The authors acknowledge support from the National Institutes of Health (NIH) (R01 GM084135 and R01 DK109982), a Pilot/Feasibility Award from the Texas Medical Center Digestive Disease Center under NIH P30 DK56338, and an Alagille Syndrome Accelerator Award from The Medical Foundation.

All animals were housed in a barrier animal facility at Baylor College of Medicine per Institutional Animal Care and Use Committee guidelines and under approved animal protocols.
1. Collection of Mouse Liver Tissue
<ol>
	<li>Preparation of mouse for liver harvest
	<ol>
		<li>Euthanize the mouse using isoflurane.</li>
		<li>Perform cervical dislocation of the mouse to ensure death.</li>
		<li>Make a transverse incision approximately one inch below the rib cage.</li>
		<li>Expose the entire ventral surface of the liver.</li>
	</ol>
	</li>
	<li>Collection of the mouse liver
	<ol>
		<li>Carefully, with small scissors, cut through the ligaments connecting the liver to other organs in the abdomen.</li>
		<li>Cut through the common BD to detach the liver from the intestine.</li>
		<li>Carefully remove the liver by holding onto the gallbladder and immediately place in a 50 mL tube filled to three-quarters by 4% paraformaldehyde (PFA).</li>
	</ol>
	</li>
</ol>
2. Fixation and Embedding the Liver in Paraffin
<ol>
	<li>Fixation
	<ol>
		<li>Fix the liver tissue for 48 h in 4% PFA at 4 &#176;C.</li>
		<li>Wash the tissue with 70% EtOH for 1 h at 4 &#176;C.</li>
		<li>Wash the tissue twice with 95% EtOH for 1 h each at 4 &#176;C.</li>
		<li>Wash the tissue twice with 100% EtOH for 1 h each at 4 &#176;C.</li>
	</ol>
	</li>
	<li>Clearing
	<ol>
		<li>Wash the liver tissue with clearing agent (Table of Materials) three times for 30 min each at room temperature. 
		NOTE: The liver should feel rigid following the third wash.</li>
	</ol>
	</li>
	<li>Embedding in paraffin
	<ol>
		<li>Place the tissue cassette in a tissue mold in paraffin wax for 3 washes, 30 min each. Wax should be preheated to 60 &#176;C.</li>
		<li>Fill the tissue mold with paraffin wax to three-quarters height and keep on a heating block at 60 &#176;C.</li>
		<li>Place the liver in the mold with the ventral side facing up.</li>
		<li>Carefully remove the mold from the heating block.</li>
		<li>Place the top of the cassette on the mold and top off with hot liquid paraffin.</li>
		<li>Allow the mold and block to cool to room temperature overnight. 
		NOTE: Tissue blocks can now be stored at room temperature.</li>
	</ol>
	</li>
</ol>
3. Sectioning liver tissue
<ol>
	<li>Preparation of the block for sectioning
	<ol>
		<li>Place the mold on ice for 5 min before removing the block from the mold.</li>
		<li>Place the block on ice with a lab tissue paper present between block and ice.</li>
		<li>Keep the block on ice when not sectioning for best tissue slicing results.</li>
	</ol>
	</li>
	<li>Sectioning the liver blocks
	<ol>
		<li>Using a microtome, begin by sectioning through the superficial, dorsal side of the liver. Sections should be 5 &#181;m.</li>
		<li>Check the superficial sections under a dissection microscope to ensure sections are not sheared or folded.</li>
		<li>Take a section of the liver that includes the caudate lobe. 
		NOTE: For some blocks, you will have the left, medial, right and caudate lobes on the same tissue slice.</li>
		<li>For those blocks where all four lobes are not present on the same slide, continue to slice until the left, medial and right lobes are present on the same slide.</li>
	</ol>
	</li>
</ol>
4. Immunohistochemistry for wsCK and &#945;SMA
<ol>
	<li>Processing of slides for immunohistochemistry
	<ol>
		<li>Select one slide per genotype to be analyzed.</li>
		<li>Wash the slide for 15 min in Xylene, 100% EtOH, 95% EtOH and finally 70% EtOH (3 x 5 min in each solution).</li>
		<li>Wash the slide for 5 min in deionized H2O.</li>
		<li>Immerse the slide in the antigen retrieval solution (Tris-based, high pH).</li>
		<li>Heat under pressure in a pressure cooker for 3 min at 10 psi.</li>
		<li>Allow the slide to cool to room temperature (approximately 35 min).</li>
	</ol>
	</li>
	<li>Blocking the tissue sections
	<ol>
		<li>Using a Pap Pen, outline the sections on the slide.</li>
		<li>Apply phosphate-buffered saline (PBS) + 0.1% Tween to cover the section twice, 5 min each.</li>
		<li>Make blocking buffer by mixing Normal Goat Serum (NGS) at 1:50 in PBS + 0.3% Triton. To have enough buffer for both blocking and primary antibody application, 100 &#181;L per section is sufficient.</li>
		<li>Apply 100 &#181;L of blocking solution per section.</li>
		<li>Incubate the slides covered with the blocking solution at 4 &#176;C for 1 h.</li>
	</ol>
	</li>
	<li>Staining for wsCK and &#945;SMA 
	<ol>
		<li>Dilute anti-CK8 and anti-CK19 antibodies16 (Developmental Studies Hybridoma Bank, TROMA-I and TROMA-III, respectively) 1:20 in blocking buffer to stain for wsCK. Dilute the anti-&#945;SMA antibody17 (Table of Materials) to 1:200 in the same buffer.</li>
		<li>Apply 100 &#181;L of the diluted antibody solution containing all three antibodies to each section.</li>
		<li>Incubate the slides covered with the antibody solution at 4 &#176;C overnight.</li>
		<li>Wash the slides with PBS + 0.1% Triton three times, 5 min each.</li>
		<li>Dilute secondary antibodies (anti-rat-Alexa488 and anti-mouse-Cy5) 1:200 in PBS + 0.3% Triton.</li>
		<li>Apply 100 &#181;L of the secondary antibody solution containing both secondary antibodies to the slides.</li>
		<li>Incubate at room temperature for 1 h.</li>
	</ol>
	</li>
	<li>DAPI nuclear staining and mounting
	<ol>
		<li>Wash the slides three times, 5 min each.</li>
		<li>Apply 100 &#181;L of DAPI (1:3000) to each section for 10 min.</li>
		<li>Apply Antifade Mounting Medium (Table of Materials) to the slides and place a glass coverslip on top of the tissue sections. Leave the slides at 4 &#176;C overnight. Seal the slides the next day.</li>
		<li>Store the slides at 4 &#176;C and image within 1 week of mounting.</li>
	</ol>
	</li>
</ol>
5. Imaging and Quantification of BDs
<ol>
	<li>Imaging liver sections
	<ol>
		<li>Prior to imaging, blind yourself to the genotype of the sample with help from a lab member. Ensure all imaging files are devoid of genotype or other specific identifying information besides an animal/sample number.</li>
		<li>Using a fluorescent microscope, take 20x images at 1x zoom of each section and ensure that every PV&#160;across the liver is imaged. Include the left, medial, right and caudate lobes. 
		NOTE: We usually find 60-90 portal tracts per animal depending on the size of the liver.</li>
		<li>To identity the PVs, look for &#945;SMA plus wsCK staining. Structures that are &#945;SMA positive but lack wsCK staining are not portal structures.</li>
	</ol>
	</li>
	<li>Identification and counting of BDs
	<ol>
		<li>Create a spreadsheet with the following columns: Animal/Sample Number, Image Number, Number of PVs, and Number of BDs.</li>
		<li>Going through each image, identify and record the number of PVs per image.</li>
		<li>Identify patent BDs in each image by the presence of cholangiocytes (wsCK+) surrounding a definable lumen. Structures should be distinct and separated by mesenchyme from other wsCK+ cells.</li>
		<li>Count each patent BD and place in the same column as the image number.</li>
		<li>Do this for each image taken of a PV.</li>
		<li>Calculate the sum of all PVs and all BDs in the liver sample.</li>
		<li>Calculate the BD to PV ratio for the liver sample.</li>
	</ol>
	</li>
</ol>

<ol>
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J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Update+on+the+etiologies+and+management+of+neonatal+cholestasis.">Update on the etiologies and management of neonatal cholestasis.</a> Clin Perinatol. 29 (1), 159-180 (2002).</li><li>Roskams, T. 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=Nomenclature+of+the+finer+branches+of+the+biliary+tree:+canals,+ductules,+and+ductular+reactions+in+human+livers.">Nomenclature of the finer branches of the biliary tree: canals, ductules, and ductular reactions in human livers.</a> Hepatology. 39 (6), 1739-1745 (2004).</li><li>Oda, T., 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=Mutations+in+the+human+Jagged1+gene+are+responsible+for+Alagille+syndrome.">Mutations in the human Jagged1 gene are responsible for Alagille syndrome.</a> Nature Genetics. 16 (3), 235 (1997).</li><li>Li, L., 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=Alagille+syndrome+is+caused+by+mutations+in+human+Jagged1,+which+encodes+a+ligand+for+Notch1.">Alagille syndrome is caused by mutations in human Jagged1, which encodes a ligand for Notch1.</a> Nature Genetics. 16 (3), 243 (1997).</li><li>Xue, Y., 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=Embryonic+lethality+and+vascular+defects+in+mice+lacking+the+Notch+ligand+Jagged1.">Embryonic lethality and vascular defects in mice lacking the Notch ligand Jagged1.</a> Human Molecular Genetics. 8 (5), 723-730 (1999).</li><li>Thakurdas, S. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Jagged1+heterozygosity+in+mice+results+in+a+congenital+cholangiopathy+which+is+reversed+by+concomitant+deletion+of+one+copy+of+Poglut1+(Rumi).">Jagged1 heterozygosity in mice results in a congenital cholangiopathy which is reversed by concomitant deletion of one copy of Poglut1 (Rumi).</a> Hepatology. 63 (2), 550-565 (2016).</li><li>Hadchouel, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Paucity+of+interlobular+bile+ducts.">Paucity of interlobular bile ducts.</a> Seminars in Diagnostic Pathology. 9 (1), 24-30 (1992).</li><li>Emerick, K. M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Features+of+Alagille+syndrome+in+92+patients:+frequency+and+relation+to+prognosis.">Features of Alagille syndrome in 92 patients: frequency and relation to prognosis.</a> Hepatology. 29 (3), 822-829 (1999).</li><li>Poncy, 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=Transcription+factors+SOX4+and+SOX9+cooperatively+control+development+of+bile+ducts.">Transcription factors SOX4 and SOX9 cooperatively control development of bile ducts.</a> Dev Biol. 404 (2), 136-148 (2015).</li><li>Hofmann, J. J., 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=Jagged1+in+the+portal+vein+mesenchyme+regulates+intrahepatic+bile+duct+development:+insights+into+Alagille+syndrome.">Jagged1 in the portal vein mesenchyme regulates intrahepatic bile duct development: insights into Alagille syndrome.</a> Development. 137 (23), 4061-4072 (2010).</li><li>McCright, B., Lozier, J., Gridley, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+mouse+model+of+Alagille+syndrome:+Notch2+as+a+genetic+modifier+of+Jag1+haploinsufficiency.">A mouse model of Alagille syndrome: Notch2 as a genetic modifier of Jag1 haploinsufficiency.</a> Development. 129 (4), 1075-1082 (2002).</li><li>Andersson, E. R., 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=Mouse+Model+of+Alagille+Syndrome+and+Mechanisms+of+Jagged1+Missense+Mutations.">Mouse Model of Alagille Syndrome and Mechanisms of Jagged1 Missense Mutations.</a> Gastroenterology. 154 (4), 1080-1095 (2018).</li><li>Loomes, K. 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The authors have no conflict of interest.

Analysis of BD development and repair in mice is an important tool in studying the pathogenesis and mechanism of cholestatic disorders. In addition, development of new therapies is in part dependent upon establishing a reproducible and preferably quantifiable phenotype. Current phenotyping in mouse models usually involves serum chemistry, liver histology and immunostaining for cell-type specific markers. Although these techniques generate valuable information about the structure and function of the biliary system, they d...

The biliary tree is a critical part of the mammalian liver, allowing the passage of bile from hepatocytes into the gut. Intrahepatic bile ducts (BDs) are formed by cholangiocytes, which differentiate from bipotential hepatoblasts through Notch and TGF&#946; signaling1,2. Proper specification and commitment of cholangiocytes and their assembly into mature BDs are critical for the development of the intrahepatic biliary tree. As the liver grows during development or upon organ regeneration, the biliary system needs to develop along the liver to ensure proper bile drainage. Moreover, a number of syndromic and non-syndromic diseases result in the paucity of intrahepatic BDs3. In addition, a number of acute and chronic liver diseases give rise to so-called ductular reactions in the liver, which are defined as the presence of a significant number of cells that express biliary markers but do not necessarily arise from biliary cells or form patent BDs4. In the multisystem disorder Alagille syndrome (ALGS), haploinsufficiency of the Notch ligand jagged1 (JAG1) results in poor BD formation and cholestasis5,6. Our lab recently demonstrated that a previously generated Jag1 heterozygous mouse line7 is an animal model of BD paucity in ALGS8. In this mouse model of ALGS, cholangiocytes are still present. However, they fail to commit to incorporation into mature, patent BDs8. Therefore, analysis of the liver in a model of BD paucity requires more than the apparent presence or absence of cholangiocytes. It is important to accurately assess the degree to which mature BDs are present in the liver.
In anatomic pathology, there are accepted quantitative methods for assessing whether BD paucity exists9. For example, studies on ALGS in human patients often quantify the BD to portal vein (PV) ratio by analyzing at least 10 portal vessels per liver biopsy9,10. Analysis of the shape and overall presence or absence of patent BDs, combined with serum chemistry, can provide valuable information about BD development in mice11,12,13. However, mice can lose a significant number of BDs with only a modest increase in serum bilirubin level8. Accordingly, a quantitative method that evaluates the number of BDs present per PV can provide a more direct measure of the degree of BD paucity in mice. In a recent report, we quantified the number of BDs per PV across all liver lobes and reported a significant decrease in the BD to PV ratio in Jag1+/&#8211; animals8. During the course of our analysis, we noticed that despite the significant variation in the degree of inflammatory response and ductular reactions, the BD to PV ratio does not show much variability8. Moreover, quantification of the BD to PV ratio allowed us to demonstrate that removing one copy of the glycosyltransferase gene Poglut1 in Jag1+/&#8211; animals can significantly improve their BD paucity8. In a Jag1+/+ background, conditional loss of Poglut1 in vascular smooth muscle cells results in a progressive increase in BD numbers, which is modest (20-30%) at P7 but becomes prominent in adults8. Again, this technique allowed us to show that even at P7, the increase in BD density in these animals is statistically significant. Of note, the increased BD density in this genotype at four months of age was validated through resin cast analysis as well.8 These observations and other reports which measured BD density in different ALGS mouse models14,15 prompted us to incorporate this method into our overall strategy to analyze biliary defects in various mutant and transgenic mice.
Here, we detail a straightforward technique which can be used to examine the degree of BD paucity in mouse models of liver disease (Figure 1). In this method, co-staining with cholangiocyte markers cytokeratin (CK) 8 and CK19 (hereafter wide-spectrum CK, wsCK) is used to visualize BDs and unincorporated cholangiocytes in the mouse liver. An antibody against alpha-smooth muscle actin (&#945;SMA) is added to the staining to label vessels. Systematic analysis of the BD to PV ratio in a section covering all liver lobes ensures that a large number of PVs are analyzed for each genotype. Since our method relies on quantifying BDs and PVs in 2D images, it is not suitable for studying the effects of a given mutation on the 3D structure of the biliary tree or the integrity of the small biliary conduits. Nevertheless, it provides a simple and objective strategy for investigators to assess biliary development in the mouse.

<table>
	<tbody>
		<tr>
			<td>Isothesia (Isoflurane)</td>
			<td>Henry Schein</td>
			<td>11695-6776-2</td>
			<td></td>
		</tr>
		<tr>
			<td>Desiccator</td>
			<td>Bel-Art</td>
			<td>16-800-552</td>
			<td></td>
		</tr>
		<tr>
			<td>10% PFA</td>
			<td>Electron Microscopy Sciences</td>
			<td>15712</td>
			<td></td>
		</tr>
		<tr>
			<td>50mL tube</td>
			<td>ThermoScientific</td>
			<td>339653</td>
			<td></td>
		</tr>
		<tr>
			<td>70% Ethanol</td>
			<td>Decon Laboratories</td>
			<td>2401</td>
			<td></td>
		</tr>
		<tr>
			<td>95% Ethanol</td>
			<td>Decon Laboratories</td>
			<td>2801</td>
			<td></td>
		</tr>
		<tr>
			<td>100% Ethanol</td>
			<td>Decon Laboratories</td>
			<td>2701</td>
			<td></td>
		</tr>
		<tr>
			<td>HistoChoice</td>
			<td>VWR Life Sciences</td>
			<td>H103-4L</td>
			<td>clearing agent</td>
		</tr>
		<tr>
			<td>Omnisette Tissue Cassette</td>
			<td>Fisher HealthCare</td>
			<td>15-197-710E</td>
			<td></td>
		</tr>
		<tr>
			<td>Macrosette</td>
			<td>Simport</td>
			<td>M512</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraplast X-TRA</td>
			<td>McCormick Scientific</td>
			<td>39503002</td>
			<td>Parrafin</td>
		</tr>
		<tr>
			<td>Tissue Mold</td>
			<td>Fisher Scientific</td>
			<td>62528-32</td>
			<td></td>
		</tr>
		<tr>
			<td>Microtome</td>
			<td>Microm</td>
			<td>HM 325</td>
			<td></td>
		</tr>
		<tr>
			<td>Superfrost Plus Microscope Slides</td>
			<td>Fisher Scientific</td>
			<td>12-550-15</td>
			<td></td>
		</tr>
		<tr>
			<td>Xylene</td>
			<td>Fisher Scientific</td>
			<td>C8H10</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris-Based Antigen Retrieval</td>
			<td>Vector Laboratories</td>
			<td>H-3301</td>
			<td></td>
		</tr>
		<tr>
			<td>Pressure Cooker</td>
			<td>Instant Pot</td>
			<td>Lux Mini</td>
			<td></td>
		</tr>
		<tr>
			<td>Mini Pap Pen</td>
			<td>Life Technologies</td>
			<td>8877</td>
			<td></td>
		</tr>
		<tr>
			<td>Polyoxyethylene 20 Sorbitan Monolaurate (Tween-20)</td>
			<td>J.T. Baker</td>
			<td>X251-07</td>
			<td></td>
		</tr>
		<tr>
			<td>Octyl Phenol Ethoxylate (Triton-X-100)</td>
			<td>J.T. Baker</td>
			<td>X198-07</td>
			<td></td>
		</tr>
		<tr>
			<td>Normal Goat Serum</td>
			<td>Jackson Immunoresearch</td>
			<td>005-000-121</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-CK8</td>
			<td>Developmental Studies Hybridoma Bank</td>
			<td>TROMA-I</td>
			<td>Antibody Registry ID AB531826</td>
		</tr>
		<tr>
			<td>anti-CK19</td>
			<td>Developmental Studies Hybridoma Bank</td>
			<td>TROMA-III</td>
			<td>Antibody Registry ID AB2133570</td>
		</tr>
		<tr>
			<td>anti-&#945;SMA</td>
			<td>Sigma Aldrich</td>
			<td>A2547, Clone 1A4</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-rat-Alexa488</td>
			<td>ThermoFisher</td>
			<td>A21208</td>
			<td></td>
		</tr>
		<tr>
			<td>anti-mouse-Cy5</td>
			<td>Jackson Immunoresearch</td>
			<td>715-175-151</td>
			<td></td>
		</tr>
		<tr>
			<td>DAPI</td>
			<td>Vector Laboratories</td>
			<td>H-1000</td>
			<td></td>
		</tr>
		<tr>
			<td>22x50 micro cover glass</td>
			<td>VWR Life Sciences</td>
			<td>48393 059</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorescence Microscope</td>
			<td>Leica</td>
			<td>DMI6000 B</td>
			<td></td>
		</tr>
		<tr>
			<td>Kimwipes</td>
			<td>Kimtech Science</td>
			<td>05511</td>
			<td></td>
		</tr>
		<tr>
			<td>VECTASHIELD</td>
			<td>Vector Laboratories</td>
			<td>H-1000</td>
			<td>Antifade Mounting Medium</td>
		</tr>
	</tbody>
</table>

determining bile duct density in the mouse liver

Mouse is broadly used as a model organism to study biliary diseases. To evaluate the development and function of the biliary system, various techniques are used, including serum chemistry, histological analysis, and immunostaining for specific markers. Although these techniques can provide important information about the biliary system, they often do not present a full picture of bile duct (BD) developmental defects across the whole liver. This is in part due to the robust ability of the mouse liver to drain the bile even in animals with significant impairment in biliary development. Here we present a simple method to calculate the average number of BDs associated with each portal vein (PV) in sections covering all lobes of mutant/transgenic mice. In this method, livers are mounted and sectioned in a stereotypic manner to facilitate comparison among various genotypes and experimental conditions. BDs are identified via light microscopy of cytokeratin-stained cholangiocytes, and then counted and divided by the total number of PVs present in liver section. As an example, we show how this method can clearly distinguish between wild-type mice and a mouse model of Alagille syndrome. The method presented here cannot substitute for techniques that visualize the three-dimensional structure of the biliary tree. However, it offers an easy and direct way to quantitatively assess BD development and the degree of ductular reaction formation in mice.

We previously documented biliary defects in Jag1+/&#8211; animals, a mouse model of ALGS8. To determine the BD to PV ratio, we sectioned P30 mouse livers and co-stained them for CK8 and CK19 (wsCK) along with the vascular marker &#945;SMA. We then imaged all the PVs in each of the liver lobes. As shown in Figure 2A, we defined PVs as &#945;SMA-stained vessels that have adjacent wsCK staining (arrowheads). The &#945;SMA-stained...

Watch this Scientific Journal Video about Determining Bile Duct Density in the Mouse Liver at JoVE.com

Determining Bile Duct Density in the Mouse Liver

We present a rather simple and sensitive method for accurate quantification of bile duct density in the mouse liver. This method can aid in determining the effects of genetic and environmental modifiers and the effectiveness of potential therapies in mouse models of biliary diseases.

Mouse is broadly used as a model organism to study biliary diseases. To evaluate the development and function of the biliary system, various techniques ...

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Research

JoVE Journal

Developmental Biology

6.8K Views.  Baylor College of Medicine. We present a rather simple and sensitive method for accurate quantification of bile duct density in the mouse liver. This method can aid in determining the effects of genetic and environmental modifiers and the effectiveness of potential therapies in mouse models of biliary diseases.

Video: Determining Bile Duct Density in the Mouse Liver

Stimulation of Notch Signaling in Mouse Osteoclast Precursors

Notch signaling is a key component of multiple physiological and pathological processes. The nature of Notch signaling, however, makes in vitro investigation of its varying and sometimes contradictory roles a challenge. As a component of direct cell-cell communication with both receptors and ligands bound to the plasma membrane, Notch signaling cannot be activated in vitro by simple addition of ligands to culture media, as is possible with many other signaling pathways. Instead, Notch ligands must be presented to cells in an immobilized state. 
Variations in methods of Notch signaling activation can lead to different outcomes in cultured cells. In osteoclast precursors, in particular, differences in methods of Notch stimulation and osteoclast precursor culture and differentiation have led to disagreement over whether Notch signaling is a positive or negative regulator of osteoclast differentiation. While closer comparisons of osteoclast differentiation under different Notch stimulation conditions in vitro and genetic models have largely resolved the controversy regarding Notch signaling and osteoclasts, standardized methods of continuous and temporary stimulation of Notch signaling in cultured cells could prevent such discrepancies in the future.
This protocol describes two methods for stimulating Notch signaling specifically in cultured mouse osteoclast precursors, though these methods should be applicable to any adherent cell type with minor adjustments. The first method produces continuous stimulation of Notch signaling and involves immobilizing Notch ligand to a tissue culture surface prior to the seeding of cells. The second, which uses Notch ligand bound to agarose beads allows for temporary stimulation of Notch signaling in cells that are already adhered to a culture surface. This protocol also includes methods for detecting Notch activation in osteoclast precursors as well as representative transcriptional markers of Notch signaling activation.

Notch signaling is a form of cellular communication that relies upon direct contact between cells. To properly induce Notch signaling in vitro, Notch ligands must be presented to cells in an immobilized state. This protocol describes methods for in vitro stimulation of Notch signaling in mouse osteoclast precursors.

Notch signaling is a key component of multiple physiological and pathological processes. The nature of Notch signaling, however, makes in vitro ...

Histological Analyses of Acute Alcoholic Liver Injury in Zebrafish

Alcoholic Liver Disease (ALD) refers to damage to the liver due to acute or chronic alcohol abuse. It is among the leading causes of alcohol-related morbidity and mortality and affects more than 2 million people in the United States. A better understanding of the cellular and molecular mechanisms underlying alcohol-induced liver injury is crucial for developing effective treatment for ALD. Zebrafish larvae exhibit hepatic steatosis and fibrogenesis after just 24 h of exposure to 2% ethanol, making them useful for the study of acute alcoholic liver injury. This work describes the procedure for acute ethanol treatment in zebrafish larvae and shows that it causes steatosis and swelling of the hepatic blood vessels. A detailed protocol for Hematoxylin and Eosin (H&#38;E) staining that is optimized for the histological analysis of the zebrafish larval liver, is also described. H&#38;E staining has several unique advantages over immunofluorescence, as it marks all liver cells and extracellular components simultaneously and can readily detect hepatic injury, such as steatosis and fibrosis. Given the increasing usage of zebrafish in modeling toxin and virus-induced liver injury, as well as inherited liver diseases, this protocol serves as a reference for the histological analyses performed in all these studies.

This protocol describes histological analyses of the livers from zebrafish larvae that have been treated with 2% ethanol for 24 h. Such acute ethanol treatment results in hepatic steatosis and swelling of the hepatic vasculature.

Alcoholic Liver Disease (ALD) refers to damage to the liver due to acute or chronic alcohol abuse. It is among the leading causes of alcohol-related ...

Quantifying Branching Density in Rat Mammary Gland Whole-mounts Using the Sholl Analysis Method

An increasing number of studies are utilizing the rodent mammary gland as an endpoint for assessing the developmental toxicity of a chemical exposure. The effects these exposures have on mammary gland development are typically evaluated using either basic dimensional measurements or by scoring morphological characteristics. However, the broad range of methods for interpreting developmental changes could lead to inconsistent translations across laboratories. A common method of assessment is needed so that proper interpretations can be formed from data being compared across studies. The present study describes the application of the Sholl analysis method to quantify mammary gland branching characteristics. The Sholl method was originally developed for use in quantifying neuronal dendritic patterns. By using ImageJ, an open-source image analysis software package, and a plugin developed for this analysis, the mammary gland branching density and the complexity of a mammary gland from a peripubertal female rat were determined. The methods described here will enable the use of the Sholl analysis as an effective tool for quantifying an important characteristic of mammary gland development.

Mammary gland development in the rodent has typically been evaluated using descriptive assessments or by measuring basic physical attributes. Branching density is an indicator of mammary development that is difficult to quantify objectively. This protocol describes a reliable method for the quantitative assessment of mammary gland branching characteristics.

An increasing number of studies are utilizing the rodent mammary gland as an endpoint for assessing the developmental toxicity of a chemical exposure. The ...

Live Imaging of Mouse Secondary Palate Fusion

The fusion of the secondary palatal shelves to form the intact secondary palate is a key process in mammalian development and its disruption can lead to cleft secondary palate, a common congenital anomaly in humans. Secondary palate fusion has been extensively studied leading to several proposed cellular mechanisms that may mediate this process. However, these studies have been mostly performed on fixed embryonic tissues at progressive timepoints during development or in fixed explant cultures analyzed at static timepoints. Static analysis is limited for the analysis of dynamic morphogenetic processes such a palate fusion and what types of dynamic cellular behaviors mediate palatal fusion is incompletely understood. Here we describe a protocol for live imaging of ex vivo secondary palate fusion in mouse embryos. To examine cellular behaviors of palate fusion, epithelial-specific Keratin14-cre was used to label palate epithelial cells in ROSA26-mTmGflox reporter embryos. To visualize filamentous actin, Lifeact-mRFPruby reporter mice were used. Live imaging of secondary palate fusion was performed by dissecting recently-adhered secondary palatal shelves of embryonic day (E) 14.5 stage embryos and culturing in agarose-containing media on a glass bottom dish to enable imaging with an inverted confocal microscope. Using this method, we have detected a variety of novel cellular behaviors during secondary palate fusion. An appreciation of how distinct cell behaviors are coordinated in space and time greatly contributes to our understanding of this dynamic morphogenetic process. This protocol can be applied to mutant mouse lines, or cultures treated with pharmacological inhibitors to further advance understanding of how secondary palate fusion is controlled.

Here, we present a protocol for live imaging of mouse secondary palate fusion using confocal microscopy. This protocol can be used in combination with a variety of fluorescent reporter mouse lines, and with pathway inhibitors for mechanistic insight. This protocol can be adapted for live imaging in other developmental systems.

The fusion of the secondary palatal shelves to form the intact secondary palate is a key process in mammalian development and its disruption can lead to ...

Dissection and Immunofluorescent Staining of Mushroom Body and Photoreceptor Neurons in Adult Drosophila melanogaster Brains

Nervous system development involves a sequential series of events that are coordinated by several signaling pathways and regulatory networks. Many of the proteins involved in these pathways are evolutionarily conserved between mammals and other eukaryotes, such as the fruit fly Drosophila melanogaster, suggesting that similar organizing principles exist during the development of these organisms. Importantly, Drosophila has been used extensively to identify cellular and molecular mechanisms regulating processes that are required in mammals including neurogenesis, differentiation, axonal guidance, and synaptogenesis. Flies have also been used successfully to model a variety of human neurodevelopmental diseases. Here we describe a protocol for the step-by-step microdissection, fixation, and immunofluorescent localization of proteins within the adult Drosophila brain. This protocol focuses on two example neuronal populations, mushroom body neurons and retinal photoreceptors, and includes optional steps to trace individual mushroom body neurons using Mosaic Analysis with a Repressible Cell Marker (MARCM) technique. Example data from both wild-type and mutant brains are shown along with a brief description of a scoring criteria for axonal guidance defects. While this protocol highlights two well-established antibodies for investigating the morphology of mushroom body and photoreceptor neurons, other Drosophila brain regions and the localization of proteins within other brain regions can also be investigated using this protocol.

Dissection and Immunofluorescent Staining of Mushroom Body and Photoreceptor Neurons in Adult Drosophila melanogaster Brains

This protocol describes the dissection and immunostaining of adult Drosophila melanogaster brain tissues. Specifically, this protocol highlights the use of Drosophila mushroom body and photoreceptor neurons as example neuronal subsets that can be accurately used to uncover general principles underlying many aspects of neuronal development.

Nervous system development involves a sequential series of events that are coordinated by several signaling pathways and regulatory networks. Many of the ...

A Novel Use of Three-dimensional High-frequency Ultrasonography for Early Pregnancy Characterization in the Mouse

High-frequency ultrasonography (HFUS) is a common method to non-invasively monitor the real-time development of the human fetus in utero. The mouse is routinely used as an in vivo model to study embryo implantation and pregnancy progression. Unfortunately, such murine studies require pregnancy interruption to enable follow-up phenotypic analysis. To address this issue, we used three-dimensional (3-D) reconstruction of HFUS imaging data for early detection and characterization of murine embryo implantation sites and their individual developmental progression in utero. Combining HFUS imaging with 3-D reconstruction and modeling, we were able to accurately quantify embryo implantation site number as well as monitor developmental progression in pregnant C57BL6J/129S mice from 5.5 days post coitus (d.p.c.) through to 9.5 d.p.c. with the use of a transducer. Measurements included: number, location, and volume of implantation sites as well as inter-implantation site spacing; embryo viability was assessed by cardiac activity monitoring. In the immediate post-implantation period (5.5 to 8.5 d.p.c.), 3-D reconstruction of the gravid uterus in both mesh and solid overlay format enabled visual representation of the developing pregnancies within each uterine horn. As genetically engineered mice continue to be used to characterize female reproductive phenotypes derived from uterine dysfunction, this method offers a new approach to detect, quantify, and characterize early implantation events in vivo. This novel use of 3-D HFUS imaging demonstrates the ability to successfully detect, visualize, and characterize embryo-implantation sites during early murine pregnancy in a non-invasive manner. The technology offers a significant improvement over current methods, which rely on the interruption of pregnancies for gross tissue and histopathologic characterization. Here we use a video and text format to describe how to successfully perform ultrasounds of early murine pregnancy to generate reliable and reproducible data with reconstruction of the uterine form in mesh and solid 3-D images.

Mice are widely used to study gestational biology. However, pregnancy termination is required for such studies which precludes longitudinal investigations and necessitates the use of large numbers of animals. Therefore, we describe a non-invasive technique of high-frequency ultrasonography for early detection and monitoring of post-implantation events in the pregnant mouse.

High-frequency ultrasonography (HFUS) is a common method to non-invasively monitor the real-time development of the human fetus in utero. The mouse is ...

A Familial Hypercholesterolemia Human Liver Chimeric Mouse Model Using Induced Pluripotent Stem Cell-derived Hepatocytes

Familial hypercholesterolemia (FH) is mostly caused by low-density lipoprotein receptor (LDLR) mutations and results in an increased risk of early-onset cardiovascular disease due to marked elevation of LDL cholesterol (LDL-C) in blood. Statins are the first line of lipid-lowering drugs for treating FH and other types of hypercholesterolemia, but new approaches are emerging, in particular PCSK9 antibodies, which are now being tested in clinical trials. To explore novel therapeutic approaches for FH, either new drugs or new formulations, we need appropriate in vivo models. However, differences in the lipid metabolic profiles compared to humans are a key problem of the available animal models of FH. To address this issue, we have generated a human liver chimeric mouse model using FH induced pluripotent stem cell (iPSC)-derived hepatocytes (iHeps). We used Ldlr-/-/Rag2-/-/Il2rg-/- (LRG) mice to avoid immune rejection of transplanted human cells and to assess the effect of LDLR-deficient iHeps in an LDLR null background. Transplanted FH iHeps could repopulate 5-10% of the LRG mouse liver based on human albumin staining. Moreover, the engrafted iHeps responded to lipid-lowering drugs and recapitulated clinical observations of increased efficacy of PCSK9 antibodies compared to statins. Our human liver chimeric model could thus be useful for preclinical testing of new therapies to FH. Using the same protocol, similar human liver chimeric mice for other FH genetic variants, or mutations corresponding to other inherited liver diseases, may also be generated.

Here, we present a protocol to generate a human liver chimeric mouse model of familial hypercholesterolemia using human induced pluripotent stem cell-derived hepatocytes. This is a valuable model for testing new therapies for hypercholesterolemia.

Familial hypercholesterolemia (FH) is mostly caused by low-density lipoprotein receptor (LDLR) mutations and results in an increased risk of early-onset ...

Visualizing the Node and Notochordal Plate In Gastrulating Mouse Embryos Using Scanning Electron Microscopy and Whole Mount Immunofluorescence

The post-implantation mouse embryo undergoes major shape changes after the initiation of gastrulation and morphogenesis. A hallmark of morphogenesis is the formation of the transient organizers, the node and notochordal plate, from cells that have passed through the primitive streak. The proper formation of these signaling centers is essential for the development of the body plan and techniques to visualize them are of high interest to mouse developmental biologists. The node and notochordal plate lie on the ventral surface of gastrulating mouse embryos around embryonic day (E) 7.5 of development. The node is a cup-shaped structure whose cells possess a single slender cilium each. The proper subcellular localization and rotation of the cilia in the node pit determines left-right asymmetry. The notochordal plate cells also possess single cilia albeit shorter than those of the node cells. The notochordal plate forms the notochord which acts as an important signaling organizer for somitogenesis and neural patterning. Because the cells of the node and notochordal plate are transiently present on the surface and possess cilia, they can be visualized using scanning electron microscopy (SEM). Among other techniques used to visualize these structures at the cellular level is whole mount immunofluorescence (WMIF) using the antibodies against the proteins that are highly expressed in the node and notochordal plate. In this report, we describe our optimized protocols to perform SEM and WMIF of the node and notochordal plate in developing mouse embryos to help in the assessment of tissue shape and cellular organization in wild-type and gastrulation mutant embryos.

The node and notochordal plate are transient signaling organizers in developing mouse embryos that can be visualized using several techniques. Here, we describe in detail how to perform two of the techniques to study their structure and morphogenesis: 1) scanning electron microscopy (SEM); and 2) whole mount immunofluorescence (WMIF).

The post-implantation mouse embryo undergoes major shape changes after the initiation of gastrulation and morphogenesis. A hallmark of morphogenesis is ...

Generation of Organoids from Mouse Extrahepatic Bile Ducts

Cholangiopathies, which affect extrahepatic bile ducts (EHBDs), include biliary atresia, primary sclerosing cholangitis, and cholangiocarcinoma. They have no effective therapeutic options. Tools to study EHBD are very limited. Our purpose was to develop an organ-specific, versatile, adult stem cell-derived, preclinical cholangiocyte model that can be easily generated from wild type and genetically engineered mice. Thus, we report on the novel technique of developing an EHBD organoid (EHBDO) culture system from adult mouse EHBDs. The model is cost-efficient, able to be readily analyzed, and has multiple downstream applications. Specifically, we describe the methodology of mouse EHBD isolation and single cell dissociation, organoid culture initiation, propagation, and long-term maintenance and storage. This manuscript also describes EHBDO processing for immunohistochemistry, fluorescent microscopy, and mRNA abundance quantitation by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). This protocol has significant advantages in addition to producing EHBD-specific organoids. The use of a conditioned medium from L-WRN cells significantly reduces the cost of this model. The use of mouse EHBDs provides almost unlimited tissue for culture generation, unlike human tissue. Generated mouse EHBDOs contain a pure population of epithelial cells with markers of endodermal progenitor and differentiated biliary cells. Cultured organoids maintain homogenous morphology through multiple passages and can be recovered after a long-term storage period in liquid nitrogen. The model allows for the study of biliary progenitor cell proliferation, can be manipulated pharmacologically, and may be generated from genetically engineered mice. Future studies are needed to optimize culture conditions in order to increase plating efficiency, evaluate functional cell maturity, and direct cell differentiation. Development of co-culture models and a more biologically neutral extracellular matrix are also desirable.

This protocol describes the production of a mouse extrahepatic bile duct 3-dimensional organoid system. These biliary organoids can be maintained in culture to study cholangiocyte biology. Biliary organoids express markers of both progenitor and biliary cells and are composed of polarized epithelial cells.

Cholangiopathies, which affect extrahepatic bile ducts (EHBDs), include biliary atresia, primary sclerosing cholangitis, and cholangiocarcinoma. They have ...

Recapitulating Suckling-to-Weaning Transition In Vitro using Fetal Intestinal Organoids

At the end of the suckling period, many mammalian species undergo major changes in the intestinal epithelium that are associated with the capability to digest solid food. This process is termed suckling-to-weaning transition and results in the replacement of neonatal epithelium with adult epithelium which goes hand in hand with metabolic and morphological adjustments. These complex developmental changes are the result of a genetic program that is intrinsic to the intestinal epithelial cells but can, to some extent, be modulated by extrinsic factors. Prolonged culture of mouse primary intestinal epithelial cells from late fetal period, recapitulates suckling-to-weaning transition in vitro. Here, we describe a detailed protocol for mouse fetal intestinal organoid culture best suited to model this process in vitro. We describe several useful assays designed to monitor the change of intestinal functions associated with suckling-to-weaning transition over time. Additionally, we include an example of an extrinsic factor that is capable to affect suckling-to-weaning transition in vivo, as a representation of modulating the timing of suckling-to-weaning transition in vitro. This in vitro approach can be used to study molecular mechanisms of the suckling-to-weaning transition as well as modulators of this process. Importantly, with respect to animal ethics in research, replacing in vivo models by this in vitro model contributes to refinement of animal experiments and possibly to a reduction in the use of animals to study gut maturation processes.

This protocol describes how to mimic suckling-to-weaning transition in vitro using mouse late fetal intestinal organoids cultured for 30 days.

At the end of the suckling period, many mammalian species undergo major changes in the intestinal epithelium that are associated with the capability to ...