Avustralya Nükleer Bilimi ve Mühendisliği Enstitüsü destek kabul edilmektedir. TCK AINSE ödül layık görüldü. Epigenomic Tıp Laboratuarı, Ulusal Sağlık ve Tıbbi Araştırma Konseyi (566.559) Avustralya tarafından desteklenmektedir. LM Melbourne Araştırma (University of Melbourne) ve Biyomedikal Görüntüleme CRC ek burs tarafından desteklenmektedir. Monash Micro Görüntüleme desteği (Dr Stephen Cody ve Iska Carmichael), bu iş için çok değerli idi.

<html> Hücre Hazırlık <ol><li> 37, epidermal büyüme faktörü, sığır hipofiz ekstresi ve 20 mg / ml gentamisin ile desteklenmiş ° C ve% 5 CO 2; İnsan keratinositler (FEP-1811) (Invitrogen K-SFM) keratinosit Serum Ücretsiz Orta yetiştirildiği. </li><li> Tripsin-EDTA (0.05% v / v) ile ayırarak, tek bir hücre süspansiyonu hazırlanmıştır </li><li> Hücreler 8-iyi Lab Tek II microchamber slaytlar ekilirler (10.000 hücrelerinin / iyi) ve slaytlar, 37 ° C&#39;de ve% 5 CO 2 3 gün inkübe edildi . </li></ol> Işınlama <ol><li> Hücreler 137 Cs kaynak (Nordion Uluslararası, ON, Kanada; 20.6 saniye / Gy Gammacell 1000 Elite ışınlama) kullanarak 2 Gy ile buz üzerinde ışınlanmış </li><li> Işınlanmamış kontrolü ve 2 Gy ışınlanmış hücreleri 37 ° C ve% 5 CO 2 &#39;de 1 saat inkübe edildi. </li></ol> Immünofloresan boyaması <ol><li> Medya kapalı uçlu ve hücreler başına 300μl PBS (w / o Ca 2 + veya Mg 2 +) ile yıkanmış ve 5 dakika boyunca bir orbital karıştırıcı döndürüldü. </li><li> Tampon kapalı uçlu ve paraformaldehid her bir kuyunun eklendi ve slaytlar için oda sıcaklığında 10 dakika inkübe edildi taze hazırlanmış% 4 (v / v) 100μl oldu. Tüm inkubasyon nemlendirilmiş bir boyama çukur yapıldı </li><li> Hücreler daha sonra PBS (w / o Ca 2 + ve Mg 2 +) ile yıkandı. 5 dakika için bir yörünge karıştırıcı bir Coplin kavanoz ve döndürülebilir Slaytlar yerleştirildi. Bu yıkama adımı iki kere daha tekrarlandı. </li><li> Tampon kapalı uçlu ve aşırı PBS hafifçe lekelenen. </li><li> Hücreler 100ml Triton X-100 (0.1% v / v) başına ve oda sıcaklığında 10 dakika inkübasyon kullanarak permeabilize. </li><li> Hücreler PBS ile yıkandı (w / o Ca 2 + ve Mg 2 +) adım 3 ve 4 yukarıda açıklandığı gibi. </li><li> Non-spesifik protein bağlanma, oda sıcaklığında ve 20 dakika inkübasyon başına 100 ml (% 1 v / v) BSA ile bloke edildi. </li><li> Aşırı BSA kapalı uçlu ve 100μl Birincil fare monoklonal anti-fosfor-H2AX histon antikor (% 1 BSA, 1:500 sulandırılmış; Millipore), oda sıcaklığında 1 saat inkübasyon için her kuyuya eklendi. </li><li> Hücreler PBS ile yıkandı (w / o Ca 2 + veya Mg 2 +), 3 ve 4 yukarıdaki adımları açıklanan ve ikincil antikor 100μl (Alexa Fluor 488 keçi anti-fare IgG ile inkübe% 1 BSA, 1:500 seyreltilmiş ; Invitrogen) karanlıkta, oda sıcaklığında 45 dakika boyunca iyi ortalama. (Antikor Seyreltilmiş prosedür boyunca karanlıkta tutulmuştur) </li><li> Hücreler PBS ile yıkandı (w / o Ca 2 + ve Mg 2 +) adım 3 ve 4 yukarıda açıklandığı gibi. Ancak, ışığa maruz folyo kullanılarak en aza indirildi. </li><li> De ortalama ve oda sıcaklığında 10 dakika inkübasyon, Nükleer counterstaining 100ml TOPRO3 (Invitrogen 1:500 seyreltilmiş) ile yapıldı </li><li> Hücreler PBS (w / o Ca 2 + ve Mg 2 +) ile yıkandı 10 yukarıda adımda açıklandığı gibi. </li><li> Odaları dikkatle slaytlar çıkarıldı, aşırı nem, lekelenen ve slaytlar kuru hava için izin verildi. </li><li> ALTIN ​​anti-fade çözüm (Invitrogen) uzatmak Bir damla başına eklendi ve slaytlar monte edildi (22x50 mm lamel) ve slayt kenarlarında herhangi bir aşırı sıvı lekelenen oldu. </li><li> Slaytları oje ile sızdırmazlık önce oda sıcaklığında bir 30 dakika daha karanlıkta tutulmuştur. </li><li> Slaytlar gecede 4 saklandı ° C analizden önce karanlıkta. </li></ol> Mikroskopi / Analiz <ol><li> (- Alexa Fluor 488 keçi anti-fare IgG γH2AX) ve (TOPRO 3) uzak kırmızı lazerler Zeiss LSM510 Meta Konfokal Microscpe standart GFP kullanarak görüntü elde etmek için kullanılır. Tipik olarak, 63 x immersiyon yağı objektif lens kullanılır. Görüntüler bir adım boyutu 0,5 mikron ile Z-serisi bir desen elde edilir. Çekirdekleri farklı düzlemlerde odakları mevcut kaybını en aza indirmek için bir adım boyutu 0,5 mikron seçildi. Analizi sırasında, bireysel uçakları deconvoluted ve odakları örtüşme (Top-şapka filtre uygulanan) en aza indirmek için azami Yansıtılan görüntüyü üretmek için yığılmış. </li><li> Metamorph (Moleküler Cihazlar, ABD) odaklarının sayısı analiz etmek için kullanılır oldu. Bu program arka plan dışlamak için eşik uygulandıktan sonra, her hücrede odaklarının sayısı quantitates. Bilgi, daha fazla analiz için bir Microsoft Excel kaydedilir. </li></ol><img src="/files/ftp_upload/1957/1957fig1.jpg" alt="Şekil 1" /> Şekil 1 γH2AX odakları (yeşil), tedavi edilmezse insan keratinositler ve 2 Gy ile ışınlanmış ve 37 1 saat daha inkübe hücrelerinde İmmünofloresan görselleştirme ° C,% 5 CO 2 . DNA TOPRO-3 (mavi) ile boyandı. Görüntüler Zeiss LSM 510 Meta Konfokal mikroskop kullanılarak elde edildi. Bar = 10 mm. e_content &quot;&gt; <img src="/files/ftp_upload/1957/1957fig2.jpg" alt="Şekil 2" /> Şekil 2, insan keratinositler ve 2 Gy ile ışınlanmış ve 37 1 saat daha inkübe hücrelerinde γH2AX odakları (yeşil) İmmünofloresan görselleştirme ° C,% 5 CO 2 . Görüntüler tüm odakları satın sağlamak için 0,5 mm Z-kesit (1-9) kullanarak Zeiss LSM 510 Meta Konfokal mikroskop kullanılarak elde edildi. Görüntüler daha sonra Metamorph kullanarak kantitatif için yığılmış. DNA TOPRO-3 (mavi) ile boyandı. Yığılmış γH2AX ve mavi görüntüleri görünüm için yığılmış. Bar = 10 mm.

<ol>
	<li>Rogakou, E. P., Boon, C., Redon, C., Bonner, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Megabase+chromatin+domains+involved+in+DNA+double-strand+breaks+in+vivo.">Megabase chromatin domains involved in DNA double-strand breaks in vivo.</a> J. Cell Biol. 146, 905-916 (1999).</li><li>Bonner, W. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Gamma+H2AX+and+cancer.">Gamma H2AX and cancer.</a> Nature Reviews Cancer. 8 (12), 957-967 (2008).</li><li>Savic, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Formation+of+Dynamic+[gamma]-H2AX+Domains+along+Broken+DNA+Strands+Is+Distinctly+Regulated+by+ATM+and+MDC1+and+Dependent+upon+H2AX+Densities+in+Chromatin.">Formation of Dynamic [gamma]-H2AX Domains along Broken DNA Strands Is Distinctly Regulated by ATM and MDC1 and Dependent upon H2AX Densities in Chromatin.</a> Molecular Cell. 34 (3), 298-310 (2009).</li><li>Downs, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Binding+of+chromatin-modifying+activities+to+phosphorylated+histone+H2A+at+DNA+damage+sites.">Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites.</a> Mol Cell. 16 (6), 979-990 (2004).</li><li>Chowdhury, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=[gamma]-H2AX+Dephosphorylation+by+Protein+Phosphatase+2A+Facilitates+DNA+Double-Strand+Break+Repair.">[gamma]-H2AX Dephosphorylation by Protein Phosphatase 2A Facilitates DNA Double-Strand Break Repair.</a> Molecular Cell. 20 (5), 801-809 (2005).</li><li>Nakada, S., Chen, G., Gingras, A., Durocher, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PP4+is+a+gamma+H2AX+phosphatase+required+for+recovery+from+the+DNA+damage+checkpoint.">PP4 is a gamma H2AX phosphatase required for recovery from the DNA damage checkpoint.</a> EMBO Rep. 9 (10), 1019-1026 (2008).</li><li>Altaf, M., Auger, A., Covic, M., C&#244;t&#233;, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Connection+between+histone+H2A+variants+and+chromatin+remodeling+complexes.">Connection between histone H2A variants and chromatin remodeling complexes.</a> Biochem Cell Biol. 87 (1), 35-50 (2009).</li><li>Kusch, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Acetylation+by+Tip60+Is+Required+for+Selective+Histone+Variant+Exchange+at+DNA+Lesions.">Acetylation by Tip60 Is Required for Selective Histone Variant Exchange at DNA Lesions.</a> Science. 306, 2084-2087 (2004).</li><li>Hurlin, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Progression+of+human+papillomavirus+type+18-immortalized+human+keratinocytes+to+a+malignant+phenotype.">Progression of human papillomavirus type 18-immortalized human keratinocytes to a malignant phenotype.</a> Proc Natl Acad Sci U S A. 88 (2), 570-574 (1991).</li><li>Dickey, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=H2AX:+functional+roles+and+potential+applications.">H2AX: functional roles and potential applications.</a> Chromosoma. , (2009).</li></ol>

(Γ-ışınları) iyonize radyasyon, hızla γH2AX odakları formu ve odaklar numaraları için aşağıdaki maruziyet 30-60 dakika 2 ila maksimum ulaşır. Bu nedenle, 1 saat ışınlama sonrası bir zaman noktasında ilk DSB oluşumunu yansıtmaktadır. Biz deneyimiz için klinik olarak anlamlı bir radyasyon dozu 2 Gy kullandık. Ancak, yöntem ilk DSB oluşumu tespiti için 4 Gy radyasyon dozları için kullanılır; odakları önemli bir örtüşme yüksek dozlarda doğru kantitatif engellemektedir. ΓH2...

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">	
		
		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>Keratinocyte-Serum Free Medium (K-SFM)</td>
<td>Media</td>
<td>Invitrogen</td>
<td>17005042</td>
<td>Keratinocyte media supplemented with human recombinant Epidermal Growth Factor 1-53 (EGF 1-53), and Bovine Pituitary Extract (BPE).</td>
</tr>
<tr>
<td>Lab Tek lI Chamber Slides (8-well)</td>
<td>Chamber Slides</td>
<td>Nunc Denmark</td>
<td>NUN154534</td>
<td>&nbsp;</td>
<tr>
<td>Coverslips (22x50mm)</td>
<td>Coverslips</td>
<td>Menzel-Gl&auml;ser</td>
<td>CS2250100</td>
<td>&nbsp;</td>
<tr>
<td>Bovine Serum Albumin (BSA)</td>
<td>&nbsp;</td>
<td>Sigma-Aldrich</td>
<td>A7906</td>
<td>BSA (1%) is used to block any non-specific antibody binding. Primary and secondary antibodies are diluted in BSA.</td>
</tr>
<tr>
<td>PBS (without Ca2+ and Mg2+)</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>17-517Q</td>
<td>&nbsp;</td>
<tr>
<td>0.5% Trypsin-EDTA x10</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>15400-054</td>
<td>Trypsin-EDTA (0.05%) used to detach cells from culture flasks.</td>
</tr>
<tr>
<td>Triton X-100</td>
<td>Reagent</td>
<td>Sigma-Aldrich</td>
<td>T8787</td>
<td>Triton X-100 (0.1%) used to permeabilise cells.</td>
</tr>
<tr>
<td>Paraformaldehyde</td>
<td>Reagent</td>
<td>Sigma-Aldrich</td>
<td>158127</td>
<td>Paraformaldehyde (4%) used to fix cells.</td>
</tr>
<tr>
<td>Mouse monoclonal anti-phospho histone-H2AX antibody</td>
<td>Primary Antibody</td>
<td>Millipore</td>
<td>16193</td>
<td>Dilution of primary antibody (1:500), in 1% BSA.</td>
</tr>
<tr>
<td>Alexa Fluor 488 goat anti-mouse IgG (H+L)</td>
<td>Secondary Antibody</td>
<td>Invitrogen</td>
<td>11029</td>
<td>Dilution of secondary antibody (1:500), in 1% BSA.</td>
</tr>
<tr>
<td>TOPRO3</td>
<td>DNA Stain</td>
<td>Invitrogen</td>
<td>T3605</td>
<td>DNA stain commonly used: 4,6-diamidino-2-phenylindole dihydrochloride (DAPI). Can only be used with microscopes with the appropriate excitation laser.</td>
</tr>
<tr>
<td>ProLong Gold</td>
<td>Anti-fade solution</td>
<td>Invitrogen</td>
<td>P36930</td>
<td>Refractive index of 1.42 at 20&deg;C.</td>
</tr>
<tr>
<td>Tissue Culture Flask, Vented Cap</td>
<td>Culture Flask</td>
<td>BD Falcon</td>
<td>353112</td>
<td>&nbsp;</td>
<tr>
<td>Tissue Culture Dish (150x25mm)</td>
<td>Petridish</td>
<td>BD Falcon</td>
<td>353025</td>
<td>&nbsp;</td>
<tr>
<td>Coplin Jar, glass</td>
<td>&nbsp;</td>
<td>Grale Scientific P/L</td>
<td>1771-OG</td>
<td>&nbsp;</td>
<tr>
<td>Staining Trough</td>
<td>&nbsp;</td>
<td>Grale Scientific P/L</td>
<td>V1991.99</td>
<td>&nbsp;</td>
<tr>
<td>Gammacell 1000 Elite Irradiator</td>
<td>Gamma Irradiator</td>
<td>Nordion International Inc.</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Zeiss LSM 510 Meta Confocal</td>
<td>Confocal Microscope</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<tr>
<td>Metamorph</td>
<td>Software for Imaging analysis</td>
<td>Molecular Devices, USA</td>
<td>&nbsp;</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>

quantification of &gamma;h2ax foci in response to ionising radiation

Endojen metabolik süreçleri ya da ya da dışsal kaynaklar tarafından indüklenen DNA çift iplikli sonları (DSBs), hayatta kalma ve genomik bütünlüğünün korunması açısından en kritik DNA lezyonlar vardır. DSBs indüksiyon erken bir cevap γH2AX oluşturan, son derece korunmuş C-terminal SQEY motifi, serin-139 kalıntı H2A histon varyant, H2AX fosforilasyon.<sup&gt; 1</sup&gt;. DSBs indüksiyonu takiben, H2AX hızla fosfatidil-inosito 3-kinaz (Pikk) proteinleri aile, ataksi telenjiektazi mutasyona uğramış (ATM), DNA-protein kinaz katalitik subunit ve ATM ve RAD3 ilgili fosforile (ATR)<sup&gt; 2</sup&gt;. Tipik olarak, sadece birkaç baz çifti (bp) kromatin, DNA hasarı sinyalizasyon ve onarımı konusunda değişiklikler önemi göz önüne alındığında, ancak, önemli bir sinyal amplifikasyonu var, bir DSB sorumlu tutulmaktadır. H2AX fosforilasyonu DSB başına toplam hücresel H2AX yaklaşık% 0.03 etkileyen, ağırlıklı olarak kromatin bitişik alanlarda ATM yayılır aracılı<sup&gt; 2,3</sup&gt;. Bu kolayca görüntülenebilmekte ve immünofloresan mikroskobu ile quantitated DSB ve ayrık γH2AX odaklarının oluşmasına sonuçları site çevreleyen kromatin ~ 2 MBP bölgeleri kapsayan yaklaşık 2000 H2AX molekülleri fosforilasyon karşılık gelen<sup&gt; 2</sup&gt;. DSB az γH2AX kaybı onarım yansıtır, ancak DSBs komple tamir tanımlar ne gibi bazı tartışmalar var, ancak her iki DNA ipliklerini rejoining yeterli olduğunu ileri sürülmüştür, o da öne sürülmüştür yeniden takiben eski haline orijinal sıkıştırma kromatin devlet gerekli<sup&gt; 4-8</sup&gt;. ΓH2AX disappearence en azından bir kısmını içerir fosfatazlar, fosfataz 2A ve fosfataz 4C tarafından Defosforilasyon<sup&gt; 5,6</sup&gt;. Ayrıca, tekrar dağıtılmasıyla γH2AX kaldırılması H2A.Z histon döviz içeren suçlanmıştır.<sup&gt; 7,8</sup&gt;. Önemlisi, γH2AX odakları kantitatif analizi, tıp ve nükleer araştırma uygulamaları geniş bir yol açmıştır. Burada ilk DNA hasarı γ-ışınlanmış yapışık insan keratinositler γH2AX odaklarının tespiti ve kantitatif değerlendirilmesi için en sık kullanılan immünofloresan yöntemi göstermektedir<sup&gt; 9</sup&gt;.

Watch this Scientific Journal Video about Quantification of Î³H2AX Foci in Response to Ionising Radiation at JoVE.com

Quantification of &amp;#947;H2AX Foci in Response to Ionising Radiation

Bir moleküler marker olarak γH2AX oluşumu kullanarak DNA çift iplikli çizgiler Niceleme radyasyon biyoloji paha biçilmez bir araç haline gelmiştir. Burada hücreler radyasyona maruz kaldıktan sonra γH2AX odakları ölçümü için immünofloresan testinin kullanımını göstermek.

İyonlaştırıcı Radyasyon Cevabı γH2AX Foci Kantitasyonu

DNA double-strand breaks (DSBs), which are induced by either endogenous metabolic processes or by exogenous sources, are one of the most critical DNA ...

quantification-of-h2ax-foci-in-response-to-ionising-radiation

Research

JoVE Journal

Biology

Quantification of &gamma;H2AX Foci in Response to Ionising Radiation

20.3K Görüntüleme.  The Alfred Medical Research and Education Precinct. Bir moleküler marker olarak γH2AX oluşumu kullanarak DNA çift iplikli çizgiler Niceleme radyasyon biyoloji paha biçilmez bir araç haline gelmiştir. Burada hücreler radyasyona maruz kaldıktan sonra γH2AX odakları ölçümü için immünofloresan testinin kullanımını göstermek.

Video: Quantification of &#947;H2AX Foci in Response to Ionising Radiation

Quantitation of &gamma;H2AX Foci in Tissue Samples

DNA double-strand breaks (DSBs) are particularly lethal and genotoxic lesions, that can arise either by endogenous (physiological or pathological) processes or by exogenous factors, particularly ionizing radiation and radiomimetic compounds. Phosphorylation of the H2A histone variant, H2AX, at the serine-139 residue, in the highly conserved C-terminal SQEY motif, forming &gamma;H2AX, is an early response to DNA double-strand breaks1. This phosphorylation event is mediated by the phosphatidyl-inosito 3-kinase (PI3K) family of proteins, ataxia telangiectasia mutated (ATM), DNA-protein kinase catalytic subunit and ATM and RAD3-related (ATR)2. Overall, DSB induction results in the formation of discrete nuclear &gamma;H2AX foci which can be easily detected and quantitated by immunofluorescence microscopy2. Given the unique specificity and sensitivity of this marker, analysis of &gamma;H2AX foci has led to a wide range of applications in biomedical research, particularly in radiation biology and nuclear medicine. The quantitation of &gamma;H2AX foci has been most widely investigated in cell culture systems in the context of ionizing radiation-induced DSBs. Apart from cellular radiosensitivity, immunofluorescence based assays have also been used to evaluate the efficacy of radiation-modifying compounds. In addition, &gamma;H2AX has been used as a molecular marker to examine the efficacy of various DSB-inducing compounds and is recently being heralded as important marker of ageing and disease, particularly cancer3. Further, immunofluorescence-based methods have been adapted to suit detection and quantitation of &gamma;H2AX foci ex vivo and in vivo4,5. Here, we demonstrate a typical immunofluorescence method for detection and quantitation of &gamma;H2AX foci in mouse tissues.

Quantitation of &amp;#947;H2AX Foci in Tissue Samples

Quantitation of DNA double-strand breaks on the basis of &gamma;H2AX foci has become an invaluable tool, particularly in radiation biology, for the evaluation of tissue radiosensitivity and effects of radiation modifying compounds. Here we demonstrate the use of an immunofluorescence assay for quantitation of &gamma;H2AX foci in tissue samples.

Doku Örnekleri γH2AX Foci kantitasyonu

DNA double-strand breaks (DSBs) are particularly lethal and genotoxic lesions, that can arise either by endogenous (physiological or pathological) ...

Biyoloji

Evaluation of the Spatial Distribution of &gamma;H2AX following Ionizing Radiation

An early molecular response to DNA double-strand breaks (DSBs) is phosphorylation of the Ser-139 residue within the terminal SQEY motif of the histone H2AX1,2. This phosphorylation of H2AX is mediated by the phosphatidyl-inosito 3-kinase (PI3K) family of proteins, ataxia telangiectasia mutated (ATM), DNA-protein kinase catalytic subunit and ATM and RAD3-related (ATR)3. The phosphorylated form of H2AX, referred to as &gamma;H2AX, spreads to adjacent regions of chromatin from the site of the DSB, forming discrete foci, which are easily visualized by immunofluorecence microscopy3. Analysis and quantitation of &gamma;H2AX foci has been widely used to evaluate DSB formation and repair, particularly in response to ionizing radiation and for evaluating the efficacy of various radiation modifying compounds and cytotoxic compounds4.
Given the exquisite specificity and sensitivity of this de novo marker of DSBs, it has provided new insights into the processes of DNA damage and repair in the context of chromatin. For example, in radiation biology the central paradigm is that the nuclear DNA is the critical target with respect to radiation sensitivity. Indeed, the general consensus in the field has largely been to view chromatin as a homogeneous template for DNA damage and repair. However, with the use of &gamma;H2AX as molecular marker of DSBs, a disparity in &gamma;-irradiation-induced &gamma;H2AX foci formation in euchromatin and heterochromatin has been observed5-7. Recently, we used a panel of antibodies to either mono-, di- or tri- methylated histone H3 at lysine 9 (H3K9me1, H3K9me2, H3K9me3) which are epigenetic imprints of constitutive heterochromatin and transcriptional silencing and lysine 4 (H3K4me1, H3K4me2, H3K4me3), which are tightly correlated actively transcribing euchromatic regions, to investigate the spatial distribution of &gamma;H2AX following ionizing radiation8. In accordance with the prevailing ideas regarding chromatin biology, our findings indicated a close correlation between &gamma;H2AX formation and active transcription9. Here we demonstrate our immunofluorescence method for detection and quantitation of &gamma;H2AX foci in non-adherent cells, with a particular focus on co-localization with other epigenetic markers, image analysis and 3D-modeling.

Evaluation of the Spatial Distribution of &amp;#947;H2AX following Ionizing Radiation

Microscopic analysis of &gamma;H2AX foci, which form following the phosphorylation of H2AX at Ser-139 in response to DNA double-strand breaks, has become an invaluable tool in radiation biology. Here we used an antibody to mono-methylated histone H3 at lysine 4 as an epigenetic marker of actively transcribing euchromatin, to evaluate the spatial distribution of radiation-induced &gamma;H2AX formation within the nucleus.

Radyasyondan aşağıdaki γH2AX Mekansal Dağılımı Değerlendirilmesi

An early molecular response to DNA double-strand breaks (DSBs) is phosphorylation of the Ser-139 residue within the terminal SQEY motif of the histone ...

Two- and Three-Dimensional Live Cell Imaging of DNA Damage Response Proteins

Double-strand breaks (DSBs) are the most deleterious DNA lesions a cell can encounter. If left unrepaired, DSBs harbor great potential to generate mutations and chromosomal aberrations1. To prevent this trauma from catalyzing genomic instability, it is crucial for cells to detect DSBs, activate the DNA damage response (DDR), and repair the DNA. When stimulated, the DDR works to preserve genomic integrity by triggering cell cycle arrest to allow for repair to take place or force the cell to undergo apoptosis. The predominant mechanisms of DSB repair occur through nonhomologous end-joining (NHEJ) and homologous recombination repair (HRR) (reviewed in2). There are many proteins whose activities must be precisely orchestrated for the DDR to function properly. Herein, we describe a method for 2- and 3-dimensional (D) visualization of one of these proteins, 53BP1.
The p53-binding protein 1 (53BP1) localizes to areas of DSBs by binding to modified histones3,4, forming foci within 5-15 minutes5. The histone modifications and recruitment of 53BP1 and other DDR proteins to DSB sites are believed to facilitate the structural rearrangement of chromatin around areas of damage and contribute to DNA repair6. Beyond direct participation in repair, additional roles have been described for 53BP1 in the DDR, such as regulating an intra-S checkpoint, a G2/M checkpoint, and activating downstream DDR proteins7-9. Recently, it was discovered that 53BP1 does not form foci in response to DNA damage induced during mitosis, instead waiting for cells to enter G1 before localizing to the vicinity of DSBs6. DDR proteins such as 53BP1 have been found to associate with mitotic structures (such as kinetochores) during the progression through mitosis10.
In this protocol we describe the use of 2- and 3-D live cell imaging to visualize the formation of 53BP1 foci in response to the DNA damaging agent camptothecin (CPT), as well as 53BP1's behavior during mitosis. Camptothecin is a topoisomerase I inhibitor that primarily causes DSBs during DNA replication. To accomplish this, we used a previously described 53BP1-mCherry fluorescent fusion protein construct consisting of a 53BP1 protein domain able to bind DSBs11. In addition, we used a histone H2B-GFP fluorescent fusion protein construct able to monitor chromatin dynamics throughout the cell cycle but in particular during mitosis12. Live cell imaging in multiple dimensions is an excellent tool to deepen our understanding of the function of DDR proteins in eukaryotic cells.

This protocol describes a method for visualizing a DNA double-strand break signaling protein activated in response to DNA damage as well as its localization during mitosis.

DNA Hasarı Tepki Proteinler İki ve Üç Boyutlu Canlı Hücre Görüntüleme

Double-strand breaks (DSBs) are the most deleterious DNA lesions a cell can encounter. If left unrepaired, DSBs harbor great potential to generate ...

Measuring Glutathione-induced Feeding Response in Hydra

Hydra is among the most primitive organisms possessing a nervous system and chemosensation for detecting reduced glutathione (GSH) for capturing the prey. The movement of prey organisms causes mechanosensory discharge of the stinging cells called nematocysts from hydra, which are inserted into the prey. The feeding response in hydra, which includes curling of the tentacles to bring the prey towards the mouth, opening of the mouth and consequent engulfing of the prey, is triggered by GSH present in the fluid released from the injured prey. To be able to identify the molecular mechanism of the feeding response in hydra which is unknown to date, it is necessary to establish an assay to measure the feeding response. Here, we describe a simple method for the quantitation of the feeding response in which the distance between the apical end of the tentacle and mouth of hydra is measured and the ratio of such distance before and after the addition of GSH is determined. The ratio, called the relative tentacle spread, was found to give a measure of the feeding response. This assay was validated using a starvation model in which starved hydra show an enhanced feeding response in comparison with daily fed hydra.

Here we describe a simple assay for the quantification of the feeding response in hydra induced by the reduced form of glutathione. This assay relies on measuring the distance between the apical end of the tentacle and mouth of hydra.

Hydra Glutatyon kaynaklı Besleme Tepki Ölçüm

Hydra is among the most primitive organisms possessing a nervous system and chemosensation for detecting reduced glutathione (GSH) for capturing the prey. ...

Examination of Proteins Bound to Nascent DNA in Mammalian Cells Using  BrdU-ChIP-Slot-Western Technique

Histone deacetylases 1 and 2 (HDAC1,2) localize to the sites of DNA replication. In the previous study, using a selective inhibitor and a genetic knockdown system, we showed novel functions for HDAC1,2 in replication fork progression and nascent chromatin maintenance in mammalian cells. Additionally, we used a BrdU-ChIP-Slot-Western technique that combines chromatin immunoprecipitation (ChIP) of bromo-deoxyuridine (BrdU)-labeled DNA with slot blot and Western analyses to quantitatively measure proteins or histone modification associated with nascent DNA.
Actively dividing cells were treated with HDAC1,2 selective inhibitor or transfected with siRNAs against Hdac1 and Hdac2 and then newly synthesized DNA was labeled with the thymidine analog bromodeoxyuridine (BrdU). The BrdU labeling was done at a time point when there was no significant cell cycle arrest or apoptosis due to the loss of HDAC1,2 functions. Following labeling of cells with BrdU, chromatin immunoprecipitation (ChIP) of histone acetylation marks or the chromatin-remodeler was performed with specific antibodies. BrdU-labeled input DNA and the immunoprecipitated (or ChIPed) DNA was then spotted onto a membrane using the slot blot technique and immobilized using UV. The amount of nascent DNA in each slot was then quantitatively assessed using Western analysis with an anti-BrdU antibody. The effect of loss of HDAC1,2 functions on the levels of newly synthesized DNA-associated histone acetylation marks and chromatin remodeler was then determined by normalizing the BrdU-ChIP signal obtained from the treated samples to the control samples.

In this protocol, we describe a novel BrdU-ChIP-Slot-Western technique to examine proteins and histone modifications associated with newly synthesized or nascent DNA.

Memeli Hücrelerde Nascent DNA Bound Proteinlerin incelenmesi BrdU ChIP-Slot-Batı Tekniği

Histone deacetylases 1 and 2 (HDAC1,2) localize to the sites of DNA replication. In the previous study, using a selective inhibitor and a genetic ...

High Resolution Quantification of Crystalline Cellulose Accumulation in Arabidopsis Roots to Monitor Tissue-specific Cell Wall Modifications

Plant cells are surrounded by a cell wall, the composition of which determines their final size and shape. The cell wall is composed of a complex matrix containing polysaccharides that include cellulose microfibrils that form both crystalline structures and cellulose chains of amorphous organization. The orientation of the cellulose fibers and their concentrations dictate the mechanical properties of the cell. Several methods are used to determine the levels of crystalline cellulose, each bringing both advantages and limitations. Some can distinguish the proportion of crystalline regions within the total cellulose. However, they are limited to whole-organ analyses that are deficient in spatiotemporal information. Others relying on live imaging, are limited by the use of imprecise dyes. Here, we report a sensitive polarized light-based system for specific quantification of relative light retardance, representing crystalline cellulose accumulation in cross sections of Arabidopsis thaliana roots. In this method, the cellular resolution and anatomical data are maintained, enabling direct comparisons between the different tissues composing the growing root. This approach opens a new analytical dimension, shedding light on the link between cell wall composition, cellular behavior and whole-organ growth.

High Resolution Quantification of Crystalline Cellulose Accumulation in Arabidopsis Roots to Monitor Tissue-specific Cell Wall Modifications

Crystalline cellulose is an important constituent of the plant cell wall. However, its quantification at a cellular resolution is technically challenging. Here, we report the use of polarized light technology and root cross sections to obtain information of cell wall composition at a spatiotemporal resolution.

Kristalin Selüloz Birikimin Yüksek Çözünürlüklü Niceleme<em&gt; Arabidopsis</em&gt; Kökler Doku spesifik Hücre Duvarı Değişiklikler Monitör

Plant cells are surrounded by a cell wall, the composition of which determines their final size and shape. The cell wall is composed of a complex matrix ...

Methods to Classify Cytoplasmic Foci as Mammalian Stress Granules

Cells are often challenged by sudden environmental changes. Stress Granules (SGs), cytoplasmic ribonucleoprotein complexes that form in cells exposed to stress conditions, are implicated in various aspects of cell metabolism and survival. SGs modulate cellular signaling pathways, post-transcriptional gene expression, and stress response programs. The formation of these mRNA-containing granules is directly connected to cellular translation. SG assembly is triggered by inhibited translation initiation, and SG disassembly is promoted by translation activation or by inhibited translation elongation. This relationship is further highlighted by SG composition. Core SG components are stalled translation pre-initiation complexes, mRNA, and selected RNA-binding Proteins (RBPs). The purpose of SG assembly is to conserve cellular energy by sequestering translationally stalled housekeeping mRNAs, allowing for the enhanced translation of stress-responsive proteins. In addition to the core constituents, such as stalled translation preinitiation complexes, SGs contain a plethora of other proteins and signaling molecules. Defects in SG formation can impair cellular adaptation to stress and can thus promote cell death. SGs and similar RNA-containing granules have been linked to a number of human diseases, including neurodegenerative disorders and cancer, leading to the recent interest in classifying and defining RNA granule subtypes. This protocol describes assays to characterize and quantify mammalian SGs.

Stress Granules (SGs) are nonmembranous cytoplasmic structures that form in cells exposed to a variety of stresses. SGs contain mRNAs, RNA-binding proteins, small ribosomal subunits, translation-related factors, and various cell signaling proteins. This protocol describes a workflow that uses several experimental approaches to detect, characterize, and quantify bona fide SGs.

Sitoplazmik Odakları Memeli Stres Granülleri Olarak Sınıflandırma Yöntemleri

Cells are often challenged by sudden environmental changes. Stress Granules (SGs), cytoplasmic ribonucleoprotein complexes that form in cells exposed to ...

Intestinal Epithelial Regeneration in Response to Ionizing Irradiation

The intestinal epithelium consists of a single layer of cells yet contains multiple types of terminally differentiated cells, which are generated by the active proliferation of intestinal stem cells located at the bottom of intestinal crypts. However, during events of acute intestinal injury, these active intestinal stem cells undergo cell death. Gamma irradiation is a widely used colorectal cancer treatment, which, while therapeutically efficacious, has the side effect of depleting the active stem cell pool. Indeed, patients frequently experience gastrointestinal radiation syndrome while undergoing radiotherapy, in part due to active stem cell depletion. The loss of active intestinal stem cells in intestinal crypts activates a pool of typically quiescent reserve intestinal stem cells and induces dedifferentiation of secretory and enterocyte precursor cells. If not for these cells, the intestinal epithelium would lack the ability to recover from radiotherapy and other such major tissue insults. New advances in lineage-tracing technologies allow tracking of the activation, differentiation, and migration of cells during regeneration and have been successfully employed for studying this in the gut. This study aims to depict a method for the analysis of cells within the mouse intestinal epithelium following radiation injury.

The gastrointestinal tract is one of the most sensitive organs to injury upon radiotherapeutic cancer treatments. It is simultaneously an organ system with one of the highest regenerative capacities following such insults. The presented protocol describes an efficient method to study the regenerative capacity of the intestinal epithelium.

İyonlaştırıcı Işınlamaya Yanıt Olarak Bağırsak Epitelyal Rejenerasyonu

The intestinal epithelium consists of a single layer of cells yet contains multiple types of terminally differentiated cells, which are generated by the ...

Decellularizasyon Yoluyla İskelet Kası Yağ İnfiltrasyonunun Miktar Tayini

Decellularization-Based Quantification of Skeletal Muscle Fatty Infiltration

Fatty infiltration is the accumulation of adipocytes between myofibers in skeletal muscle and is a prominent feature of many myopathies, metabolic disorders, and dystrophies. Clinically in human populations, fatty infiltration is assessed using noninvasive methods, including computed tomography (CT), magnetic resonance imaging (MRI), and ultrasound (US). Although some studies have used CT or MRI to quantify fatty infiltration in mouse muscle, costs and insufficient spatial resolution remain challenging. Other small animal methods utilize histology to visualize individual adipocytes; however, this methodology suffers from sampling bias in heterogeneous pathology. This protocol describes the methodology to qualitatively view and quantitatively measure fatty infiltration comprehensively throughout intact mouse muscle and at the level of individual adipocytes using decellularization. The protocol is not limited to specific muscles or specific species and can be extended to human biopsy. Additionally, gross qualitative and quantitative assessments can be made with standard laboratory equipment for little cost, making this procedure more accessible across research laboratories.

Yazar Spotlight: İskelet Kası Yağ İnfiltrasyonunun Decellularizasyona Dayalı Miktar Tayini  

The present study describes decellularization-based methodologies for visualizing and quantifying intramuscular adipose tissue (IMAT) deposition through intact muscle volume, as well as quantifying metrics of individual adipocytes that comprise IMAT.

Methods Article

İyonlaştırıcı Radyasyon Cevabı γH2AX Foci Kantitasyonu