1005 (2007).</li><li>Prasad, M., Jang, A. C., Starz-Gaiano, M., Melani, M., Montell, D. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+protocol+for+culturing+Drosophila+melanogaster+stage+9+egg+chambers+for+live+imaging.">A protocol for culturing Drosophila melanogaster stage 9 egg chambers for live imaging.</a> Nat. Protoc. 2, 2467-2473 (2007).</li><li>Morris, L. X., Spradling, A. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Long-term+live+imaging+provides+new+insight+into+stem+cell+regulation+and+germline-soma+coordination+in+the+Drosophila+ovary.">Long-term live imaging provides new insight into stem cell regulation and germline-soma coordination in the Drosophila ovary.</a> Development. 138, 2207-2215 (2011).</li><li>Bianco, A., 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=Two+distinct+modes+of+guidance+signalling+during+collective+migration+of+border+cells.">Two distinct modes of guidance signalling during collective migration of border cells.</a> Nature. 448, 362-365 (2007).</li><li>Brand, A. 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There is nothing to disclose.

The Drosophila follicle is composed of only a small number of cell types, making it ideal for both morphologic and molecular analyses. Furthermore, due to the structure of the ovary, it is relatively easy to obtain large numbers of specific stages of follicle development with a common dissecting scope and minimal training. As each stage represents a short temporal window, stage isolation can provide significant molecular insights into the developmental processes occurring during that stage. For example, we have ...

Each Drosophila ovary is composed of ~16 ovarioles, or chains of sequentially maturing egg chambers or follicles. Each follicle is composed of a single oocyte, 15 germ line derived nurse or support cells, and ~650 somatic cells termed follicle cells (Figure 1A). Drosophila oogenesis is divided into 14 morphologically defined stages of development1. Each stage of follicle development is observed many times within a single fly,&#160;making it relatively easy to isolate a substantial number of stage-specific follicles.
The mid-to-late stages of oogenesis (Stages 10B-14) are particularly well suited for stage isolation (Figure 1). At Stage 10B (S10B), the follicle is fully elongated (i.e. its length is equal to that of a Stage 14 (S14) follicle, see Figure 1 and Figure 2H) and half the length of the follicle is composed of nurse cells while the other half is the oocyte (Figure 1C). At this stage the nurse cells undergo dramatic actin remodeling, strengthening the cortical actin and generating parallel bundles of actin filaments2. At the same time, a population of follicle cells, termed centripetal cells, migrate in between the nurse cells and the oocyte, and two dorsal groups of follicle cells become specified to undergo migration to form the dorsal appendages, tubular respiratory apparatuses for the embryo3. The nurse cells then contract (S11), squeezing their cytoplasmic contents into the oocyte in a process called nurse cell dumping, which provides the oocyte with the factors necessary for it to complete embryogenesis (Figure 1D). The nurse cells then undergo cell death (S12-S13)4, and the follicle cells secrete and pattern the eggshell5 (Figures 1E-G). Thus, the end of oogenesis is rich with important developmental and morphogenetic processes.
Isolated mid-to-late stage follicles (S10B-S14) can be used for a variety of purposes, including molecular analyses. For example, mRNA from staged follicles can be isolated for RT-PCR, microarray, or RNA-seq analyses. This allows one to look at gene expression within a short developmental window, with only a few cell types present, and determine how gene expression is changed by either pharmacologic or genetic perturbations. Stage isolation can also be used to look at proteins by western blotting. Such analysis is important because it allows one to quantify the level of protein expression in wild-type versus mutants at specific stages. While one could use immunofluorescent analyses to achieve similar results, quantification of fluorescence is less robust due to the strict requirements that all of the pixels be within the linear range of detection6. Additionally, western blot analysis may provide other information, such as if the protein is posttranslationally modified or is expressed from a specific splice isoform. Isolated stages can also be used for further protein purification, including subcellular fractionation or coimmunoprecipitation.
Stage-specific follicle isolation can also be used for in vitro development assays7 and live-imaging8. Isolated S10B-S13 follicles will continue to develop to S14 in simple culture media (see below). It is important to note that S10A follicles will not progress through nurse cell dumping using the culture conditions discussed in this manuscript. We have used S10B in vitro development assays to define the role of prostaglandins, both pharmacologically and genetically, in regulating actin remodeling by using nurse cell dumping and development as read-outs7,9. Similarly, the later stages of development can also be isolated to determine the effects of pharmacologic treatments or genetic manipulations on particular processes such as centripetal cell migration, dorsal appendage migration/formation10, and nurse cell death. Such assays can be used to perform dominant interaction screens or assays; for example, while heterozygosity for mutations in pxt or fascin alone have no effect on S10B in vitro development, follicles from double heterozygotes exhibit nurse cell dumping defects and a block in development9.
Additionally, because S10B-13 can develop in culture, all of the processes that occur during this time can be observed by live-imaging. Such imaging can be performed simply using transmitted light (if one is only interested in gross changes in morphology) or with confocal microscopy using transgenic flies expressing fluorescent probes or follicles stained with live imaging dyes. Live imaging is being used to substantially advance our understanding of developmental processes. Indeed, live imaging of late stage follicles has expanded the knowledge of dorsal appendage migration, an example of tubulogenesis10. We expect that live imaging of additional late stage processes, including actin dynamics during nurse cell dumping, will provide novel insights into these developmental events. It is important to note that while S10A and early stages of follicle development will not continue to develop into a S14 in culture, live-imaging of events occurring during those stages of development is possible using alternative culture conditions11-14 (see Discussion for more information).
Here we provide detailed protocols for isolating late stage follicles for either in vitro development and live-imaging, or molecular analyses (mRNA and protein isolation).

<table border="0" cellpadding="0" cellspacing="0" width="1098">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="17">
			<td height="17" style="height:17px;width:253px;">Active Dry Yeast</td>
			<td style="width:195px;">Genesee Scientific</td>
			<td style="width:227px;">62-103</td>
			<td style="width:424px;">Any source of Active Dry Yeast is fine</td>
		</tr>
		<tr height="17">
			<td height="17" style="height:17px;">Grace&#8217;s Insect Media</td>
			<td>Lonza</td>
			<td>04-457F</td>
			<td></td>
		</tr>
		<tr height="17">
			<td height="17" style="height:17px;">Heat Inactivated Fetal Bovine Serum</td>
			<td>Atlanta Biologicals</td>
			<td>S11050H</td>
			<td>Any Heat Inactivated FBS should work</td>
		</tr>
		<tr height="17">
			<td height="17" style="height:17px;">10x Pen/Strep</td>
			<td>Gibco/Invitrogen</td>
			<td>15140-122</td>
			<td></td>
		</tr>
		<tr height="17">
			<td height="17" style="height:17px;">Pin Vises and Needles</td>
			<td>Ted Pella, Inc.</td>
			<td>13561-10</td>
			<td></td>
		</tr>
		<tr height="17">
			<td height="17" style="height:17px;">Spot Plate, Nine Well</td>
			<td>Corning</td>
			<td>7220-85</td>
			<td></td>
		</tr>
		<tr height="17">
			<td height="17" style="height:17px;">#5 Dumont forceps</td>
			<td>Fine Science Tools</td>
			<td>11252-20</td>
			<td></td>
		</tr>
		<tr height="17">
			<td height="17" style="height:17px;">24 multi-well plates</td>
			<td>Becton Dickinson</td>
			<td>35 3226</td>
			<td>Any 24-well tissue culture dish should work</td>
		</tr>
		<tr height="17">
			<td height="17" style="height:17px;">Coverslip Bottom Dishes (35mm)</td>
			<td>MatTek Corporation</td>
			<td>P35G-1.0-14-C</td>
			<td>Coverslip thickness will depend on the microscope/objective being used</td>
		</tr>
		<tr height="17">
			<td height="17" style="height:17px;">Glass pipettes</td>
			<td>Corning</td>
			<td colspan="2">7095B-5x (for transferring follicles)</td>
		</tr>
		<tr height="17">
			<td height="17" style="height:17px;">Glass pipettes - long</td>
			<td>Corning</td>
			<td colspan="2">7095B-9 (for producing pulled pipettes)</td>
		</tr>
		<tr height="18">
			<td height="18" style="height:19px;">Sample pestle (1.5 &#956;l; RNase/DNase free)</td>
			<td>Research Products International</td>
			<td>199228</td>
			<td>Any plastic pestle that fits 1.5 &#956;l microfuge tubes can be used</td>
		</tr>
		<tr height="17">
			<td height="17" style="height:17px;">Trizol</td>
			<td>Invitrogen</td>
			<td>15596-018</td>
			<td></td>
		</tr>
	</tbody>
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the utility of stage-specific mid-to-late drosophila follicle isolation

Drosophila oogenesis or follicle development has been widely used to advance the understanding of complex developmental and cell biologic processes. This methods paper describes how to isolate mid-to-late stage follicles (Stage 10B-14) and utilize them to provide new insights into the molecular and morphologic events occurring during tight windows of developmental time. Isolated follicles can be used for a variety of experimental techniques, including in vitro development assays, live imaging, mRNA expression analysis and western blot analysis of proteins. Follicles at Stage 10B (S10B) or later will complete development in culture; this allows one to combine genetic or pharmacologic perturbations with in vitro development to define the effects of such manipulations on the processes occurring during specific periods of development. Additionally, because these follicles develop in culture, they are ideally suited for live imaging studies, which often reveal new mechanisms that mediate morphological events. Isolated follicles can also be used for molecular analyses. For example, changes in gene expression that result from genetic perturbations can be defined for specific developmental windows. Additionally, protein level, stability, and/or posttranslational modification state during a particular stage of follicle development can be examined through western blot analyses. Thus, stage-specific isolation of Drosophila follicles provides a rich source of information into widely conserved processes of development and morphogenesis.

When isolating specific stages of Drosophila follicle development it is essential to be able to accurately distinguish the different morphological stages. This is somewhat challenging for S10A and S10B, as the nurse cells and the oocyte each take up half the length of the follicle at these stages (Figure&#160;1B compared to 1C). However, S10A follicles are shorter in length than S10B follicles, as the S10B follicles are fully elongated and thus equal in length to a S14 follicle ...

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The Utility of Stage-specific Mid-to-late Drosophila Follicle Isolation

Stage-specific isolation of mid-to-late Drosophila follicles is useful for a variety of purposes. Such follicles develop in culture, which allows for genetic and/or pharmacologic manipulations to be coupled with in vitro development assays and live imaging. Additionally, follicles can be used for molecular studies, such as isolating mRNA and protein.

The Utility of Stage-specific Mid-to-late Drosophila Follicle Isolation

Drosophila oogenesis or follicle development has been widely used to advance the understanding of complex developmental and cell biologic processes. This ...

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Biology

11.2K Views.  University of Iowa Carver College of Medicine. Stage-specific isolation of mid-to-late Drosophila follicles is useful for a variety of purposes. Such follicles develop in culture, which allows for genetic and/or pharmacologic manipulations to be coupled with in vitro development assays and live imaging. Additionally, follicles can be used for molecular studies, such as isolating mRNA and protein.

Video: The Utility of Stage-specific Mid-to-late Drosophila Follicle Isolation

Targeted Expression of GFP in the Hair Follicle Using Ex Vivo Viral Transduction

There are many cell types in the hair follicle, including hair matrix cells which form the hair shaft and stem cells which can initiate the hair shaft during early anagen, the growth phase of the hair cycle, as well as pluripotent stem cells that play a role in hair follicle growth but have the potential to differentiate to non-follicle cells such as neurons. These properties of the hair follicle are discussed. The various cell types of the hair follicle are potential targets for gene therapy. Gene delivery system for the hair follicle using viral vectors or liposomes for gene targeting to the various cell types in the hair follicle and the results obtained are also discussed.

The hair follicle is a highly complex appendage of the skin containing a multiplicity of cell types. The follicle undergoes constant cycling through the life of the organism including growth and resorption with growth dependent on specific stem cells. The targeting of the follicle by genes and stem cells to change its properties, in particular, the nature of the hair shaft is, discussed. Hair follicle delivery systems are described, such as liposomes and viral vectors for gene therapy. The nature of the hair follicle stem cells is discussed, in particular, its pluripotency.

There are many cell types in the hair follicle, including hair matrix cells which form the hair shaft and stem cells which can initiate the hair shaft ...

Fluorescent Labeling of Drosophila Heart Structures

The Drosophila melanogaster dorsal vessel, or heart, is a tubular structure comprised of a single layer of contractile cardiomyocytes, pericardial cells that align along each side of the heart wall, supportive alary muscles and, in adults, a layer of ventral longitudinal muscle cells. The contractile fibers house conserved constituents of the muscle cytoarchitecture including densely packed bundles of myofibrils and cytoskeletal/submembranous protein complexes, which interact with homologous components of the extracellular matrix. Here we describe a protocol for the fixation and the fluorescent labeling of particular myocardial elements from the hearts of dissected larvae and semi-intact adult Drosophila. Specifically, we demonstrate the labeling of sarcomeric F-actin and of &alpha;-actinin in larval hearts. Additionally, we perform labeling of F-actin and &alpha;-actinin in myosin-GFP expressing adult flies and of &alpha;-actinin and pericardin, a type IV extracellular matrix collagen, in wild type adult hearts. Particular attention is given to a mounting strategy for semi-intact adult hearts that minimizes handling and optimizes the opportunity for maintaining the integrity of the cardiac tubes and the associated tissues. These preparations are suitable for imaging via fluorescent and confocal microscopy. Overall, this procedure allows for careful and detailed analysis of the structural characteristics of the heart from a powerful genetically tractable model system.

Fluorescent Labeling of Drosophila Heart Structures

Here we describe a basic protocol for fluorescent labeling of different elements of heart tubes from larva and adult Drosophila melanogaster. These specimens are well-suited for imaging via fluorescent or confocal microscopy. This technique permits detailed structural analysis of the features of the hearts from a powerful model organism.

The Drosophila melanogaster dorsal vessel, or heart, is a tubular structure comprised of a single layer of contractile cardiomyocytes, pericardial cells ...

Visualizing the Beating Heart in Drosophila

The Drosophila heart has recently emerged as a good model system for examining the genetic, cellular, and molecular mechanisms underlying function in myogenic hearts. A key step in examining heart function in the fly is finding a way to access the heart in a manner that preserves its myogenic function while still allowing the beating heart organ to be observed and recorded. Two different methods for observing and recording the beating heart in both larva and adult Drosophila are described here. Our semi-intact preparation using adult flies allows clear visualization of the abdominal heart without interference from the pigmented cuticle and overlying fat bodies. To record larval heart beats it is necessary to immobilize the larva, which minimizes body wall movements thereby reducing heart movements that are not associated with myocardial contractions. Our methodologies produce stable adult and larval heart preparations that can beat for hours at rates of 1-3 Hz.

Visualizing the Beating Heart in Drosophila

Technique required for visualizing the beating heart in larval and adult Drosophila are presented. Each life stage requires a different methodology.

The Drosophila heart has recently emerged as a good model system for examining the genetic, cellular, and molecular mechanisms underlying function in ...

Isolation and Purification of Drosophila Peripheral Neurons by Magnetic Bead Sorting

The Drosophila peripheral nervous system (PNS) is a powerful model for investigating the complex processes of neuronal development and dendrite morphogenesis at the functional and molecular levels. To aid in these analyses, we have developed a strategy for the isolation of a subclass of PNS neurons called dendritic arborization (da) neurons that have been widely used for studying dendrite morphogenesis1,2. These neurons are very difficult to isolate as a pure population, due in part to their extremely low occurrence and their difficult-to-reach location below the tough chitinous larval cuticle. Our newly developed method overcomes these challenges, and is based on a fast and specific cell enrichment using antibody-coated magnetic beads. For our magnetic bead sorting studies, we have used age-matched third instar larvae expressing a mouse CD8 tagged GFP fusion protein (UAS-mCD8-GFP)3 under the control of either the class IV dendritic arborization (da) neuron-specific pickpocket (ppk)-GAL4 driver4 or the control of the pan-da neuron-specific GAL421-7 driver5. Although this protocol has been optimized for isolating PNS cells which are attached to the inner wall of the larval cuticle, by varying a few parameters, the same protocol could be used to isolate many different cell types attached to the cuticle at larval or pupal stages of development (e.g. epithelia, muscle, oenocytes etc.), or other cell types from larval organs depending upon the GAL4-specific driver expression pattern. The RNA isolated by this method is of high quality and can be readily used for downstream genomic analyses such as microarray gene expression profiling studies. This approach offers a powerful new tool to perform studies on isolated Drosophila dendritic arborization (da) neurons thereby providing novel insights into the molecular mechanisms underlying dendrite morphogenesis.

Isolation and Purification of Drosophila Peripheral Neurons by Magnetic Bead Sorting

In this video-article we present a method for the isolation and purification of Drosophila peripheral neurons using a fast magnetic bead assisted cell sorting strategy. RNA obtained from the isolated cells can be readily used for downstream applications including microarray analyses.

The Drosophila peripheral nervous system (PNS) is a powerful model for investigating the complex processes of neuronal development and dendrite ...

Isolation of Drosophila melanogaster Testes

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.

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 assays.

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

Isolation and Purification of Kinesin from Drosophila Embryos

Motor proteins move cargos along microtubules, and transport them to specific sub-cellular locations. Because altered transport is suggested to underlie a variety of neurodegenerative diseases, understanding microtubule based motor transport and its regulation will likely ultimately lead to improved therapeutic approaches. Kinesin-1 is a eukaryotic motor protein which moves in an anterograde (plus-end) direction along microtubules (MTs), powered by ATP hydrolysis. Here we report a detailed purification protocol to isolate active full length kinesin from Drosophila embryos, thus allowing the combination of Drosophila genetics with single-molecule biophysical studies. Starting with approximately 50 laying cups, with approximately 1000 females per cup, we carried out overnight collections. This provided approximately 10 ml of packed embryos. The embryos were bleach dechorionated (yielding approximately 9 grams of embryos), and then homogenized. After disruption, the homogenate was clarified using a low speed spin followed by a high speed centrifugation. The clarified supernatant was treated with GTP and taxol to polymerize MTs. Kinesin was immobilized on polymerized MTs by adding the ATP analog, 5'-adenylyl imidodiphosphate at room temperature. After kinesin binding, microtubules were sedimented via high speed centrifugation through a sucrose cushion. The microtubule pellet was then re-suspended, and this process was repeated. Finally, ATP was added to release the kinesin from the MTs. High speed centrifugation then spun down the MTs, leaving the kinesin in the supernatant. This kinesin was subjected to a centrifugal filtration using a 100 KD cut off filter for further purification, aliquoted, snap frozen in liquid nitrogen, and stored at -80 &deg;C. SDS gel electrophoresis and western blotting was performed using the purified sample. The motor activity of purified samples before and after the final centrifugal filtration step was evaluated using an in vitro single molecule microtubule assay. The kinesin fractions before and after the centrifugal filtration showed processivity as previously reported in literature. Further experiments are underway to evaluate the interaction between kinesin and other transport related proteins.

Isolation and Purification of Kinesin from Drosophila Embryos

This is a protocol to isolate active full length Kinesin from Drosophila embryos for single-molecule biophysical studies. We show how to collect embryos, make the embryo lysate, and then polymerize microtubules (MTs). Kinesin is purified by immobilizing it on the MTs, spinning down the Kinesin-MT complexes, and then releasing the kinesin from the MTs via ATP addition.

Motor proteins move cargos along microtubules, and transport them to specific sub-cellular locations. Because altered transport is suggested to underlie a ...

Live Imaging of Apoptotic Cell Clearance during Drosophila Embryogenesis

The proper elimination of unwanted or aberrant cells through apoptosis and subsequent phagocytosis (apoptotic cell clearance) is crucial for normal development in all metazoan organisms. Apoptotic cell clearance is a highly dynamic process intimately associated with cell death; unengulfed apoptotic cells are barely seen in vivo under normal conditions. In order to understand the different steps of apoptotic cell clearance and to compare 'professional' phagocytes - macrophages and dendritic cells to 'non-professional' - tissue-resident neighboring cells, in vivo live imaging of the process is extremely valuable. Here we describe a protocol for studying apoptotic cell clearance in live Drosophila embryos. To follow the dynamics of different steps in phagocytosis we use specific markers for apoptotic cells and phagocytes. In addition, we can monitor two phagocyte systems in parallel: 'professional' macrophages and 'semi-professional' glia in the developing central nervous system (CNS). The method described here employs the Drosophila embryo as an excellent model for real time studies of apoptotic cell clearance.

Live Imaging of Apoptotic Cell Clearance during Drosophila Embryogenesis

Here we describe an effective method for studying dynamics of apoptotic cell clearance in vivo. This method employs live Drosophila embryos as a powerful model for monitoring phagocytosis of apoptotic cells using specific labeling of apoptotic cells and phagocytes.

The  proper elimination of unwanted or aberrant cells through apoptosis and  subsequent phagocytosis (apoptotic cell clearance) is crucial for normal  ...

Affinity-based Isolation of Tagged Nuclei from Drosophila Tissues for Gene Expression Analysis

Drosophila melanogaster embryonic and larval tissues often contain a highly heterogeneous mixture of cell types, which can complicate the analysis of gene expression in these tissues. Thus, to analyze cell-specific gene expression profiles from Drosophila tissues, it may be necessary to isolate specific cell types with high purity and at sufficient yields for downstream applications such as transcriptional profiling and chromatin immunoprecipitation. However, the irregular cellular morphology in tissues such as the central nervous system, coupled with the rare population of specific cell types in these tissues, can pose challenges for traditional methods of cell isolation such as laser microdissection and fluorescence-activated cell sorting (FACS). Here, an alternative approach to characterizing cell-specific gene expression profiles using affinity-based isolation of tagged nuclei, rather than whole cells, is described. Nuclei in the specific cell type of interest are genetically labeled with a nuclear envelope-localized EGFP tag using the Gal4/UAS binary expression system. These EGFP-tagged nuclei can be isolated using antibodies against GFP that are coupled to magnetic beads. The approach described in this protocol enables consistent isolation of nuclei from specific cell types in the Drosophila larval central nervous system at high purity and at sufficient levels for expression analysis, even when these cell types comprise less than 2% of the total cell population in the tissue. This approach can be used to isolate nuclei from a wide variety of Drosophila embryonic and larval cell types using specific Gal4 drivers, and may be useful for isolating nuclei from cell types that are not suitable for FACS or laser microdissection.

Affinity-based Isolation of Tagged Nuclei from Drosophila Tissues for Gene Expression Analysis

Drosophila tissues often contain a heterogeneous mixture of cell types.&#160;To examine gene expression in specific cell types from a particular tissue, nuclei can be genetically tagged and subsequently isolated using an affinity-based approach. Isolated nuclei can be used for downstream applications such as gene expression analysis and chromatin immunoprecipitation.

Drosophila melanogaster embryonic and larval tissues often contain a highly heterogeneous mixture of cell types, which can complicate the analysis of gene ...

Isolation of Neonatal Extrahepatic Cholangiocytes

The intra and extrahepatic bile ducts of the liver are developmentally distinct, and may be differentially affected by certain diseases. However, differences between intra and extrahepatic cholangiocytes, and between neonatal and adult cells, are not well understood.
Methods for the isolation of cholangiocytes from intrahepatic bile ducts are well established1-4. Isolation of extrahepatic ductal cells, especially from the neonate, has not yet been described, although this would be of great benefit in understanding the differences between distinct cholangiocyte populations and in studying diseases such as biliary atresia that appear to target the extrahepatic ducts. Described here is an optimized technique to isolate both neonatal and adult mouse extrahepatic bile duct cells. This technique yields a pure cell population with minimal contamination from mesenchymal cells like fibroblasts.
This method is based on the removal of the extrahepatic ducts and gallbladder, followed by meticulous dissection and scraping to remove fat and fibroblast layers. Structures are embedded in thick layers of collagen and cultured for approximately 3 weeks to allow outgrowth of cholangiocytes in monolayers, which can then be trypsinized and re plated for experimental use.

A technique to isolate cholangiocytes from the extrahepatic bile ducts of neonatal mice is described. The ducts are meticulously dissected, and then cells are isolated by outgrowth in thick collagen gels. This method provides a useful tool for studying extrahepatic bile duct development and pathology.

The intra and extrahepatic bile ducts of the liver are developmentally distinct, and may be differentially affected by certain diseases. However, ...

Isolation of Murine Valve Endothelial Cells

Normal valve structures consist of stratified layers of specialized extracellular matrix (ECM) interspersed with valve interstitial cells (VICs) and surrounded by a monolayer of valve endothelial cells (VECs). VECs play essential roles in establishing the valve structures during embryonic development, and are important for maintaining life-long valve integrity and function. In contrast to a continuous endothelium over the surface of healthy valve leaflets, VEC disruption is commonly observed in malfunctioning valves and is associated with pathological processes that promote valve disease and dysfunction. Despite the clinical relevance, focused studies determining the contribution of VECs to development and disease processes are limited. The isolation of VECs from animal models would allow for cell-specific experimentation. VECs have been isolated from large animal adult models but due to their small population size, fragileness, and lack of specific markers, no reports of VEC isolations in embryos or adult small animal models have been reported. Here we describe a novel method that allows for the direct isolation of VECs from mice at embryonic and adult stages. Utilizing the Tie2-GFP reporter model that labels all endothelial cells with Green Fluorescent Protein (GFP), we have been successful in isolating GFP-positive (and negative) cells from the semilunar and atrioventricular valve regions using fluorescence activated cell sorting (FACS). Isolated GFP-positive VECs are enriched for endothelial markers, including CD31 and von Willebrand Factor (vWF), and retain endothelial cell expression when cultured; while, GFP-negative cells exhibit molecular profiles and cell shapes consistent with VIC phenotypes. The ability to isolate embryonic and adult murine VECs allows for previously unattainable molecular and functional studies to be carried out on a specific valve cell population, which will greatly improve our understanding of valve development and disease mechanisms.

The ability to isolate heart valve endothelial cells (VECs) is critical for understanding mechanisms of valve development, maintenance, and disease. Here we describe the isolation of VECs from embryonic and adult Tie2-GFP mice using FACS that will allow for studies determining the contribution of VECs in developmental and disease processes.

Normal valve structures consist of stratified layers of specialized extracellular matrix (ECM) interspersed with valve interstitial cells (VICs) and ...