Name: Author Spotlight: Optimizing Supraclavicular Brown Adipose Tissue Extraction for Genetic Analysis
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This work is supported by NIDDK of the NIH under Award Number R01DK116899, USDA/ARS under Award Number 3092-51000-064-000D, and a pilot award from the Baylor College of Medicine Cardiovascular Research Institute. The flowcharts were produced using BioRender.

The animal procedures were approved by the Institutional Animal Care and Use Committee at Baylor College of Medicine. All procedures were performed on C57BL/6J male mice aged 3 weeks and 3 months old. Prior to the dissection, all mice were euthanized using the approved rodent carbon dioxide euthanasia procedure. See the Table of Materials for details related to all materials, reagents, and instruments used in this protocol.
1. Dissection of scBAT
<ol>
	<li>Place the mouse ca...

Morphological and Molecular Characterization of the scBAT in Mice

<ol>
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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=Identification+and+importance+of+brown+adipose+tissue+in+adult+humans.">Identification and importance of brown adipose tissue in adult humans.</a> N Engl J Med. 360 (15), 1509-1517 (2009).</li><li>van Marken Lichtenbelt, W. D., 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=Cold-activated+brown+adipose+tissue+in+healthy+men.">Cold-activated brown adipose tissue in healthy men.</a> N Engl J Med. 360 (15), 1500-1508 (2009).</li><li>Virtanen, K. 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=Functional+brown+adipose+tissue+in+healthy+adults.">Functional brown adipose tissue in healthy adults.</a> N Engl J Med. 360 (15), 1518-1525 (2009).</li><li>Cypess, A. 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=Anatomical+localization,+gene+expression+profiling+and+functional+characterization+of+adult+human+neck+brown+fat.">Anatomical localization, gene expression profiling and functional characterization of adult human neck brown fat.</a> Nat Med. 19 (5), 635-639 (2013).</li><li>Leitner, B. P., 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=Mapping+of+human+brown+adipose+tissue+in+lean+and+obese+young+men.">Mapping of human brown adipose tissue in lean and obese young men.</a> Proc Natl Acad Sci U S A. 114 (32), 8649-8654 (2017).</li><li>Mo, Q., 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=Identification+and+characterization+of+a+supraclavicular+brown+adipose+tissue+in+mice.">Identification and characterization of a supraclavicular brown adipose tissue in mice.</a> JCI Insight. 2 (11), e93166 (2017).</li><li>Shi, 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=Gene+Expression+Analysis+of+Environmental+Temperature+and+High-Fat+Diet-Induced+Changes+in+Mouse+Supraclavicular+Brown+Adipose+Tissue.">Gene Expression Analysis of Environmental Temperature and High-Fat Diet-Induced Changes in Mouse Supraclavicular Brown Adipose Tissue.</a> Cells. 10 (6), 1370 (2021).</li><li>Chang, 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=Loss+of+perivascular+adipose+tissue+on+peroxisome+proliferator-activated+receptor-gamma+deletion+in+smooth+muscle+cells+impairs+intravascular+thermoregulation+and+enhances+atherosclerosis.">Loss of perivascular adipose tissue on peroxisome proliferator-activated receptor-gamma deletion in smooth muscle cells impairs intravascular thermoregulation and enhances atherosclerosis.</a> Circulation. 126 (9), 1067-1078 (2012).</li><li>Ye, 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=Developmental+and+functional+characteristics+of+the+thoracic+aorta+perivascular+adipocyte.">Developmental and functional characteristics of the thoracic aorta perivascular adipocyte.</a> Cell Mol Life Sci. 76 (4), 777-789 (2019).</li><li>de Jong, J. M., Larsson, O., Cannon, B., Nedergaard, 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+stringent+validation+of+mouse+adipose+tissue+identity+markers.">A stringent validation of mouse adipose tissue identity markers.</a> Am J Physiol Endocrinol Metab. 308 (12), E1085-E1105 (2015).</li><li>Fu, 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=Neural+crest+cells+differentiate+into+brown+adipocytes+and+contribute+to+periaortic+arch+adipose+tissue+formation.">Neural crest cells differentiate into brown adipocytes and contribute to periaortic arch adipose tissue formation.</a> Arterioscler Thromb Vasc Biol. 39 (8), 1629-1644 (2019).</li><li>Tucker, D. K., Foley, J. F., Bouknight, S. A., Fenton, S. 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In this protocol, we present in detail the procedures for dissecting and processing scBAT for H&#38;E and gene expression analyses. Because scBAT resides in the intermediate layer of the neck and lies along the large veins, the isolation of this depot requires precise technique. Specifically, to gain a clear view of the depot, we recommend placing the mouse under a dissecting microscope after the neck has been opened. Using a pair of superfine point forceps to peel scBAT off the salivary gland and surrounding veins, care...

The increasing prevalence of obesity in the U.S. and worldwide has ignited great interest in understanding its etiology and identifying potential treatments1,2. Adipose tissue plays a vital role in metabolism, and dysregulation of the adipose tissue can lead to the development of obesity. Generally, there are two types of adipose tissues, white and brown adipose tissue. While white adipose tissue (WAT) can store chemical energy and secrete endocrine factors, brown adipose tissue (BAT) can use chemical energy to generate heat and maintain body temperature in the cold3,4. Because of this unique ability, activation of BAT can also increase energy expenditure and improve insulin sensitivity5.
BAT exerts its function through non-shivering thermogenesis, a process mediated by uncoupling protein 1 (UCP1)6. Mammals, including mice and humans, possess varying amounts of BAT. The classical view of BAT is that these adipose tissues are more abundant in mice and infants than in adult humans. iBAT, located in the upper dorsal flank between the scapulae, is the most studied BAT depot in mice. By applying radioisotope imaging and biopsy tests, recent studies identified several BAT depots in adult humans. Some of them, including the depots found in the deep neck and supraclavicular region, had not previously been identified in mice or other model animals7,8,9,10,11. Among these BAT depots, the scBAT is the most frequently seen depot in adult humans. To better understand the origin and molecular contribution of these newly found BAT depots in humans, it is essential to identify equivalent depots in mice that allow genetic and molecular manipulations to trace and test the functional role of these depots. Thus, we and others identified a few previously unknown BAT depots in different anatomical locations in mice, including scBAT12,13, thoracic perivascular BAT14,15, perirenal BAT16, and periaortic BAT17. Mouse scBAT anatomically resembles human scBAT and morphologically resembles classical iBAT, expressing high levels of UCP112.
Unlike mouse iBAT, which can be readily dissected, scBAT is situated in the intermediate layer of the mouse neck, beneath the salivary glands and along the external jugular vein. Isolation of this depot for histological and molecular analyses can be challenging. Here, we describe in detail the procedure for dissecting scBAT from postnatal and adult mice and processing this depot for histology and gene expression analysis.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>95% Dehydrant Alcohol (Flex 95)</td>
			<td>Epredia</td>
			<td>8201</td>
			<td></td>
		</tr>
		<tr>
			<td>100% Dehydrant Alcohol (Flex 100)</td>
			<td>Epredia</td>
			<td>8101</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well PCR plate</td>
			<td>Bio-Rad</td>
			<td>MLL9601</td>
			<td></td>
		</tr>
		<tr>
			<td>Aurum Binding Mini Column</td>
			<td>Bio-Rad</td>
			<td>7326826</td>
			<td></td>
		</tr>
		<tr>
			<td>Aurum High Stringency Wash</td>
			<td>Bio-Rad</td>
			<td>7326803</td>
			<td></td>
		</tr>
		<tr>
			<td>Aurum Low Stringency Wash</td>
			<td>Bio-Rad</td>
			<td>7326804</td>
			<td></td>
		</tr>
		<tr>
			<td>Base Molds (for embedding)</td>
			<td>Tissue-Tek</td>
			<td>4122</td>
			<td></td>
		</tr>
		<tr>
			<td>BD PrecisionGlide Needle 21g x 1 1/2&#34;</td>
			<td>Becton Dickinson</td>
			<td>305167</td>
			<td></td>
		</tr>
		<tr>
			<td>C1000 Touch Thermal Cycler</td>
			<td>Bio-Rad</td>
			<td>1840148</td>
			<td></td>
		</tr>
		<tr>
			<td>Capless Microcentrifuge Tubes 2 mL</td>
			<td>Fisherbrand</td>
			<td>02-681-453</td>
			<td></td>
		</tr>
		<tr>
			<td>Centrifuge&#160;</td>
			<td>Eppendorf</td>
			<td>5430R</td>
			<td></td>
		</tr>
		<tr>
			<td>CFX Opus 96 Real-Time PCR Instrument</td>
			<td>Bio-Rad</td>
			<td>12011319</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroform</td>
			<td>Thermo Scientific Chemicals</td>
			<td>383760010</td>
			<td></td>
		</tr>
		<tr>
			<td>Cytoseal 60 Low-viscosity mounting medium</td>
			<td>Epredia</td>
			<td>83104</td>
			<td></td>
		</tr>
		<tr>
			<td>DEPC-Treated Water</td>
			<td>Ambion</td>
			<td>AM 9906</td>
			<td></td>
		</tr>
		<tr>
			<td>Dissecting Microscope</td>
			<td>Nikon</td>
			<td>SMZ1500</td>
			<td></td>
		</tr>
		<tr>
			<td>DNase Dilution Solution</td>
			<td>Bio-Rad</td>
			<td>7326805</td>
			<td></td>
		</tr>
		<tr>
			<td>DNase I</td>
			<td>Bio-Rad</td>
			<td>7326828</td>
			<td></td>
		</tr>
		<tr>
			<td>dNTPs</td>
			<td>Invitrogen</td>
			<td>18427013</td>
			<td></td>
		</tr>
		<tr>
			<td>Elution solution</td>
			<td>Bio-Rad</td>
			<td>7326801</td>
			<td></td>
		</tr>
		<tr>
			<td>EM 400 embedding medium paraffin</td>
			<td>Leica Biosystems</td>
			<td>3801320</td>
			<td></td>
		</tr>
		<tr>
			<td>Eosin Y (0.5% w/v)</td>
			<td>RICCA</td>
			<td>2858-16</td>
			<td></td>
		</tr>
		<tr>
			<td>Formula R Infiltration medium paraffin</td>
			<td>Leica Biosystems</td>
			<td>3801470</td>
			<td></td>
		</tr>
		<tr>
			<td>Genemark Nutator Gyromixer 349</td>
			<td>Bio Express</td>
			<td>S-3200-2</td>
			<td></td>
		</tr>
		<tr>
			<td>Gill #3 Hematoxylin</td>
			<td>Sigma-Aldrich</td>
			<td>GHS332-1L</td>
			<td></td>
		</tr>
		<tr>
			<td>HCl (for HCL-Ethanol)</td>
			<td>Fisher Chemical</td>
			<td>A142212</td>
			<td></td>
		</tr>
		<tr>
			<td>IP VI Embedding Cassettes</td>
			<td>Leica Biosystems</td>
			<td>39LC-550-5-L</td>
			<td></td>
		</tr>
		<tr>
			<td>Koptec&#39;s Pure Ethanol - 200 Proof (for 70% Ethanol)</td>
			<td>Decon Labs</td>
			<td>V1001</td>
			<td></td>
		</tr>
		<tr>
			<td>MgCl2 (25 mM)</td>
			<td>Thermo Fisher Scientific</td>
			<td>R0971</td>
			<td></td>
		</tr>
		<tr>
			<td>Microcentrifuge Tubes 1.7 mL</td>
			<td>Avantor</td>
			<td>87003-294</td>
			<td></td>
		</tr>
		<tr>
			<td>Microseal &#39;B&#39; Seals (adhseive seals)</td>
			<td>Bio-Rad</td>
			<td>MSB1001</td>
			<td></td>
		</tr>
		<tr>
			<td>Microtome</td>
			<td>Leica Biosystems</td>
			<td>RM2245</td>
			<td></td>
		</tr>
		<tr>
			<td>Molecular Biology Grade Water</td>
			<td>Corning</td>
			<td>46-000-CM</td>
			<td></td>
		</tr>
		<tr>
			<td>Mortar Coors Tek</td>
			<td>Thomas Scientific</td>
			<td>60310</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl (for 0.85% saline)</td>
			<td>Fisher Bioreagents</td>
			<td>BP358-212</td>
			<td></td>
		</tr>
		<tr>
			<td>NanoDrop Spectrophotometer</td>
			<td>NanoDrop Technologies</td>
			<td>ND-1000 UV/Vis</td>
			<td></td>
		</tr>
		<tr>
			<td>Oligo dT</td>
			<td>Invitrogen</td>
			<td>18418020</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraffin Section Flotation Bath</td>
			<td>Boekel Scientific</td>
			<td>14792V</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde (PFA)</td>
			<td>Sigma-Aldrich</td>
			<td>P6148-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>PCR Tube Strip</td>
			<td>Avantor</td>
			<td>76318-802</td>
			<td></td>
		</tr>
		<tr>
			<td>Pestle by Coors Tek</td>
			<td>Thomas Scientific</td>
			<td>60311</td>
			<td></td>
		</tr>
		<tr>
			<td>Pestle Pellet Motor</td>
			<td>Kimble</td>
			<td>749540-0000</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffer Saline (PBS)</td>
			<td>Sigma-Aldrich</td>
			<td>D8537-500ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Precision Model 19 Vacuum Oven&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>CAT# 51221162</td>
			<td></td>
		</tr>
		<tr>
			<td>Primer: 36B4&#160; (forward) 10 &#956;M 
			5&#39; TGA AGT GCT CGA CAT CAC AGA GCA 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>Primer: 36B4 (reverse) 10 &#956;M 
			5&#39; GCT TGT ACC CAT TGA TGA TGG AGT GT 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>Primer: Fabp4 (forward) 10 &#956;M 
			5&#8217; ACA CCG AGA TTT CCT TCA AAC TG 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>Primer: Fabp4 (reverse) 10 &#956;M 
			5&#8217; CCA TCT AGG GTT ATG ATG CTC TTC A 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>Primer: Glut 4 (forward primer) 10 &#956;M 
			5&#8217; CTG ATT CTG CTG CCC TTC TGT CCT 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>Primer: Glut 4 (reverse) 10 &#956;M 
			5&#8217; GAC ATT GGA CGC TCT CTC TCC AAC TT 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>Primer: PPARg (forward) 10 &#956;M 
			5&#8217; AGG GCG ATC TTG ACA GGA AAG ACA 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>Primer: PPARg (reserve) 10 &#956;M 
			5&#8217; AAA TTC GGA TGG CCA CCT CTT TGC 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>Primer: Ppargc1a (reverse) 10 &#956;M 
			5&#39; ATG TTG CGA CTG CGG TTG TGT ATG 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>Primer: Ppargc1a(forward) 10 &#956;M 
			5&#39; ACG TCC CTG CTC AGA GCT TCT CA 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>Primer: Ucp1 (forward) 10 &#956;M 
			5&#8217; AGC CAC CAC AGA AAG CTT GTC AAC 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>Primer: Ucp1 (reverse) 10 &#956;M 
			5&#8217; ACA GCT TGG TAC GCT TGG GTA CTG 3&#8217;</td>
			<td></td>
			<td></td>
			<td>Chen lab Oligo database</td>
		</tr>
		<tr>
			<td>RNA isolation solution (PureZol)</td>
			<td>Bio-Rad</td>
			<td>7326880</td>
			<td></td>
		</tr>
		<tr>
			<td>RNase Away (surface decontaminant)</td>
			<td>Thermo Scientific</td>
			<td>1437535</td>
			<td></td>
		</tr>
		<tr>
			<td>RNase H</td>
			<td>NEB</td>
			<td>M0297S</td>
			<td></td>
		</tr>
		<tr>
			<td>Rnase inhibitor (RNase Out)</td>
			<td>Invitrogen</td>
			<td>10777019</td>
			<td></td>
		</tr>
		<tr>
			<td>Scintillation Vial (glass)</td>
			<td>Electron Microscopy Sciences</td>
			<td>72632</td>
			<td></td>
		</tr>
		<tr>
			<td>Slide drying bench&#160;</td>
			<td>Electrothermal (Cole-Parmer)</td>
			<td>MH6616</td>
			<td></td>
		</tr>
		<tr>
			<td>Stainless staining rack</td>
			<td>Electron Microscopy Sciences</td>
			<td>70312-54</td>
			<td></td>
		</tr>
		<tr>
			<td>Stereo microscope (for embedding)</td>
			<td>Olympus</td>
			<td>SZ51</td>
			<td></td>
		</tr>
		<tr>
			<td>Sugical scissors</td>
			<td>McKesson</td>
			<td>43-1-104</td>
			<td></td>
		</tr>
		<tr>
			<td>Superfine point Straight Dissecting Forceps</td>
			<td>Avantor</td>
			<td>82027-402</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>Superscript III Reverse Transcriptase (Includes 5x First-Strand Buffer and 0.1M DTT)&#160;</td>
			<td>Invitrogen</td>
			<td>18080044</td>
			<td></td>
		</tr>
		<tr>
			<td>SUR-VET syringe with needle 25 G x 5/8&#34;, 1 mL</td>
			<td>Terumo</td>
			<td>100281</td>
			<td></td>
		</tr>
		<tr>
			<td>SYBR Green (qPCR enzyme master mixture)</td>
			<td>Applied Biosystems</td>
			<td>A25778</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue-Tek Manual Slide Staining Set (jars)</td>
			<td>Electron Microscopy Sciences</td>
			<td>SKU: 62540-01</td>
			<td></td>
		</tr>
		<tr>
			<td>Toluene</td>
			<td>Fisher Chemical</td>
			<td>T324-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Transfer pipette</td>
			<td>Avantor</td>
			<td>414004-005</td>
			<td></td>
		</tr>
		<tr>
			<td>Xylene</td>
			<td>Fisher Chemical</td>
			<td>X3P-1GAL</td>
			<td></td>
		</tr>
	</tbody>
</table>

dissection, histological processing, and gene expression analysis of murine supraclavicular brown adipose tissue

Brown adipose tissue (BAT)-mediated thermogenesis plays an important role in the regulation of metabolism, and its morphology and function can be greatly impacted by environmental stimuli in mice and humans. Currently, murine interscapular BAT (iBAT), which is located between two scapulae in the upper dorsal flank of mice, is the main BAT depot used by research laboratories to study BAT function. Recently, a few previously unknown BAT depots were identified in mice, including one analogous to human supraclavicular brown adipose tissue. Unlike iBAT, murine supraclavicular brown adipose tissue (scBAT) is situated in the intermediate layer of the neck and thus cannot be accessed as readily.
To facilitate the study of newly identified mouse scBAT, presented herein is a protocol detailing the steps to dissect intact scBAT from postnatal and adult mice. Due to scBAT&#39;s small size relative to other adipose depots, procedures have been modified and optimized specifically for processing scBAT. Among these modifications is the use of a dissecting microscope during tissue collection to increase the precision and homogenization of frozen scBAT samples to raise the efficiency of subsequent qPCR analysis. With these optimizations, the identification of, morphological appearance of, and molecular characterization of the scBAT can be determined in mice.

Author Spotlight: Optimizing Supraclavicular Brown Adipose Tissue Extraction for Genetic Analysis

Dissection, Histological Processing, and Gene Expression Analysis of Murine Supraclavicular Brown Adipose Tissue

Unlike iBAT, which is situated in the subcutaneous layer of the back between two scapulae, scBAT is situated in the intermediate layer of the neck, extending deep between layers of skeletal muscle and the salivary gland as it grows along the external jugular vein (Figure 1A). Dissecting scBAT is not as straightforward as iBAT. Here, we provide a detailed procedure including crucial steps for dissecting intact scBAT from postnatal and adult mice (<strong class...

Watch this Scientific Journal Video about Author Spotlight: Optimizing Supraclavicular Brown Adipose Tissue Extraction for Genetic Analysis at JoVE.com

Here, we provide a practical procedure for dissecting and performing histological and gene expression analyses of murine supraclavicular brown adipose tissue.

Brown adipose tissue (BAT)-mediated thermogenesis plays an important role in the regulation of metabolism, and its morphology and function can be greatly ...