Name: a hydrophobic tissue clearing method for rat brain tissue
Uploaded: 2020-12-23T15:00:00
Description: Watch this Scientific Journal Video about A Hydrophobic Tissue Clearing Method for Rat Brain Tissue at JoVE.com

Bu çalışma NIH hibeleri tarafından finanse edildi: NS100624, DA013137, HD043680, MH106392 & T32 Eğitim Hibesi 5T32GM081740

Tüm hayvan protokolleri Güney Carolina Üniversitesi Hayvan Bakım ve Kullanım Komitesi tarafından incelendi ve onaylandı.
1. Stok çözeltisi hazırlama
<ol><li>Çözelti 1 (1 L): 900 mL'ye deiyonize H2O, 10x fosfat tamponlu salin (PBS) ve 2 mL Triton X-100 ekleyin.</li>
	<li>Çözüm 2 (1 L): 900 mL deiyonize H2O'ya, 10x PBS'nin 100 mL'si, 2mL Ara-20 ve 1 mL'lik 10 mg/mL Heparin stok çözeltisi ekleyin.</li>
	<li>Çözelti 3 (500 mL): 400 mL Çözelti 1'e 11,5 g...

<ol>
	<li>Chung, K., 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=Structural+and+molecular+interrogation+of+intact+biological+systems.">Structural and molecular interrogation of intact biological systems.</a> Nature. 497 (7449), 332-337 (2013).</li><li>Susaki, E. 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=Whole-brain+imaging+with+single-cell+resolution+using+chemical+cocktails+and+computational+analysis.">Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis.</a> Cell. 157 (3), 726-739 (2014).</li><li>Ueda, H. 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=Tissue+clearing+and+its+applications+in+neuroscience.">Tissue clearing and its applications in neuroscience.</a> Nature Reviews Neuroscienc. 21, 298 (2020).</li><li>Renier, N., 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=iDISCO:+a+simple,+rapid+method+to+immunolabel+large+tissue+samples+for+volume+imaging.">iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging.</a> Cell. 159 (4), 896-910 (2014).</li><li>Renier, N., 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+brain+activity+by+automated+volume+analysis+of+immediate+early+genes.">Mapping of brain activity by automated volume analysis of immediate early genes.</a> Cell. 165 (7), 1789-1802 (2016).</li><li>Reid, W., 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=An+HIV-1+transgenic+rat+that+develops+HIV-related+pathology+and+immunologic+dysfunction.">An HIV-1 transgenic rat that develops HIV-related pathology and immunologic dysfunction.</a> Proceedings of the National Academy of Science U. S. A. 98, 9271-9276 (2001).</li><li>Vigorito, M., Connaghan, K. P., Chang, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+HIV-1+transgenic+rat+model+of+neuroHIV.">The HIV-1 transgenic rat model of neuroHIV.</a> Brain, Behavior, and Immunity. 48, 336-349 (2015).</li><li>McLaurin, 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=Synaptic+connectivity+in+medium+spiny+neurons+of+the+nucleus+accumbens:+A+sex-dependent+mechanism+underlying+apathy+in+the+HIV-1+transgenic+rat.">Synaptic connectivity in medium spiny neurons of the nucleus accumbens: A sex-dependent mechanism underlying apathy in the HIV-1 transgenic rat.</a> Frontiers in Behavior Neurosciences. 12, 285 (2018).</li><li>Fitting, S., Booze, R. M., Mactutus, C. F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HIV-1+proteins,+Tat+and+gp120,+target+the+developing+dopamine+system.">HIV-1 proteins, Tat and gp120, target the developing dopamine system.</a> Current HIV Research. 13, 135-137 (2015).</li><li>Javadi-Paydar, M., Roscoe, R. F., Denton, A. R., Mactutus, C. F., Booze, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HIV-1+and+cocaine+disrupt+dopamine+reuptake+and+medium+spiny+neurons+in+female+rat+striatum.">HIV-1 and cocaine disrupt dopamine reuptake and medium spiny neurons in female rat striatum.</a> PLos One. 12 (11), 0188404 (2017).</li><li>Bertrand, S. J., Mactutus, C. F., Harrod, S. B., Moran, L. M., Booze, R. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=HIV-1+proteins+dysregulate+motivational+processes+and+dopamine+circuitry.">HIV-1 proteins dysregulate motivational processes and dopamine circuitry.</a> Science Report. 8, 6152 (2018).</li><li>Denton, A. 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=Selective+monoaminergic+and+histaminergic+circuit+dysregulation+following+long-term+HIV-1+protein+exposure.">Selective monoaminergic and histaminergic circuit dysregulation following long-term HIV-1 protein exposure.</a> Journal of neurovirology. 25 (4), 540-550 (2019).</li><li>Berendse, H. W., Groenewegen, H. J., Lohman, A. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Compartmental+distribution+of+ventral+striatal+neurons+projecting+to+the+mesencephalon+in+the+rat.">Compartmental distribution of ventral striatal neurons projecting to the mesencephalon in the rat.</a> Journal of Neuroscienc. 12 (6), 2079-2103 (1992).</li><li>Peyron, C., Petit, J. M., Rampon, C., Jouvet, M., Luppi, P. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Forebrain+afferents+to+the+rat+dorsal+raphe+nucleus+demonstrated+by+retrograde+and+anterograde+tracing+methods.">Forebrain afferents to the rat dorsal raphe nucleus demonstrated by retrograde and anterograde tracing methods.</a> Neuroscience. 82 (2), 443-468 (1998).</li><li>Barrot, 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=Braking+dopamine+systems:+a+new+GABA+master+structure+for+mesolimbic+and+nigrostriatal+functions.">Braking dopamine systems: a new GABA master structure for mesolimbic and nigrostriatal functions.</a> The Journal of Neuroscience: The Official Journal of the Society for Neuroscienc. 32 (41), 14094-14101 (2012).</li><li>Roostalu, U., 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=Quantitative+whole-brain+3D+imaging+of+tyrosine+hydroxylase-labeled+neuron+architecture+in+the+mouse+MPTP+model+of+Parkinson's+disease.">Quantitative whole-brain 3D imaging of tyrosine hydroxylase-labeled neuron architecture in the mouse MPTP model of Parkinson's disease.</a> Disease Models &amp; Mechanisms. 12 (11), (2019).</li><li>Ransohoff, R., Cardona, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+myeloid+cells+of+the+central+nervous+system+parenchyma.">The myeloid cells of the central nervous system parenchyma.</a> Nature. 468, 253-262 (2010).</li><li>Rocha, M. 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=Tissue+Clearing+and+Light+Sheet+Microscopy:+Imaging+the+Unsectioned+Adult+Zebra+Finch+Brain+at+Cellular+Resolution.">Tissue Clearing and Light Sheet Microscopy: Imaging the Unsectioned Adult Zebra Finch Brain at Cellular Resolution.</a> Frontiers in Neuroanatomy. 13, 13 (2019).</li><li>Richardson, D. S., Lichtman, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clarifying+tissue+clearing.">Clarifying tissue clearing.</a> Cell. 162 (2), 246-257 (2015).</li></ol>

Doku temizleme, geleneksel IHC protokolünün sınırlamalarına bir çözüm sunar. Şeffaf olan bir örnek, sağlam dokulara hücresel düzeyde optik erişim sağlayan ışığın saçılmasını ve emilimini en aza indirir18,19. Doku temizleme teknikleri, çözücülerin yönetimi ile delipidasyon, dekolorizasyon ve kireçten arındırma yoluyla bir dokuyu şeffaf hale gelir. Doku örneğinin kırılma indeksi seçilen görüntüleme ortamının kırılma inde...

Beyinde kullanım için çeşitli doku temizleme teknikleri doğrulanmıştır: hidrojel, hidrofilik ve hidrofobik. Bu teknikler, çözücülerin yönetimi yoluyla bir dokuyu delipidasyon, dekolorizasyon ve kireçten arındırma yoluyla şeffaf hale getirmeyi amaçlamaktadır. Doku örneğinin kırılma indeksi seçilen görüntüleme ortamının kırılma indisiyle eşleştiğinde, numunenin net bir görüntüsü elde edilebilir. CLARITY gibi hidrojel bazlı teknikler, dokudaki biyomolekülleri akril bazlı hidrojellere bağlayarak güvence altına almakta, bu da yapısal hasarı ve protein kaybını önler1. Bununla birlikte, hidrojel teknikleri daha kırılgan dokulara zarar verme potansiyeline sahip olandan daha sert kimyasallar kullanır ve daha yoğun doku örnekleri hidrojel protokolü ile uyumlu olmayabilir. Bazı hidrojel teknikleri pahalı ekipman gerektirebilir veya doku genişlemesine yol açabilir. CUBIC gibi hidrofilik teknikler, doku içinde hidrojen bağları oluşumu yoluyla 3D yapıyı korur2. Doku genişlemesi bazı hidrofilik protokollerde de ortaya çıkabilir. Hidrofilik tekniklerin temizleme yeteneği genellikle daha yoğun ve kalın dokular için önemli olan hidrofobik tekniklerin sahip olduğu yetenekle eşleşmez3.
Hidrofobik teknikler genellikle hızlıdır, özel ekipman gerektirmez ve kullanımı ve depolaması kolay bir örnek üretir. iDISCO, diğer hidrofobik protokollerde meydana gelebilecek büzülmeleri ortadan kaldıran bir hidrofobik tekniktir. Başlangıçta, iDISCO doku temizleme tekniği, farelerin embriyoları ve yoğun, yetişkin organları için Renier ve ark.4 tarafından tanımlanmıştır. Bu teknik, ilk dehidrasyon adımında dokudaki suyu temizler, böylece ışık saçılmasını azaltır. Doku, derin antikor penetrasyonunu sağlamak için ön işlem sırasında permeabilize edilir. Uzak kırmızı spektrumdaki Alexa Fluor boyaları, alt dalga boylarında dokunun otoflüoresansını önlemek için immünolabeling için kullanılır5. Hidrofobik temizleme protokollerinden geçen doku kolayca işlenebilir ve Alexa Fluor boyalarının uzun ömürlü olması nedeniyle birkaç kez görüntülenebilir. Düzgün bir şekilde saklanırsa, dokular ilk işlemden sonra aylarca ila bir yıl boyunca görüntü sağlayabilir.
Mevcut protokolde hem erkek hem de kadın kontrolünde ve HIV-1 transgenik (Tg) sıçan beyinlerinde tirozin hidroksilaz (TH) antikoru, Iba1 antikoru ve Kolera Toksini Alt Ünlem B (CTB) kullanılmıştır. HIV-1 Tg sıçanı, HIV-1 viral genomu oluşturan dokuz genden yedisine sahiptir, bu da uzun süreli HIV-1 protein maruziyetinin bulaşıcı olmayan bir modeline yol açar6,7,8. Dopaminerjik değişiklikler daha önce HIV-1 Tg sıçanında gösterilmiştir ve HIV-1'in kendisi enflamatuar bir hastalıktır, bu nedenle antikor seçimi deneysel tasarım 9 , 10,11,12ile ilişkiliydi. CTB, ganglioside bağlama yoluyla nöronlara bağlanan ve beyindeki farklı projeksiyonları izlemek için kullanılabilen bir izleyicidir. CTB daha önce çekirdek akumbens'ten substantia nigra bölgesine, beynin dopaminerjik yollar13 , 14,15ile yoğun olarak ilgili iki bölgesine kadar projeksiyonları incelemek için kullanılmıştır.
Bu protokolde, TH dopamin üretimi için bir işaretleyici olarak hizmet edecek ve Iba1 aktif mikrogliayı işaretleyecek. Kullanılan TH antikor, tirozin hidroksilaz'a karşılık gelen yaklaşık 62 kDa'da tek bir bandı seçici olarak etiketler. Iba1 antikorı Iba1 karboksi-terminal dizisine karşılık gelir. Her iki antikor da tavşanda bulundu ve poliklonaldi. CTB, nöronların çekirdek akumbens bölgesinden substantia nigra bölgesine retrograd izlenmesi için kullanılacaktır. Mevcut protokol ayrıca orijinal iDISCO protokolünün iki farklı şekilde ayarlanması için bir kılavuz sunar: 1) engelleme adımlarındaki serum reaktiflerini değiştirerek arka plan boyamanın genel olarak azaltılması ve 2) kuluçka süresinin daha büyük doku örnekleri için uygun olacak şekilde ölçeklendirilmesi. Genel olarak, mevcut protokol, hidrofobik temizleme tekniklerinin sıçanın beyin dokularında mümkün olduğuna, HIV-1 viral proteinlerle ayırt edilebilir zararlı etkileşimleri olmadığına ve TH antikor, Iba1 antikor ve CTB ile uyumlu olduğuna dair sürekli kanıtlar sunmaktadır.

<table>
	<tbody>
		<tr>
			<td>Cholera Toxin Subunit B (Recombinant), Alexa Fluor 488</td>
			<td>Invitrogen</td>
			<td>C34775</td>
			<td></td>
		</tr>
		<tr>
			<td>DBE</td>
			<td>Sigma-Aldrich</td>
			<td>108014-1KG</td>
			<td></td>
		</tr>
		<tr>
			<td>DCM</td>
			<td>Sigma-Aldrich</td>
			<td>270997-100mL</td>
			<td></td>
		</tr>
		<tr>
			<td>DMSO</td>
			<td>Sigma-Aldrich</td>
			<td>472301-1L</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Fisher Chemical</td>
			<td>G46-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat anti-rabbit Alexa Fluor Plus 647</td>
			<td>Invitrogen</td>
			<td>A32733</td>
			<td></td>
		</tr>
		<tr>
			<td>Goat serum</td>
			<td>Sigma Life Science</td>
			<td>G9023-10mL</td>
			<td></td>
		</tr>
		<tr>
			<td>Heparin</td>
			<td>Acros Organics</td>
			<td>41121-0010</td>
			<td></td>
		</tr>
		<tr>
			<td>Iba1 primary antibody</td>
			<td>FUJIFILM Wako</td>
			<td>019-19741</td>
			<td></td>
		</tr>
		<tr>
			<td>Kwik-sil epoxy</td>
			<td>VWR</td>
			<td>70730-062</td>
			<td></td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>Sigma-Aldrich</td>
			<td>34860-1l-R</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Fisher Bioreagents</td>
			<td>BP2944-100</td>
			<td></td>
		</tr>
		<tr>
			<td>Perfusion machine</td>
			<td>VWR</td>
			<td>70730-062</td>
			<td>mini pump variable flow</td>
		</tr>
		<tr>
			<td>PFA</td>
			<td>Sigma-Aldrich</td>
			<td>158127-3KG</td>
			<td></td>
		</tr>
		<tr>
			<td>TH primary antibody</td>
			<td>Millipore Sigma</td>
			<td>AB152</td>
			<td></td>
		</tr>
		<tr>
			<td>TritonX-100</td>
			<td>Fisher Bioreagents</td>
			<td>BP151-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Fisher Bioreagents</td>
			<td>BP337-500</td>
			<td></td>
		</tr>
	</tbody>
</table>

a hydrophobic tissue clearing method for rat brain tissue

Hidrofobik doku temizleme yöntemleri, değiştirilmemiş doku örneklerinde ilgi molekülünün incelenmesini sağlayan kolayca ayarlanabilir, hızlı ve düşük maliyetli prosedürlerdir. Geleneksel immünolabeling prosedürleri, numunenin sağlam yapıları etiketleme ve inceleme yeteneğini kısıtlayan ince bölümlere kesilmesini gerektirir. Ancak, işlem sırasında beyin dokusu bozulmadan kalabiliyorsa, analiz için yapılar ve devreler bozulmadan kalabilir. Daha önce kurulan temizleme yöntemleri dokuyu tamamen temizlemek için önemli zaman alır ve sert kimyasallar genellikle hassas antikorlara zarar verebilir. iDISCO yöntemi dokuyu hızlı ve tamamen temizler, birçok antikorla uyumludur ve özel bir laboratuvar ekipmanı gerektirmez. Bu teknik başlangıçta fare dokusunda kullanım için doğrulandı, ancak mevcut protokol bu yöntemi kontrol ve transgenik sıçan beyinlerinin görüntü yarımkürelerine uyarlıyor. Buna ek olarak, mevcut protokol, daha az arka plan boyama ile daha net görüntüler sağlamak için önceden var olan protokolde birkaç ayarlama yapar. Iba-1 ve tirozin hidroksilaz antikorları HIV-1 transgenik sıçanda ve F344/N kontrol sıçanlarında mevcut hidrofobik doku temizleme yöntemi kullanılarak doğrulandı. Beyin, yapıların birbirinden ayrı olarak daha sık birlikte çalıştığı iç içe geçmiş bir ağdır. Beyni tek tek parçaların bir kombinasyonunun aksine bütün bir sistem olarak analiz etmek, tüm bu beyin temizleme yönteminin en büyük yararıdır.

Bu modifiye hidrofobik doku temizleme protokolü kullanılarak hem F344/N hem de HIV-1 sıçan beyin dokusunun geniş bölümlerinin tam olarak temizlenmesi sağlandı. Şekil 1, substantia nigra bölgesinde TH için tipik bir konfokal görüntü görüntüler. Şekil 1A yoğun, pozitif lekeleri temsil eder. Bu gibi yoğun alanlar pozitif lekeleme ve uygun hücre morfolojisini doğrulamak için "Z" düzlemine odaklanarak ayrıştırılabilir. <strong class="xfig...

Watch this Scientific Journal Video about A Hydrophobic Tissue Clearing Method for Rat Brain Tissue at JoVE.com

A Hydrophobic Tissue Clearing Method for Rat Brain Tissue

Burada, hedef moleküllerin sağlam beyin yapılarının bir parçası olarak görüntülenmesini sağlayan hidrofobik bir doku temizleme yöntemi sunuyoruz. Bu teknik artık F344/N kontrolü ve her iki cinsiyetten HIV-1 transgenik sıçanlar için onaylanmıştır.

Sıçan Beyin Dokusu için Hidrofobik Doku Temizleme Yöntemi

Hydrophobic tissue clearing methods are easily adjustable, fast, and low-cost procedures that allows for the study of a molecule of interest in unaltered ...

The overall goal of this clearing technique is to establish a tissue clearing method for the rat brain. This protocol can also be used for the HIV-1 transgenic rat. The main advantage of this technique is that the rat brain tissue can be left intact for clearing thus allowing for full circuit level analysis.Demonstrating the procedure will be Kristin Kirchner, a PhD candidate from my laboratory, and also Hailong Li, a research associate from my lab. After performing transcardial perfusion in a three to six week old rat, remove the brain from the skull using forceps. Then place it in a sagittal position and slice it into four equal three millimeter wide sections using a razor blade and a rat brain matrix.Fix each section in four percent PFA in a sealed five milliliter plastic tube overnight on a shaker at four degrees Celsius. On the next day, continue the fixation at room temperature for one hour. Wash each section three times with PBS for about 30 minutes per wash.Serially incubate the washed sections in 20, 40, 60, 80, and 100%methanol solution for one hour each. Repeat the dehydration with 100%methanol. Then chill the samples in 100%methanol at four degrees Celsius for 10 minutes.Prepare a solution containing 66%DCM and 33%methanol and incubate the chilled sections in this solution overnight at room temperature with shaking. On the next day, wash the sample twice with methanol for 30 minutes and chill it in 100%methanol at four degrees Celsius for 10 minutes. For bleaching, place the sample in fresh five percent hydrogen peroxide in methanol and incubate it overnight at four degrees Celsius.After the overnight incubation, serially incubate the sample in 80, 60, 40, and 20%methanol solutions for one hour each at room temperature. Then incubate the sample in PBS for one hour and wash it twice in solution one for one hour per wash. Fill a one milliliter syringe with 2.5 microliters of one percent biotin-CTB and slowly inject it into the nucleus accumbens site over 20 seconds.Leave the needle tip in place for one minute and remove it slowly over 10 seconds to prevent leakage. Incubate the sample in solution three and then solution four for two days each in a 37 degrees Celsius water bath. Then add the primary antibody and continue the incubation for seven days.Wash the sample five times in solution two for one hour per wash and store it in solution two at room temperature overnight. Incubate the sample with a secondary antibody for seven days in a 37 degrees Celsius water bath. Finally, wash it five times in solution two for one hour per wash and store it in solution two at room temperature overnight in low light.Incubate the sample serially in 20, 40, 60, 80, and 100%methanol for one hour each at room temperature. Then incubate it in fresh 100%methanol overnight. On the next day, incubate the sample in freshly prepared 66%DCM in 33%methanol for three hours at room temperature with shaking.After three hours, incubate the sample in dibenzyl ether without shaking until it is clear. Then store it in dibenzyl ether until imaging. Obtain a 3D printer chamber and secure it to a microscope slide using epoxy.Place the sample in the square space in the middle of the chamber and completely fill the chamber with dibenzyl ether. Place a 0.17 millimeter thick cover slip over the chamber and apply pressure to ensure it is in full contact with the chamber walls. Then seal the edges using epoxy.Make sure to rotate the chamber to allow air bubbles to escape from the filling inlet. Fill the chamber with additional dibenzyl ether. Then seal the filling inlet with epoxy and allow it to cure.Observe the specimen using a confocal microscope system to perform a z-scan at four times magnification. The confocal image of hydrophobically-cleared tissue sample at four times magnification shows dense TH staining in the substantia nigra area, sparse TH neurons adjacent to the substantia nigra, and a dark black area of tissue lacking TH neurons. Typical morphology of a TH-positive neuron at 20 times magnification has a large soma and several branching processes.Whereas IBA1-stained microglia have small cell bodies and shorter extending processes. The ideal confocal image shows positive and dense TH staining in the substantia nigra area with suitable fluorescence gain. Examples of poor confocal images include an improperly focused image with too much fluorescent gain, a false positive staining with bright spots not in focus with the rest of the tissue, and a high background staining as a result of using a blocking serum that does not match with a secondary antibody.Positive CTB staining in the rat brain is shown here. The long thin fibers are afferent projections along the dopaminergic pathway. Colocalization of TH and CTB makes it possible to visualize the injection site in the nucleus accumbens area which appears as a densely fluorescent green circle.Colocalization of TH and CTB in the substantia nigra is shown here. The most important things to remember in attempting this procedure are to allow the sample plenty of time to incubate in all antibody solutions and plenty of time to fully clear before imaging. The sample should have limited exposure to air as this will damage the sample.This technique is highly versatile and can be used to investigate many different proteins of interest throughout different regions of the brain. The present technique helps pave the way for neuroscientists to investigate the rat brain on a circuit level which is essential for the study of brain as a whole system.

a-hydrophobic-tissue-clearing-method-for-rat-brain-tissue

Research

JoVE Journal

Neuroscience

Preparation of Mouse Brain Tissue for Immunoelectron Microscopy

Transmission electron microscopy (TEM) is extremely useful for visualizing microglial, oligodendrocytic, astrocytic, and neuronal subcellular compartments (dendrite, dendritic spine, axon, axon terminal, perikaryon), as well as their intracellular organelles and cytoskeleton, in the central nervous system at high spatial resolution. Combined with TEM, pre-embedding immunocytochemistry allows the discrimination of cellular elements with few distinctive features and identification criteria (e.g., microglial perikarya and processes, when using an antibody against the microglia-specific marker Iba1 (ionized calcium binding adaptor molecule 1; as presented here)), identifying the neurotransmitter contents of cellular elements (e.g., serotonergic) and their ultrastructural localization of soluble or membrane-bound proteins (e.g., 5 HT1A and EphA4 receptors). Here, we describe a protocol for transcardiac perfusion of mice with acrolein fixative, removal and sectioning of the brain, as well as immunoperoxidase-diaminobenzidine (DAB) staining, resin embedding, and ultrathin sectioning of the brain sections. Upon completion of these procedures, the immunostained material is ready for examination with TEM. When rigorously performed, this technique provides an excellent compromise between optimal ultrastructural preservation and immunocytochemical detection.

We describe a protocol for transcardiac perfusion of mice, removal and sectioning of the brain, as well as immunoperoxidase staining, resin embedding, and ultrathin sectioning of the brain sections. Upon completion of these procedures, the immunostained material is ready for examination with transmission electron microscopy.

Fare Beyin Dokusu Immunoelectron Mikroskopi için hazırlanması

Transmission electron microscopy (TEM) is extremely useful for visualizing microglial, oligodendrocytic, astrocytic, and neuronal subcellular compartments ...

Nörobilim

Chromatin Immunoprecipitation from Dorsal Root Ganglia Tissue following Axonal Injury

Axons in the central nervous system (CNS) do not regenerate while those in the peripheral nervous system (PNS) do regenerate 
to a limited extent after injury (Teng et al., 2006). It is recognized that transcriptional programs essential for neurite and axonal outgrowth are 
reactivated upon injury in the PNS (Makwana et al., 2005). However the tools available to analyze neuronal gene regulation in vivo are limited and 
often challenging.
The dorsal root ganglia (DRG) offer an excellent injury model system because both the CNS and PNS are innervated by a 
bifurcated axon originating from the same soma. The ganglia represent a discrete collection of cell bodies where all transcriptional events occur, 
and thus provide a clearly defined region of transcriptional activity that can be easily and reproducibly removed from the animal. Injury of nerve 
fibers in the PNS (e.g. sciatic nerve), where axonal regeneration does occur, should reveal a set of transcriptional programs that are distinct from 
those responding to a similar injury in the CNS, where regeneration does not take place (e.g. spinal cord). Sites for transcription factor binding, 
histone and DNA modification resulting from injury to either PNS or CNS can be characterized using chromatin immunoprecipitation (ChIP). 
Here, we describe a ChIP protocol using fixed mouse DRG tissue following axonal injury. This powerful combination provides a means for characterizing the pro-regeneration chromatin environment necessary for promoting axonal regeneration.

We present a method for chromatin immunoprecipitation from dorsal root ganglia tissue following axonal injury. The approach can be used to identify specific transcription factor binding sites and epigenetic modification of histone and DNA important for the regeneration of injured axons in both the peripheral and central nervous system.

Kromatin Aksonal Yaralanma Dorsal Kök Ganglia Doku Immunoprecipitation

Axons in the central nervous system (CNS) do not regenerate while those in the peripheral nervous system (PNS) do regenerate 
to a limited extent after ...

Intact Histological Characterization of Brain-implanted Microdevices and Surrounding Tissue

Research into the design and utilization of brain-implanted microdevices, such as microelectrode arrays, aims to produce clinically relevant devices that interface chronically with surrounding brain tissue. Tissue surrounding these implants is thought to react to the presence of the devices over time, which includes the formation of an insulating "glial scar" around the devices. However, histological analysis of these tissue changes is typically performed after explanting the device, in a process that can disrupt the morphology of the tissue of interest.
Here we demonstrate a protocol in which cortical-implanted devices are collected intact in surrounding rodent brain tissue. We describe how, once perfused with fixative, brains are removed and sliced in such a way as to avoid explanting devices. We outline fluorescent antibody labeling and optical clearing methods useful for producing an informative, yet thick tissue section. Finally, we demonstrate the mounting and imaging of these tissue sections in order to investigate the biological interface around brain-implanted devices.

Here we present a histological method for capturing, labeling, optically clearing, and imaging the intact brain tissue interface around chronically implanted microdevices in rodent brain tissue. Results from the techniques comprising this method are useful for understanding the impact of various penetrating brain-implants on their surrounding tissue.

Beyin-implante Microdevices ve Çevresi Doku Bozulmamış Histolojik Karakterizasyonu

Research  into the design and utilization of brain-implanted microdevices, such as  microelectrode arrays, aims to produce clinically relevant devices ...

Immunohistochemical Analysis in the Rat Central Nervous System and Peripheral Lymph Node Tissue Sections

Immunohistochemistry (IHC) provides highly specific, reliable and attractive protein visualization. Correct performance and interpretation of an IHC-based multicolor labeling is challenging, especially when utilized for assessing interrelations between target proteins in the tissue with a high fat content such as the central nervous system (CNS).
Our protocol represents a refinement of the standard immunolabeling technique particularly adjusted for detection of both structural and soluble proteins in the rat CNS and peripheral lymph nodes (LN) affected by neuroinflammation. Nonetheless, with or without further modifications, our protocol could likely be used for detection of other related protein targets, even in other organs and species than here presented.

We here present an optimized, detailed protocol for double immunostaining in formalin-fixed, paraffin-embedded rat central nervous system (CNS) and peripheral lymph node (LN) tissue sections.

Sıçan Santral Sinir Sistemi immunohistokimyasal Analizi ve Çevresel lenf nodu Doku Bölümler

Immunohistochemistry (IHC) provides highly specific, reliable and attractive protein visualization. Correct performance and interpretation of an IHC-based ...

Primer for Immunohistochemistry on Cryosectioned Rat Brain Tissue: Example Staining for Microglia and Neurons

Immunohistochemistry is a widely used technique for detecting the presence, location, and relative abundance of antigens in situ. This introductory level protocol describes the reagents, equipment, and techniques required to complete immunohistochemical staining of rodent brain tissue, using markers for microglia and neuronal elements as an example. Specifically, this paper is a step-by-step protocol for fluorescent visualization of microglia and neurons via immunohistochemistry for Iba1 and Pan-neuronal, respectively. Fluorescence double-labeling is particularly useful for the localization of multiple proteins within the same sample, providing the opportunity to accurately observe interactions between cell types, receptors, ligands, and/or the extracellular matrix in relation to one another as well as protein co-localization within a single cell. Unlike other visualization techniques, fluorescence immunohistochemistry staining intensity may decrease in the weeks to months following staining, unless appropriate precautions are taken. Despite this limitation, in many applications fluorescence double-labeling is preferred over alternatives such as 3,3&#39;-diaminobenzidine tetrahydrochloride (DAB) or alkaline phosphatase (AP), as fluorescence is more time efficient and allows for more precise differentiation between two or more markers. The discussion includes troubleshooting tips and advice to promote success.

This introductory level protocol describes the reagents, equipment, and techniques required to complete immunohistochemical staining of rodent brains, using markers for microglia and neuronal elements as an example.

Mikroglia ve nöronlar için örnek Boyama: Cryosectioned Rat Beyin Dokusu Üzerine İmmünohistokimya için Astar

Immunohistochemistry is a widely used technique for detecting the presence, location, and relative abundance of antigens in situ. This introductory level ...

Using Fluorescence Activated Cell Sorting to Examine Cell-Type-Specific Gene Expression in Rat Brain Tissue

The brain is comprised of four primary cell types including neurons, astrocytes, microglia and oligodendrocytes. Though they are not the most abundant cell type in the brain, neurons are the most widely studied of these cell types given their direct role in impacting behaviors. Other cell types in the brain also impact neuronal function and behavior via the signaling molecules they produce. Neuroscientists must understand the interactions between the cell types in the brain to better understand how these interactions impact neural function and disease. To date, the most common method of analyzing protein or gene expression utilizes the homogenization of whole tissue samples, usually with blood, and without regard for cell type. This approach is an informative approach for examining general changes in gene or protein expression that may influence neural function and behavior; however, this method of analysis does not lend itself to a greater understanding of cell-type-specific gene expression and the effect of cell-to-cell communication on neural function. Analysis of behavioral epigenetics has been an area of growing focus which examines how modifications of the deoxyribonucleic acid (DNA) structure impact long-term gene expression and behavior; however, this information may only be relevant if analyzed in a cell-type-specific manner given the differential lineage and thus epigenetic markers that may be present on certain genes of individual neural cell types. The Fluorescence Activated Cell Sorting (FACS) technique described below provides a simple and effective way to isolate individual neural cells for the subsequent analysis of gene expression, protein expression, or epigenetic modifications of DNA. This technique can also be modified to isolate more specific neural cell types in the brain for subsequent cell-type-specific analysis.

The goal of this protocol is to use the fluorescence activated cell sorting (FACS) technique to sort specific types of neural cells for subsequent analysis of cell-type-specific gene expression, epigenetic markers, and or protein expression.

Sıçan beyin dokusunda incelemek için THP kullanılarak hücre-tipi-spesifik gen ifadesi

The brain is comprised of four primary cell types including neurons, astrocytes, microglia and oligodendrocytes. Though they are not the most abundant ...

A Rat Model of Mild Intrauterine Hypoperfusion with Microcoil Stenosis

Intrauterine hypoperfusion/ischemia is one of the major causes of intrauterine/fetal growth restriction, preterm birth, and low birth weight. Most studies of this phenomenon have been performed in either models with severe intrauterine ischemia or models with gradient degree of intrauterine hypoperfusion. No study has been performed in a model on uniform mild intrauterine hypoperfusion (MIUH). Two models have been used for studies of MIUH: a model based on suture ligation of either side of the arterial arcade formed with the uterine and ovarian arteries, and a transient model based on clipping the bilateral ovarian arteries and aorta having patency. Those two rodent models of MIUH have some limitations, e.g., not all fetuses are subjected to MIUH, depending on their position in the uterine horn. In our MIUH model, all fetuses are subjected to a comparable level of intrauterine hypoperfusion. MIUH was achieved by mild stenosis of all four arteries feeding the uterus, i.e., the bilateral uterine and ovarian arteries.
Arterial stenosis was induced by metal microcoils wrapped around the feeding arteries. Producing arterial stenosis with microcoils allowed us to control, optimize, and reproduce decreased blood flow with very little inter-animal variability and a low mortality rate, thus enabling accurate evaluation. When microcoils with an inner diameter of 0.24 mm were used, the blood flow in both the placenta and fetus was mildly decreased (approximately 30% from the pre-stenosis level in the placenta). The offspring of our MIUH model clearly demonstrates long-lasting alterations in neurological, neuroanatomical and behavioral test results.

Mild intrauterine hypoperfusion was produced by artery stenosis with metal microcoils wrapped around the uterine and ovarian arteries in rats at embryonic day 17. This procedure produced prenatal hypoperfusion and intrauterine growth restriction.

Microcoil stenoz ile hafif intrauterin hipoperfüzyon fare modeli

Intrauterine hypoperfusion/ischemia is one of the major causes of intrauterine/fetal growth restriction, preterm birth, and low birth weight. Most studies ...

Novel Passive Clearing Methods for the Rapid Production of Optical Transparency in Whole CNS Tissue

Since the development of CLARITY, a bioelectrochemical clearing technique that allows for three-dimensional phenotype mapping within transparent tissues, a multitude of novel clearing methodologies including CUBIC (clear, unobstructed brain imaging cocktails and computational analysis), SWITCH (system-wide control of interaction time and kinetics of chemicals), MAP (magnified analysis of the proteome), and PACT (passive clarity technique), have been established to further expand the existing toolkit for the microscopic analysis of biological tissues. The present study aims to improve upon and optimize the original PACT procedure for an array of intact rodent tissues, including the whole central nervous system (CNS), kidneys, spleen, and whole mouse embryos. Termed psPACT (process-separate PACT) and mPACT (modified PACT), these novel techniques provide highly efficacious means of mapping cell circuitry and visualizing subcellular structures in intact normal and pathological tissues. In the following protocol, we provide a detailed, step-by-step outline on how to achieve maximal tissue clearance with minimal invasion of their structural integrity via psPACT and mPACT.

Here, we present two novel methodologies, psPACT and mPACT, for achieving maximal optical transparency and subsequent microscopic analysis of tissue vasculature in the intact rodent whole CNS.

Roman pasif optik şeffaflık bütün sinir dokusunda hızlı üretim için yöntemleri Temizleme

Since the development of CLARITY, a bioelectrochemical clearing technique that allows for three-dimensional phenotype mapping within transparent tissues, ...

Isolation of Cerebral Capillaries from Fresh Human Brain Tissue

Understanding blood-brain barrier function under physiological and pathophysiological conditions is critical for the development of new therapeutic strategies that hold the promise to enhance brain drug delivery, improve brain protection, and treat brain disorders. However, studying the human blood-brain barrier function is challenging. Thus, there is a critical need for appropriate models. In this regard, brain capillaries isolated from human brain tissue represent a unique tool to study barrier function as close to the human in vivo situation as possible. Here, we describe an optimized protocol to isolate capillaries from human brain tissue at a high yield and with consistent quality and purity. Capillaries are isolated from fresh human brain tissue using mechanical homogenization, density-gradient centrifugation, and filtration. After the isolation, the human brain capillaries can be used for various applications including leakage assays, live cell imaging, and immune-based assays to study protein expression and function, enzyme activity, or intracellular signaling. Isolated human brain capillaries are a unique model to elucidate the regulation of the human blood-brain barrier function. This model can provide insights into central nervous system (CNS) pathogenesis, which will help the development of therapeutic strategies for treating CNS disorders.

Isolated brain capillaries from human brain tissue can be used as a preclinical model to study barrier function under physiological and pathophysiological conditions. Here, we present an optimized protocol to isolate brain capillaries from fresh human brain tissue.

Yalıtım taze insan beyin dokusundan beyin kapiller

Understanding blood-brain barrier function under physiological and pathophysiological conditions is critical for the development of new therapeutic ...

Preparation of Newborn Rat Brain Tissue for Ultrastructural Morphometric Analysis of Synaptic Vesicle Distribution at Nerve Terminals

Our laboratory and many others have exploited the high resolving power of transmission electron microscopy to study the morphology and spatial organization of synaptic vesicles. In order to obtain high-quality electron micrographs that can yield the degree of morphological detail necessary for quantitative analysis of pre-synaptic vesicle distribution, optimal specimen preparation is critical. Chemical fixation is the first step in the process of specimen preparation, and of utmost importance to preserve fine ultrastructure. Vascular fixation with a glutaraldehyde-formaldehyde solution, followed by treatment of vibratome-sectioned specimens with osmium tetroxide, stabilizes the maximum number of molecules, especially proteins and lipids, and results in superior conservation of ultrastructure. Tissue is then processed with counterstaining, sequential dehydration and resin-embedding. En bloc staining with uranyl acetate (i.e., staining of vibratome-sectioned tissue before resin embedding) enhances endogenous contrast and stabilizes cell components against extraction during specimen processing. Contrast can be further increased by applying uranyl acetate as a post-stain on ultrathin sections. Double-staining of ultrathin sections with lead citrate after uranyl acetate treatment also improves image resolution, by intensifying electron-opacity of nucleic acid-containing structures through selective binding of lead to uranyl acetate. Transmission electron microscopy is a powerful tool for characterization of the morphological details of synaptic vesicles and quantification of their size and spatial organization in the terminal bouton. However, because it uses fixed tissue, transmission electron microscopy can only provide indirect information regarding living or evolving processes. Therefore, other techniques should be considered when the main objective is to study dynamic or functional aspects of synaptic vesicle trafficking and exocytosis.

We describe procedures for processing newborn rat brain tissue to obtain high-resolution electron micrographs for morphometric analysis of synaptic vesicle distribution at nerve terminals. The micrographs obtained with these methods can also be used to study the morphology of a number of other cellular components and their dimensional structural relationships.