This study was supported by grants from the Chinese Special Fund for Postdocs (No. 2014T70392 to YF), the National Natural Science Foundation of China (No. 81673766 to YF), the New Teacher Priming Fund, the Zuoxue Foundation of Fudan University, and the Development Project of Shanghai Peak Disciplines-Integrative Medicine (20150407).

All procedures involving animal subjects followed the guidelines of the Animal Ethics Committee at Shanghai Medical College, Fudan University (Approval number 20160225-013).
1. Preparation of the Transparent Mouse Ovary
<ol>
	<li>Preparation of the solutions
	<ol>
		<li>Prepare phosphate-buffered saline (PBS) solution (1 M, pH 7.6) with 0.1% Triton X-100 (PBST). To make 1 L of 10x PBS stock solution, mix 87 g of NaCl, 3.1 g of NaH2PO4 &#183; 2H2O, and 28.7 g of Na2HPO4 &#183;12H2O. Add dH2O to 1 L and stir ~2 h. Adjust to pH 7.4 with 1 N NaOH and store at room temperature. Dilute this 10x stock solution by 1/10 using dH2O and then make 0.1% Triton X-100 in PBS.</li>
		<li>Prepare the hydrogel solution (pH 7.5) by mixings 4% (wt/vol) paraformaldehyde (PFA) solution, 4% (wt/vol) acrylamide, 0.05% (wt/vol) bisacrylamide, and 0.25% (wt/vol) VA-044 initiator in double-distilled water on ice.</li>
		<li>Prepare the clearing solution (pH 8.5) by mixing 200 mM sodium borate buffer containing 4% (wt/vol) sodium dodecyl sulfate (SDS) in double-distilled water.</li>
	</ol>
	</li>
	<li>Transcardial perfusion and ovary preparation
	<ol>
		<li>Keep all solutions on ice during all procedures.</li>
		<li>Anesthetize adult female wild type C57BL/6 mouse with an intraperitoneal injection of pentobarbital (0.35 mg/kg) solution. Once it shows no toe-pinch response, the mouse is properly anesthetized.</li>
		<li>Use sticky tape to fix the mouse with limbs stretched out on a flat foam board.</li>
		<li>Expose the heart by an incision on the xiphoid-process through the chest, skin, and bones with scissors.</li>
		<li>Make an incision into the animal&#39;s right atrium, and then perfuse the left ventricle with 20 mL of ice-cold 1x PBS at 10 mL/min.</li>
		<li>Perfuse the animal with at least 20 mL of hydrogel solution at 10 mL/min.</li>
		<li>Incise the skin over the abdomen along the medioventral line with scissors, which exposes the whole enterocoelia, and remove the intestines. Collect the ovaries as well as the uterus to maintain the integrity of ovarian morphology.</li>
		<li>Remove the fat tissues around the ovary under a microscope.</li>
	</ol>
	</li>
	<li>Degassing
	<ol>
		<li>Place the ovaries in 10 mL hydrogel solution at 4 &#176;C for fixation for 3 days.</li>
		<li>Transfer the ovary into a 5-mL tube and fill the tube with hydrogel solution. Stretch parafilm over the top of the tube and then wrap parafilm around the neck of the tube. 
		Caution: Ensure that there are no bubbles between the parafilm and the hydrogel solution.</li>
		<li>Place the tube on a shaker in the incubator at 37 &#176;C for a maximum of 3 h to allow the hydrogel to polymerize.</li>
		<li>Remove the ovary from the gel using a spatula and carefully remove the excess gel from around the ovary by tissue paper. Wash the ovary four times with 1x PBS.</li>
	</ol>
	</li>
	<li>Passive clearing
	<ol>
		<li>Submerge the ovary in 10 mL of the clearing solution. Gently shake at 80 rpm at 37 &#176;C to start the clearing process.</li>
		<li>In the first week, change the solution every 3 days. After one week, refresh the clearing solution once a week until the ovary becomes clear. Usually this process takes about 2-3 weeks. 
		NOTE: The ovary can be directly immunostained or can be stored in sodium azide (0.02%) in PBS at 4 &#176;C for several weeks before immunostaining.</li>
	</ol>
	</li>
</ol>
2. Immunostaining
<ol>
	<li>Wash the ovary twice in PBST on the day 1 at 37 &#176;C on a shaker.</li>
	<li>Incubate the ovary on a shaker in primary antibodies/PBST solution (Table 1) on day 2-3 at 37 &#176;C. In the work presented here, the primary antibodies were platelet-endothelial cell adhesion molecule 1 (CD31) and tyrosine hydroxylase diluted at 1:10 and 1:50 in PBST, respectively. 
	Caution: If two or more kinds of primary antibody are used, make sure there are different animal sources.</li>
	<li>Wash off the primary antibodies with PBST buffer at 37 &#176;C on day 4 on a shaker.</li>
	<li>Incubate the ovary with the desired secondary antibodies in PBST on day 5-6 at 37 &#176;C on a shaker. In the work presented here, the secondary antibodies were Alexa Flour 488 for tyrosine hydroxylase and Alexa Flour 594 for CD31 diluted at 1:50 in PBST.</li>
	<li>Wash off the secondary antibodies with PBST buffer at 37 &#176;C on day 7 on a shaker.</li>
	<li>Transfer the tissue into refractive index matching solution for refractive index homogenization on day 8. Put the tissue on a paper with gridlines to check its visual clarity by checking whether the gridlines can be seen. Once the tissue has been fully clarified, it can be imaged.</li>
	<li>Make a putty cylinder that could just surrounds the tissue, and then shape it into a horseshoe shape and press the outer ridge tightly onto a glass slide in order to make a sealed space. The height of the putty should be a little taller than the ovary.</li>
	<li>Place the clarified ovary carefully into the center of the putty and add refractive index matching solution. Put a glass-bottom dish over the putty tightly and use putty to fix the dish.</li>
</ol>
3. Confocal Microscopy
<ol>
	<li>For imaging with a confocal microscope, in the &#34;Ni-E&#34; panel choose the lens (in this case water immersion 25X objective lens, 1.1-NA, 2 mm-WD) with the proper working distance (in this case 2.0 mm).</li>
	<li>In the &#34;Acquisition&#34; panel, select the number of channels. Here, use three channels.
	<ol>
		<li>First, use the &#34;eye port&#34; tab and the XY controller joystick to move the tissue to the center of field by checking through the microscope eyepieces.</li>
		<li>After turning off the shutter light, click the &#34;live&#34; tab to adjust the &#34;laser power&#34;, &#34;HV (Gain)&#34;, and &#34;offset&#39; for each channel separately. Higher laser power and HV can lead to higher signals, and higher offset can reduce the background noise.</li>
		<li>Select the proper &#34;Scan size&#34; and &#34;Count&#34;. Use a scan size of 1024 x 1024 &#181;m2 and a count of 4 to 8.</li>
	</ol>
	</li>
	<li>After setting the image quality for defining the depth of the tissue in the panel &#34;Z intensity correction&#34;, and after locating the lens on the top-most layer of the ovary (in the center of the tissue) and adjusting the acquisition for the top layer, click the &#34;plus&#34; button to define the top layer.
	<ol>
		<li>Move the lens down and set the appropriate HV and laser power for the bottom of the tissue and add the lowest layer information into the Z-intensity correction table. Click on &#34;To ND&#34; to synchronize the setting with the &#34;ND acquisition&#34; panel.</li>
	</ol>
	</li>
	<li>In the &#34;ND acquisition&#34; panel, first set the number of scanning steps. Then, tick the tabs &#34;Z&#34; and &#34;Large Image&#34;.
	<ol>
		<li>Go to the &#34;Scan large image&#34; window to define the size of the field according to the border of the tissue with the help of tissue visualization through the eyepieces. Go back to the &#34;ND acquisition&#34; panel to input the size of the scanning area (&#34;fields&#34;) and choose the overlap between 10% and 15%.</li>
		<li>Click &#34;Run Z correction&#34;, not &#34;Run now&#34;, to automatically set the proper HV, laser power, and offset for each layer, and wait for the image to process.</li>
	</ol>
	</li>
</ol>
4. 3D Reconstruction of Individual Follicles and Their Vasculatures
<ol>
	<li>First, use ImageJ5 to open the original NIS file. Click the &#34;Image&#34; button and choose the &#34;Color&#34; and the &#34;Split Channels&#34;. Then, click &#34;File&#34; and separately save the channels as tiff file series by using the &#34;Image Sequences&#34; option in &#34;Save as&#34;.</li>
	<li>Use Imaris to open one of the tiff file series. Click the &#34;Edit&#34; button and choose &#34;Add channels&#34; to add the rest of the channels. The name and color of the channel can be changed in the &#34;Display Adjustment&#34; tabs. The thickness of the tissue might need to be corrected in the &#34;Image Properties&#34; panel in the drop-down list under &#34;Edit&#34;.</li>
	<li>For the 3D cropping of the final images and removal of excess parts, click the &#34;Edit&#34; button and choose &#34;Crop 3D&#34;. The size of the field can be adjusted by dragging the border.</li>
	<li>To reconstruct the vessel signals with the Filaments algorithm in the Surpass panel, click the &#34;Filaments&#34; button to create a new Filament and click next.
	<ol>
		<li>In order to define the largest and the thinnest diameter, go to the &#34;Slice&#34; panel and find the tracing vessel. The distance will be automatically shown on the &#34;Measure&#34; panel by selecting two points at the maximum width of the vessel.</li>
		<li>Go back to the &#34;Surpass&#34; panel and input the measured width and click next.</li>
	</ol>
	</li>
	<li>Adjust the starting and seed point threshold. In the &#34;Camera&#34; panel, choose &#34;Select&#34;. If some of the automatically produced spheres need to be removed, press shift and click on the point. By choosing &#34;Navigate&#34; and moving the mouse, the structure can be rotated to ensure that all the correct points have been retained, and then click next.</li>
	<li>Choose the highest threshold for the local contrast and click next. Do not select &#34;Detect Spines&#34;, and continue to finalize the reconstruction of the blood vessel cylinder. The color can be edited by clicking the &#34;Color&#34; tab. The statistical data can be extracted in the &#34;Statistic&#34; panel of the reconstructed Filament. Excess parts can be removed in the &#34;Edit&#34; panel. 
	NOTE: Other algorithms can be used for measuring the volume of total follicles or follicular walls. In the work presented here, the oocytes were marked by the autofluorescence of both secondary antibodies. Because of the large amount of data, a workstation server was used for the data analysis.</li>
</ol>
5. Statistical Analysis
NOTE: Image analysis data are presented as means &#177; standard errors.
<ol>
	<li>Perform comparisons between the follicles using independent sample t-test, and use Pearson&#39;s correlation test to compare correlation coefficients of follicular wall and capillary length. Set a value of P &#60;0.05 as the limit for statistical significance.</li>
</ol>

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The authors have nothing to disclose.

In the current study, we present 3D imaging to evaluate the relationships between capillaries and individual growing follicles. In our previous work using the same protocol 9, we studied the roles of large vasculature, interactions between follicles, and the location of follicles in intact mouse ovaries. The passive CLARITY approach allowed us to study micro- and macro-vasculatures, folliculogenesis, and the interrelationships between the corpora lutea and follicles as well as to reconstruct the o...

The follicle is the fundamental structural and functional unit of the ovary, and its development is highly related to the vasculature within the ovary. Blood vessels supply nutrition and hormones to the follicles and thus play important roles in the growth and maturation of follicles1.
A combination of technologies, including selective blood vessel markers, transgenic mouse models, and pharmaceutical development, have increased our knowledge about ovarian vascular networks, angiogenesis, and the function of blood vessels in folliculogenesis. The ovary is known as an active organ because it remodels various tissues and vascular networks during folliculogenesis and ovulation. Such active remodeling in the size and structure of vessels is required for the biological function of developing and recruiting follicles.
Traditional histological and histomorphometric methods using ovarian sections and immunolabeling of blood vessels are limited to two-dimensional (2D) images2. With the development of three-dimensional (3D) reconstruction technologies, 2D images of tissue slices can be overlapped to make a 3D structure, but this method still has some limitations &#8212; sectioning of the tissue can destroy the microstructures, some parts of the tissue are often missing, and significant labor is involved in making 3D reconstructions from images obtained from slices. Whole-tissue 3D imaging with confocal microscopy can overcome many of these limitations, but these methods are limited to the evaluation of angiogenesis in the embryonic ovary3. Using whole tissue clearing methods such as CLARITY4 can increase the visualized volume so as to solve these problems in postnatal and adult ovaries, and such methods provide optical clearance of the ovary without any structural deformations. Imaging of the 3D architecture of the intact ovary provides an accurate image database for image analysis software, such as the Imaris software package used in this work.
Remodeling of the ovary throughout adulthood is part of a dynamic physiological system, and this makes the ovary an excellent model for investigations into the regulation of angiogenesis. Furthermore, evaluating the role of ovarian blood vessels in pathologic conditions of the female reproductive system such as polycystic ovary syndrome or ovarian cancers can be studied through whole ovarian tissue imaging. The development of the passive CLARITY method and the use of advanced image analysis software have provided detailed spatial information on the relationships between blood vessels and ovarian structures such as follicles.

<table><tbody><tr><td>Acrylamide</td><td>Vetec</td><td>v900845</td><td>http://www.sigmaaldrich.com/catalog/product/vetec/v900845</td></tr><tr><td>Alexa Flour 488 (Dilution 1:50)&amp;nbsp;</td><td>Life Technologies</td><td>A11039</td><td>https://www.thermofisher.com/antibody/product/Goat-anti-Chicken-IgY-H-L-Secondary-Antibody-Polyclonal/A-11039</td></tr><tr><td>Alexa Flour 594 (Dilution 1:50)</td><td>Life Technologies</td><td>A11012</td><td>https://www.thermofisher.com/antibody/product/Goat-anti-Rabbit-IgG-H-L-Cross-Adsorbed-Secondary-Antibody-Polyclonal/A-11012</td></tr><tr><td>Bisacrylamide</td><td>Amresco</td><td>172</td><td>http://www.amresco-inc.com/BIS-ACRYLAMIDE-0172.cmsx</td></tr><tr><td>Black wall glass bottom dish (Willco-Dish)</td><td>Ted Pella</td><td>14032</td><td>http://www.tedpella.com/section_html/706dish.htm#black_wall</td></tr><tr><td>Boric acid</td><td>Sinopharm Chemical Reagent</td><td>10004818</td><td>http://en.reagent.com.cn/enshowproduct.jsp?id=10004818</td></tr><tr><td>Disodium hydrogen phosphate dodecahydrate (Na&lt;sub&gt;2&lt;/sub&gt;HPO&lt;sub&gt;4&lt;/sub&gt; 12H&lt;sub&gt;2&lt;/sub&gt;O)</td><td>Sinopharm Chemical Reagent</td><td>10020318</td><td>http://en.reagent.com.cn/enshowproduct.jsp?id=10020318</td></tr><tr><td>FocusClear</td><td>Celexplorer</td><td>FC-102</td><td>http://www.celexplorer.com/product_list.asp?MainType=107&amp;amp;BRDarea=1</td></tr><tr><td>Parafilm</td><td>Bemis</td><td>PM996</td><td>http://www.parafilm.com/products</td></tr><tr><td>Paraformaldehyde</td><td>Sinopharm Chemical Reagent</td><td>80096618</td><td>http://en.reagent.com.cn/enshowproduct.jsp?id=80096618</td></tr><tr><td>PECAM1/CD31, platelet-endothelial cell adhesion molecule 1 (Dilution 1:10)</td><td>Abcam</td><td>ab28364</td><td>http://www.abcam.com/cd31-antibody-ab28364.html</td></tr><tr><td>Photoinitiator VA044</td><td>Wako</td><td>va-044/225-02111</td><td>http://www.wako-chem.co.jp/specialty/waterazo/VA-044.htm</td></tr><tr><td>Sodium azide</td><td>Sigma</td><td>S2002</td><td>http://www.sigmaaldrich.com/catalog/product/sial/s2002?lang=en&amp;amp;region=US</td></tr><tr><td>Sodium chloride (NaCl)</td><td>Sinopharm Chemical Reagent</td><td>10019318</td><td>http://en.reagent.com.cn/enshowproduct.jsp?id=10019318</td></tr><tr><td>Sodium dihydrogen phosphate dihydrate (NaH&lt;sub&gt;2&lt;/sub&gt;PO&lt;sub&gt;4&lt;/sub&gt; 2H&lt;sub&gt;2&lt;/sub&gt;O)</td><td>Sinopharm Chemical Reagent</td><td>20040718</td><td>http://en.reagent.com.cn/enshowproduct.jsp?id=20040718</td></tr><tr><td>Sodium dodecyl sulfate</td><td>Sinopharm Chemical Reagent</td><td>30166428</td><td>http://en.reagent.com.cn/enshowproduct.jsp?id=30166428</td></tr><tr><td>Sodium hydroxide (NaOH)</td><td>Sinopharm Chemical Reagent</td><td>10019718</td><td>http://en.reagent.com.cn/enshowproduct.jsp?id=10019718</td></tr><tr><td>Triton X-100</td><td>Sinopharm Chemical Reagent</td><td>30188928</td><td>http://en.reagent.com.cn/enshowproduct.jsp?id=30188928</td></tr><tr><td>Tyrosine hydroxylase (TH, Dilution 1:50)</td><td>Abcam</td><td>ab76442</td><td>http://www.abcam.com/tyrosine-hydroxylase-phospho-s40-antibody-ab51206.html</td></tr></tbody></table>

three-dimensional reconstruction of the vascular architecture of the passive clarity-cleared mouse ovary

The ovary is the main organ of the female reproductive system and is essential for the production of female gametes and for controlling the endocrine system, but the complex structural relationships and three-dimensional (3D) vasculature architectures of the ovary are not well described. In order to visualize the 3D connections and architecture of blood vessels in the intact ovary, the first important step is to make the ovary optically clear. In order to avoid tissue shrinkage, we used the hydrogel fixation-based passive CLARITY (Clear Lipid-exchanged Acrylamide-hybridized Rigid Imaging/ Immunostaining/In situ-hybridization-compatible Tissue Hydrogel) protocol method to clear an intact ovary. Immunostaining, advanced multiphoton confocal microscopy, and 3D image-reconstructions were then used for the visualization of ovarian vessels and follicular capillaries. Using this approach, we showed a significant positive correlation (P &#60;0.01) between the length of the follicular capillaries and volume of the follicular wall.

We adapted the passive CLARITY method into a quick and simple method for passive ovary clearing while preserving the follicular and vascular architecture and obtaining the highest fluorescent signal from labeled markers of vessels and follicles. The 3D architecture of the follicular vasculature was determined by immunostaining for CD31, a marker for endothelial cells6. CD31 staining in the ovaries of adult mice was traced using the Filament algorithm and showed int...

Watch this Scientific Journal Video about Three-dimensional Reconstruction of the Vascular Architecture of the Passive CLARITY-cleared Mouse Ovary at JoVE.com

Three-dimensional Reconstruction of the Vascular Architecture of the Passive CLARITY-cleared Mouse Ovary

Here we present an adaptation of the passive CLARITY and 3D reconstruction method for visualization of the ovarian vasculature and follicular capillaries in intact mouse ovaries.

The ovary is the main organ of the female reproductive system and is essential for the production of female gametes and for controlling the endocrine ...

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Research

JoVE Journal

Biology

8.6K Views.  Fudan University. Here we present an adaptation of the passive CLARITY and 3D reconstruction method for visualization of the ovarian vasculature and follicular capillaries in intact mouse ovaries.

Video: Three-dimensional Reconstruction of the Vascular Architecture of the Passive CLARITY-cleared Mouse Ovary

An Orthotopic Model of Serous Ovarian Cancer in Immunocompetent Mice for in vivo Tumor Imaging and Monitoring of Tumor Immune Responses

Background: Ovarian cancer is generally diagnosed at an advanced stage where the case/fatality ratio is high and thus remains the most lethal of all gynecologic malignancies among US women 1,2,3. Serous tumors are the most widespread forms of ovarian cancer and 4,5 the Tg-MISIIR-TAg transgenic represents the only mouse model that spontaneously develops this type of tumors. Tg-MISIIR-TAg mice express SV40 transforming region under control of the Mullerian Inhibitory Substance type II Receptor (MISIIR) gene promoter 6. Additional transgenic lines have been identified that express the SV40 TAg transgene, but do not develop ovarian tumors. Non-tumor prone mice exhibit typical lifespan for C57Bl/6 mice and are fertile. These mice can be used as syngeneic allograft recipients for tumor cells isolated from Tg-MISIIR-TAg-DR26 mice.
Objective: Although tumor imaging is possible 7, early detection of deep tumors is challenging in small living animals. To enable preclinical studies in an immunologically intact animal model for serous ovarian cancer, we describe a syngeneic mouse model for this type of ovarian cancer that permits in vivo imaging, studies of the tumor microenvironment and tumor immune responses.
Methods: We first derived a TAg+ mouse cancer cell line (MOV1) from a spontaneous ovarian tumor harvested in a 26 week-old DR26 Tg-MISIIR-TAg female. Then, we stably transduced MOV1 cells with TurboFP635 Lentivirus mammalian vector that encodes Katushka, a far-red mutant of the red fluorescent protein from sea anemone Entacmaea quadricolor with excitation/emission maxima at 588/635 nm 8,9,10. We orthotopically implanted MOV1Kat in the ovary 11,12,13,14 of non-tumor prone Tg-MISIIR-TAg female mice. Tumor progression was followed by in vivo optical imaging and tumor microenvironment was analyzed by immunohistochemistry.
Results: Orthotopically implanted MOV1Kat cells developed serous ovarian tumors. MOV1Kat tumors could be visualized by in vivo imaging up to three weeks after implantation (fig. 1) and were infiltrated with leukocytes, as observed in human ovarian cancers 15 (fig. 2).
Conclusions: We describe an orthotopic model of ovarian cancer suitable for in vivo imaging of early tumors due to the high pH-stability and photostability of Katushka in deep tissues. We propose the use of this novel syngeneic model of serous ovarian cancer for in vivo imaging studies and monitoring of tumor immune responses and immunotherapies.

An Orthotopic Model of Serous Ovarian Cancer in Immunocompetent Mice for in vivo Tumor Imaging and Monitoring of Tumor Immune Responses

To study in vivo tumor growth and tumor microenvironment, we used a syngeneic and orthotopic mouse model of ovarian cancer in immunocompetent animals. We transduced a mouse tumor cell line (MOV1) with Katushka fluorescent protein (MOV1KAT) and here we show its orthotopic implantation in ovary and in vivo imaging.

Background: Ovarian cancer is generally diagnosed at an advanced stage where the case/fatality ratio is high and thus remains the most lethal of all ...

Immunology and Infection

Three-dimensional Rendering and Analysis of Immunolabeled, Clarified Human Placental Villous Vascular Networks

Nutrient and gas exchange between mother and fetus occurs at the interface of the maternal intervillous blood and the vast villous capillary network that makes up much of the parenchyma of the human placenta. The distal villous capillary network is the terminus of the fetal blood supply after several generations of branching of vessels extending out from the umbilical cord. This network has a contiguous cellular sheath, the syncytial trophoblast barrier layer, which prevents mixing of fetal blood and the maternal blood in which it is continuously bathed. Insults to the integrity of the placental capillary network, occurring in disorders such as maternal diabetes, hypertension and obesity, have consequences that present serious health risks for the fetus, infant, and adult. To better define the structural effects of these insults, a protocol was developed for this study that captures capillary network structure on the order of 1 - 2 mm3 wherein one can investigate its topological features in its full complexity. To accomplish this, clusters of terminal villi from placenta are dissected, and the trophoblast layer and the capillary endothelia are immunolabeled. These samples are then clarified with a new tissue clearing process which makes it possible to acquire confocal image stacks to z- depths of ~1 mm. The three-dimensional renderings of these stacks are then processed and analyzed to generate basic capillary network measures such as volume, number of capillary branches, and capillary branch end points, as validation of the suitability of this approach for capillary network characterization.

This study presents a protocol for the reversible tissue clearing, immunostaining, 3D-rendering and analysis of vascular networks in human placenta villi samples on the order of 1 - 2 mm3.

Nutrient and gas exchange between mother and fetus occurs at the interface of the maternal intervillous blood and the vast villous capillary network that ...

Developmental Biology

Whole Mount Immunofluorescence and Follicle Quantification of Cultured Mouse Ovaries

Research in the field of mammalian reproductive biology often involves evaluating the overall health of ovaries and testes. Specifically, in females, ovarian fitness is often assessed by visualizing and quantifying follicles and oocytes. Because the ovary is an opaque three-dimensional tissue, traditional approaches require laboriously slicing the tissue into numerous serial sections in order to visualize cells throughout the entire organ. Furthermore, because quantification by this method typically entails scoring only a subset of the sections separated by the approximate diameter of an oocyte, it is prone to inaccuracy. Here, a protocol is described that instead utilizes whole organ tissue clearing and immunofluorescence staining of mouse ovaries to visualize follicles and oocytes. Compared to more traditional approaches, this protocol is advantageous for visualizing cells within the ovary for numerous reasons: 1) the ovary remains intact throughout sample preparation and processing; 2) small ovaries, which are difficult to section, can be examined with ease; 3) cellular quantification is more readily and accurately achieved; and 4) the whole organ imaged.

Here, we present a protocol to quantify follicles in cultured ovaries of young mice without serial sectioning. Using whole organ immunofluorescence and tissue clearing, physical sectioning is replaced with optical sectioning. This method of sample preparation and visualization maintains organ integrity and facilitates automated quantification of specific cells.

Research in the field of mammalian reproductive biology often involves evaluating the overall health of ovaries and testes. Specifically, in females, ...

Ovarian Tissue Culture to Visualize Phenomena in Mouse Ovary

Mammalian females periodically ovulate an almost constant number of oocytes during each estrus cycle. To sustain such regularity and periodicity, regulation occurs at the hypothalamic-pituitary-gonadal axis level and on developing follicles in the ovary. Despite active studies, follicle development mechanisms are not clear because of the several steps involved from the dormant primordial follicle activation to ovulation, and because of the regulation complexity that differs at each follicular stage. To investigate the mechanisms of follicle development, and the dynamics of follicles throughout the estrus cycle, we developed a mouse ovarian tissue culture model that can be used to observe follicle development using a microscope. Systematic follicle development, periodical ovulation, and follicle atresia can all be reproduced in the cultured ovary model, and the culture conditions can be experimentally modulated. Here, we demonstrate the usefulness of this method in the study of the regulatory mechanisms of follicle development and other ovarian phenomena.

Ovarian tissue cultures can be used as models of follicle development, ovulation, and follicle atresia and indicate regulatory mechanisms of dynamic ovarian processes.

Mammalian females periodically ovulate an almost constant number of oocytes during each estrus cycle. To sustain such regularity and periodicity, ...

Imaging Cleared Intact Biological Systems at a Cellular Level by 3DISCO

Tissue clearing and subsequent imaging of transparent organs is a powerful method to analyze fluorescently labeled cells and molecules in 3D, in intact organs. Unlike traditional histological methods, where the tissue of interest is sectioned for fluorescent imaging, 3D imaging of cleared tissue allows examination of labeled cells and molecules in the entire specimen. To this end, optically opaque tissues should be rendered transparent by matching the refractory indices throughout the tissue. Subsequently, the tissue can be imaged at once using laser-scanning microscopes to obtain a complete high-resolution 3D image of the specimen. A growing list of tissue clearing protocols including 3DISCO, CLARITY, Sca/e, ClearT2, and SeeDB provide new ways for researchers to image their tissue of interest as a whole. Among them, 3DISCO is a highly reproducible and straightforward method, which can clear different types of tissues and can be utilized with various microscopy techniques. This protocol describes this straightforward procedure and presents its various applications. It also discusses the limitations and possible difficulties and how to overcome them.

To obtain high-resolution images of fluorescently labeled cells within large tissues, ideally, the biological samples should be imaged without sectioning. 3DISCO is a straightforward tissue clearing procedure based on sequential incubation with organic solvents. Upon clearing, the organs become transparent allowing an end-to-end laser scan of the specimen.

Tissue clearing and subsequent imaging of transparent organs is a powerful method to analyze fluorescently labeled cells and molecules in 3D, in intact ...

Neuroscience

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

The three-dimensional folding of chromosomes compartmentalizes the genome and and can bring distant functional elements, such as promoters and enhancers, into close spatial proximity 2-6. Deciphering the relationship between chromosome organization and genome activity will aid in understanding genomic processes, like transcription and replication. However, little is known about how chromosomes fold. Microscopy is unable to distinguish large numbers of loci simultaneously or at high resolution. To date, the detection of chromosomal interactions using chromosome conformation capture (3C) and its subsequent adaptations required the choice of a set of target loci, making genome-wide studies impossible 7-10.
We developed Hi-C, an extension of 3C that is capable of identifying long range interactions in an unbiased, genome-wide fashion. In Hi-C, cells are fixed with formaldehyde, causing interacting loci to be bound to one another by means of covalent DNA-protein cross-links. When the DNA is subsequently fragmented with a restriction enzyme, these loci remain linked. A biotinylated residue is incorporated as the 5' overhangs are filled in. Next, blunt-end ligation is performed under dilute conditions that favor ligation events between cross-linked DNA fragments. This results in a genome-wide library of ligation products, corresponding to pairs of fragments that were originally in close proximity to each other in the nucleus. Each ligation product is marked with biotin at the site of the junction. The library is sheared, and the junctions are pulled-down with streptavidin beads. The purified junctions can subsequently be analyzed using a high-throughput sequencer, resulting in a catalog of interacting fragments.
Direct analysis of the resulting contact matrix reveals numerous features of genomic organization, such as the presence of chromosome territories and the preferential association of small gene-rich chromosomes. Correlation analysis can be applied to the contact matrix, demonstrating that the human genome is segregated into two compartments: a less densely packed compartment containing open, accessible, and active chromatin and a more dense compartment containing closed, inaccessible, and inactive chromatin regions. Finally, ensemble analysis of the contact matrix, coupled with theoretical derivations and computational simulations, revealed that at the megabase scale Hi-C reveals features consistent with a fractal globule conformation.

The Hi-C method allows unbiased, genome-wide identification of chromatin interactions (1). Hi-C couples proximity ligation and massively parallel sequencing. The resulting data can be used to study genomic architecture at multiple scales: initial results identified features such as chromosome territories, segregation of open and closed chromatin, and chromatin structure at the megabase scale.

The three-dimensional folding of chromosomes compartmentalizes the genome and and can bring distant functional elements, such as promoters and enhancers, ...

Accurate Follicle Enumeration in Adult Mouse Ovaries

Sexually reproducing female mammals are born with their entire lifetime supply of oocytes. Immature, quiescent oocytes are found within primordial follicles, the storage unit of the female germline. They are non-renewable, thus their number at birth and subsequent rate of loss largely dictates the female fertile lifespan. Accurate quantification of primordial follicle numbers in women and animals is essential for determining the impact of medicines and toxicants on the ovarian reserve. It is also necessary for evaluating the need for, and success of, existing and emerging fertility preservation techniques. Currently, no methods exist to accurately measure the number of primordial follicles comprising the ovarian reserve in women. Furthermore, obtaining ovarian tissue from large animals or endangered species for experimentation is often not feasible. Thus, mice have become an essential model for such studies, and the ability to evaluate primordial follicle numbers in whole mouse ovaries is a critical tool. However, reports of absolute follicle numbers in mouse ovaries in the literature are highly variable, making it difficult to compare and/or replicate data. This is due to a number of factors including strain, age, treatment groups, as well as technical differences in the methods of counting employed. In this article, we provide a step-by-step instructional guide for preparing histological sections and counting primordial follicles in mouse ovaries using two different methods: [1] stereology, which relies on the fractionator/optical dissector technique; and [2] the direct count technique. Some of the key advantages and drawbacks of each method will be highlighted so that reproducibility can be improved in the field and to enable researchers to select the most appropriate method for their studies.

Here, we describe, compare, and contrast two different techniques for accurate follicle counting of fixed mouse ovarian tissues.

Sexually reproducing female mammals are born with their entire lifetime supply of oocytes. Immature, quiescent oocytes are found within primordial ...

Whole Ovary Immunofluorescence, Clearing, and Multiphoton Microscopy for Quantitative 3D Analysis of the Developing Ovarian Reserve in Mouse

Female fertility and reproductive lifespan depend on the quality and quantity of the ovarian oocyte reserve. An estimated 80% of female germ cells entering meiotic prophase I are eliminated during Fetal Oocyte Attrition (FOA) and the first week of postnatal life. Three major mechanisms regulate the number of oocytes that survive during development and establish the ovarian reserve in females entering puberty. In the first wave of oocyte loss, 30-50% of the oocytes are eliminated during early FOA, a phenomenon that is attributed to high Long interspersed nuclear element-1 (LINE-1) expression. The second wave of oocyte loss is the elimination of oocytes with meiotic defects by a meiotic quality checkpoint. The third wave of oocyte loss occurs perinatally during primordial follicle formation when some oocytes fail to form follicles. It remains unclear what regulates each of these three waves of oocyte loss and how they shape the ovarian reserve in either mice or humans.
Immunofluorescence and 3D visualization have opened a new avenue to image and analyze oocyte development in the context of the whole ovary rather than in less informative 2D sections. This article provides a comprehensive protocol for whole ovary immunostaining and optical clearing, yielding preparations for imaging using multiphoton microscopy and 3D modeling using commercially available software. It shows how this method can be used to show the dynamics of oocyte attrition during ovarian development in C57BL/6J mice and quantify oocyte loss during the three waves of oocyte elimination. This protocol can be applied to prenatal and early postnatal ovaries for oocyte visualization and quantification, as well as other quantitative approaches. Importantly, the protocol was strategically developed to accommodate high-throughput, reliable, and repeatable processing that can meet the needs in toxicology, clinical diagnostics, and genomic assays of ovarian function.

Here, we present an optimized protocol for imaging entire ovaries for quantitative and qualitative analyses using whole-mount immunostaining, multiphoton microscopy, and 3D visualization and analysis. This protocol accommodates high-throughput, reliable, and repeatable processing that is applicable for toxicology, clinical diagnostics, and genomic assays of ovarian function.

Female fertility and reproductive lifespan depend on the quality and quantity of the ovarian oocyte reserve. An estimated 80% of female germ cells ...

Retinal Pericytes Visualization Using Tissue-Clearing and Fluorescent Labeling

3D Visualization of Retinal Vascular Pericytes in Mice by Immunostaining

Retinal pericytes are essential for vascular development and stability of the retina, playing a key role in maintaining the integrity of the retinal vasculature. To provide a detailed view of the morphological characteristics of pericytes, this study described a new approach combining the retro-orbital injection of a fluorescent agent, immunofluorescent-staining, and tissue-clearing treatment. Firstly, the fluorescent tomato lectin was injected into the retro-orbital sinus of the live mouse to label the retinal vasculature. After 5 min, the mouse was sacrificed, and its intact retina was carefully removed from the retinal cup and immunofluorescently stained with platelet-derived growth factor receptor &#946; to reveal the pericytes. Additionally, the stained retina was treated with tissue-clearing reagent and whole mounted on the microscope slide. Through these approaches, the retinal vasculature and pericytes were clearly observed in the transparent retina. Under a confocal microscope, we obtained more opportunities to take high-resolution images for further reconstructing and analyzing the morphological characteristics of pericytes along the retinal vascular tree in a three-dimensional view. Methodologically, this protocol offers an effective approach for visualizing pericytes within the retinal vasculature, providing valuable insights into their role under both physiological and pathological conditions.

The pericytes in retinal vasculature were examined by immunofluorescent staining with platelet-derived growth factor receptor &#946; after retro-orbital injection of fluorescent tomato lectin. The labeled retina was further treated with the tissue-clearing method and whole mounted for visualizing the three-dimensional views of pericytes surrounding retinal vasculature under a confocal microscope.

Retinal pericytes are essential for vascular development and stability of the retina, playing a key role in maintaining the integrity of the retinal ...

Biochemistry

Generation of Mice Derived from Induced Pluripotent Stem Cells

The production of induced pluripotent stem cells (iPSCs) from somatic cells provides a means to create valuable tools for basic research and may also produce a source of patient-matched cells for regenerative therapies. iPSCs may be generated using multiple protocols and derived from multiple cell sources. Once generated, iPSCs are tested using a variety of assays including immunostaining for pluripotency markers, generation of three germ layers in embryoid bodies and teratomas, comparisons of gene expression with embryonic stem cells (ESCs) and production of chimeric mice with or without germline contribution2. Importantly, iPSC lines that pass these tests still vary in their capacity to produce different differentiated cell types2. This has made it difficult to establish which iPSC derivation protocols, donor cell sources or selection methods are most useful for different applications.
The most stringent test of whether a stem cell line has sufficient developmental potential to generate all tissues required for survival of an organism (termed full pluripotency) is tetraploid embryo complementation (TEC)3-5. Technically, TEC involves electrofusion of two-cell embryos to generate tetraploid (4n) one-cell embryos that can be cultured in vitro to the blastocyst stage6. Diploid (2n) pluripotent stem cells (e.g. ESCs or iPSCs) are then injected into the blastocoel cavity of the tetraploid blastocyst and transferred to a recipient female for gestation (see Figure 1). The tetraploid component of the complemented embryo contributes almost exclusively to the extraembryonic tissues (placenta, yolk sac), whereas the diploid cells constitute the embryo proper, resulting in a fetus derived entirely from the injected stem cell line.
Recently, we reported the derivation of iPSC lines that reproducibly generate adult mice via TEC1. These iPSC lines give rise to viable pups with efficiencies of 5-13%, which is comparable to ESCs3,4,7 and higher than that reported for most other iPSC lines8-12. These reports show that direct reprogramming can produce fully pluripotent iPSCs that match ESCs in their developmental potential and efficiency of generating pups in TEC tests. At present, it is not clear what distinguishes between fully pluripotent iPSCs and less potent lines13-15. Nor is it clear which reprogramming methods will produce these lines with the highest efficiency. Here we describe one method that produces fully pluripotent iPSCs and "all- iPSC" mice, which may be helpful for investigators wishing to compare the pluripotency of iPSC lines or establish the equivalence of different reprogramming methods.

Generating induced pluripotent stem cell (iPSC) lines produces lines of differing developmental potential even when they pass standard tests for pluripotency. Here we describe a protocol to produce mice derived entirely from iPSCs, which defines the iPSC lines as possessing full pluripotency1.

The production of induced pluripotent stem cells (iPSCs) from somatic cells provides a means to create valuable tools for basic research and may also ...

Three-dimensional Reconstruction of the Vascular Architecture of the Passive CLARITY-cleared Mouse Ovary

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Chapters in this video

An Orthotopic Model of Serous Ovarian Cancer in Immunocompetent Mice for in vivo Tumor Imaging and Monitoring of Tumor Immune Responses

Three-dimensional Rendering and Analysis of Immunolabeled, Clarified Human Placental Villous Vascular Networks

Whole Mount Immunofluorescence and Follicle Quantification of Cultured Mouse Ovaries

Ovarian Tissue Culture to Visualize Phenomena in Mouse Ovary

Imaging Cleared Intact Biological Systems at a Cellular Level by 3DISCO

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

Accurate Follicle Enumeration in Adult Mouse Ovaries

Whole Ovary Immunofluorescence, Clearing, and Multiphoton Microscopy for Quantitative 3D Analysis of the Developing Ovarian Reserve in Mouse

3D Visualization of Retinal Vascular Pericytes in Mice by Immunostaining

Generation of Mice Derived from Induced Pluripotent Stem Cells