我々は、彼らのコラボレーションのための臨床病理学、ウィーン、オーストリアの大学の研究所で教授Dontscho Kerjaschki、コリーナマイルホーファーとシグルドリーガーに感謝。

細胞の培養<ol><li>グルタミンとF - 12ハムの培地私は10％ウシ胎児血清、50 U / mlペニシリン、および50μg/ mlの硫酸ストレプトマイシン（Invitrogen）を含むの標準的な細胞培養の手順を使用して、チャイニーズハムスター卵巣細胞（CHO - K1）を成長する。 </li><li>無血清培地に培地を交換する。 CyDye DIGEフルーアと異なる時間点Cy3またはCy5最小限の色素（以下、節の細胞表面のラベルを参照）にあった細胞表面タンパク質にラベルを付けます。 </li><li> CyDye DIGEフルーアCy2と、各時点とラベルからの細胞のプールが同数。それぞれの2 - Dゲルのための内部標準としてこれらを使用してください。 </li><li>実験の大半は、CHO - K1細胞で行うことができますが、マウス胚線維芽細胞（3T3 L1）とマウスの腹水リンパ腫リンパ芽球（EL4）も（データは示さず）が使用できます。 </li><li>グルタミンIIを含むDMEM培地での後者の2つの種類の細胞を成長させる、しかし、そうでない場合は、CHO - K1細胞に使用する同一の条件を使用してください。 </li></ol>細胞表面のラベリング<ol><li>慎重に数えて、5〜10 x106細胞のアリコートに分割し、非酵素的に接着細胞を切り離します。懸濁液中で増殖する細胞の場合は、切り離し手順を省略します。 </li><li> 5分間、約800 × gで細胞懸濁液を遠心してください。培地を含む上清を取り除く。 </li><li> 1ミリリットルの氷冷ハンクス平衡塩溶液（HBSS）pH8.5中でresuspendionでペレットを洗浄してください。 4 800 XG℃で2分間で遠心分離。 </li><li>上清を除去し、200μlの氷冷標識バッファー（HBSS pHは8.5、1 Mの尿素）で細胞ペレットを再懸濁します。 </li><li>暗所で氷上で20分間、600 pmolのCyDye DIGEフルーア最小限の色素との完全な細胞にラベルを付けます。 </li><li>リジン20μlの10mMのを加えて反応をクエンチ。 10分間インキュベートする。 </li><li> 4 800 × gで遠心分離℃で2分間に続いて500μlのHBSS pHを7.4に再懸濁によって二回表面標識細胞を洗う。 </li></ol>細胞溶解と分画<ol><li> 150μlの冷溶解バッファー（7 M尿素、2 Mチオ尿素、4％CHAPS、30mMのトリス、5mMの酢酸マグネシウムのpH 8.5）で表面標識細胞を溶解する。時々ボルテックスしながら少なくとも1時間氷上にしておきます。 </li><li> 4℃で10 000 × gでライセートを遠心℃で5分間。上清を新しいチューブに移す。このサンプルは、すべての細胞タンパク質を含有する非画したサンプルです。 </li><li>並行して、前の2次元ゲル電気泳動への膜と細胞質分画に（膜分画キットを使用して、Pierce）を分画するし、上記のように、細胞ペレットを洗浄する。膜画分は、内部と細胞表面の膜タンパク質が含まれています。 </li><li>比較のために、標準的なEttan DIGEの手順3を実行し、溶解、ラベル、および、最終的に、細胞を分画する。 Dクワントキット（GEヘルスケア） - 2を用いてサンプル中のタンパク質濃度を決定する。 </li></ol> 2次元電気泳動<ol><li>イモビのDryStripゲル、イモビDryStrip Reswellingトレイ、一晩450μlのDeStreakの補液で24センチメートル（0.5％、IPGバッファー）を用いてpH 3 - 11NL（24センチ）再水和。 </li><li>マニホールドの陽極カップローディングでDryStripゲルをイモビ、指示に従ってEttan IPGphor II IEF Systemを使用して等電点電気泳動（IEF）を実行するCyDye標識サンプル（50μgの総タンパク質量に相当）適用されます。 </li><li> IEF後、大（26 × 20センチ）12.5％ポリアクリルアミドゲル（SDS - PAGE）上の二つの手順と場所でストリップを平衡化します。 0.5％アガロース（ブロモフェノールブルーを含むバッファを実行しているの）とのオーバーレイ。色素フロントがゲルの底に達するまで30分間、5 W /ゲルで、その後15 W /ゲルでEttan DALTtwelve大きな垂直軸システムを用いて2次元電気泳動を実行します。 </li></ol>イメージングとデータ解析<ol><li> 2次元電気泳動を完了した後、台風9410可変モードのイメージャを使用してCy2と、Cy3またはCy5用ゲルをスキャン。 </li><li>膜画分、細胞質分画、およびDeCyder 2次元差分解析ソフトウェア4を使用して非画した試料からスポットマップを比較する。 </li></ol>後染色<ol><li>イメージング後、銀は標準的な手順5にしたがってゲルを染色。 </li></ol>タンパク質の同定<ol><li> 、収穫の成長、などの非画したサンプルのため、上記の分取量（10 x106 CHO細胞から約1 mgの総タンパク質）の細胞を、洗浄し、溶解する。スパイクとしてCy5標識細胞表面標識サンプル（上記参照）を使用し、そしてタンパク質の非標識取量と一緒に適用されます。 </li><li>上記のような2次元電気泳動を行うが、今回は、aplly 600μgのラベルの付いていないセルは、アノードカップのアプリケーションによってスパイクラベル付け50μgの細胞表面と一緒にライセート。正しいスポットピッキングを可能にするために、基準マーカを使用して、となる配置提言3に記載のゲルキャスティングの前にガラス板をトゥイーン。 </li><li>ディープパープルの全タンパク質染色3を使って総タンパク質の染色をCy5で細胞表面のスポットのマップを、得るためにCy5をチャネルでゲルをスキャンします。 </li><li> DeCyder 2次元ソフトウェアを使用して2つのスポットのマップを一緒に一致させるとCy 5標識細胞表面タンパク質に対応する全てのスポットのピックリストを作成します。 Ettanのスポット処理ステーションを使用して細胞表面タンパク質を選んで、ゲルプラグから抽出し、EttanのDigesterを使ってtrypsinate。 MALDI - TOF質量分析法を用いて識別する。 </li></ol> 表1。Ettan DIGEの実験は図1の細胞表面タンパク質標識プロトコールに従ってラベル血清枯渇細胞からサ ​​ンプルを用いて行った。 <table style="width: 517px; height: 139px;" border="1" cellspacing="0" cellpadding="0"><tbody><tr><td style="text-align:center; font-weight:bold">サンプル</td><td style="text-align:center; font-weight:bold">血清枯渇の時間</td><td style="text-align:center; font-weight:bold"> CyDyeでLabelled </td><td style="text-align:center; font-weight:bold">ゲル番号</td></tr><tr><td style="text-align:center;"> 1 </td><td style="text-align:center;"> - </td><td style="text-align:center;"> CY 3、CY 2 </td><td style="text-align:center;"> 1 </td></tr><tr><td style="text-align:center;"> 2 </td><td style="text-align:center;"> 30分</td><td style="text-align:center;"> CY 5、CY 2 </td><td style="text-align:center;"> 1 </td></tr><tr><td style="text-align:center;"> 3 </td><td style="text-align:center;"> 2時間</td><td style="text-align:center;"> CY 3、CY 2 </td><td style="text-align:center;"> 2 </td></tr><tr><td style="text-align:center;"> 4 </td><td style="text-align:center;"> 4時間</td><td style="text-align:center;"> CY 5、CY 2 </td><td style="text-align:center;"> 2 </td></tr><tr><td style="text-align:center;"> 5 </td><td style="text-align:center;"> 16時間</td><td style="text-align:center;"> CY 5、CY 2 </td><td style="text-align:center;"> 3 </td></tr></tbody></table>

<ol>
	<li>Jang, J. H., Hanash, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Profiling+of+the+cell+surface+proteome.">Profiling of the cell surface proteome.</a> Proteomics. 3, 1947-1954 (2003).</li><li>Shin, B. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Global+profiling+of+the+cell+surface+proteome+of+cancer+cells+uncovers+an+abundance+of+proteins+with+chaperone+function.">Global profiling of the cell surface proteome of cancer cells uncovers an abundance of proteins with chaperone function.</a> J Biol Chem. 9, 7607-7616 (2003).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Ettan+DIGE+System+User+Manual.">Ettan DIGE System User Manual.</a> GE Healthcare user manual 18-1164-40. , (2006).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DeCyder+2-D+Differential+Analysis+Software+v+6.0.+GE+Healthcare+data+file+11-0011-98+Edition+AA.">DeCyder 2-D Differential Analysis Software v 6.0. GE Healthcare data file 11-0011-98 Edition AA.</a> , (2004).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=2-D+Electrophoresis+using+immobilized+pH+gradients,+principles+and+methods.">2-D Electrophoresis using immobilized pH gradients, principles and methods.</a> GE Healthcare handbook 80-6429-60 Edition AB. , (2002).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CyDye+DIGE+fluors+and+labeling+kits.+GE+Healthcare+data+file+18-1164-84+Edition+AB.">CyDye DIGE fluors and labeling kits. GE Healthcare data file 18-1164-84 Edition AB.</a> , (2003).</li><li>Mayrhofer, C., Krieger, S., Allmaier, G., Kerjaschki, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DIGE+compatible+labeling+of+surface+proteins+on+vital+cells+in+vitro+and+in+vivo.">DIGE compatible labeling of surface proteins on vital cells in vitro and in vivo.</a> Proteomics. 2, 579-5785 (2006).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selective+labeling+of+cell-surface+proteins+using+CyDye+DIGE+Fluor+minimal+dyes.+GE+Healthcare+Application+Note+11-0033-92+Edition+AB.">Selective labeling of cell-surface proteins using CyDye DIGE Fluor minimal dyes. GE Healthcare Application Note 11-0033-92 Edition AB.</a> , (2005).</li></ol>

タンパク質濃度 twoラベリングワークフローの概要を図1に示されています。細胞表面タンパク質標識プロトコールに従ってラベル際に細胞がまだそのままなので、唯一の細胞表面タンパク質は、染料にさらされている。細胞内部だけでなく外部の標識とタンパク質が（図1）ラベルが付いている前に、標準的なEttan DIGEプロトコールでは、細胞を溶解している。細胞表面タン?...

<!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>CyDye DIGE Kit, 2 nmol</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>28-9345-30</td>
<td>&nbsp;</td>
<tr>
<td>2-D Quant Kit</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>80-6484-51</td>
<td>&nbsp;</td>
<tr>
<td>IPG Buffer pH 3-11NL</td>
<td>Reagent</td>
<td>GE Heallthcare</td>
<td>17-6004-40</td>
<td>&nbsp;</td>
<tr>
<td>Immobiline DryStrip pH 3-11NL, 24 cm</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-6003-77</td>
<td>&nbsp;</td>
<tr>
<td>IPGbox</td>
<td>Tool</td>
<td>GE Healthcare</td>
<td>28-9334-65</td>
<td>&nbsp;</td>
<tr>
<td>IPGbox kit</td>
<td>Tool</td>
<td>GE Healthcare</td>
<td>28-9334-92</td>
<td>&nbsp;</td>
<tr>
<td>DeStreak Rehydration solution</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-6003-19</td>
<td>&nbsp;</td>
<tr>
<td>Immobiline DryStrip Cover Fluid</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1335-01</td>
<td>&nbsp;</td>
<tr>
<td>Ettan IPGphor 3 IEF Unit</td>
<td>Instrument</td>
<td>GE Healthcare</td>
<td>11-0033-64</td>
<td>&nbsp;</td>
<tr>
<td>Ettan IPGphor Manifold</td>
<td>Instrument component</td>
<td>GE Healthcare</td>
<td>80-6498-38</td>
<td>&nbsp;</td>
<tr>
<td>Ettan DALTtwelve Gel Caster </td>
<td>Tool</td>
<td>GE Healthcare</td>
<td>80-6467-22</td>
<td>&nbsp;</td>
<tr>
<td>Ettan DALTtwelve Separation Unit and Power Supply/Control Unit</td>
<td>Instrument</td>
<td>GE Healthcare</td>
<td>80-6466-46</td>
<td>230 V unit: 80-6466-27</td>
</tr>
<tr>
<td>Typhoon 9410 Variable Mode Imager</td>
<td>Instrument</td>
<td>GE Healthcare</td>
<td>63-0055-81</td>
<td>&nbsp;</td>
<tr>
<td>Ettan Spot Picker</td>
<td>Instrument</td>
<td>GE Healthcare</td>
<td>18-1145-28</td>
<td>&nbsp;</td>
<tr>
<td>Ettan Digester</td>
<td>Instrument</td>
<td>GE Healthcare</td>
<td>18-1142-68</td>
<td>&nbsp;</td>
<tr>
<td>Ettan Spotter</td>
<td>Instrument</td>
<td>GE Healthcare</td>
<td>18-1142-67</td>
<td>&nbsp;</td>
<tr>
<td>Ettan MALDI-TOF</td>
<td>Instrument</td>
<td>GE Healthcare</td>
<td>18-1142-33</td>
<td>&nbsp;</td>
<tr>
<td>DeCyder 2-D Differential Analysis Software</td>
<td>Other</td>
<td>GE Healthcare</td>
<td>28-4012-01</td>
<td>&nbsp;</td>
<tr>
<td>ImageQuant Analysis Software</td>
<td>Other</td>
<td>GE Healthcare</td>
<td>28-9236-62</td>
<td>&nbsp;</td>
<tr>
<td>Urea</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1319-01</td>
<td>&nbsp;</td>
<tr>
<td>CHAPS</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1314-01</td>
<td>&nbsp;</td>
<tr>
<td>PlusOne Dithiothreitol (DTT)</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1318-01</td>
<td>&nbsp;</td>
<tr>
<td>Bromophenol Blue</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1329-01</td>
<td>&nbsp;</td>
<tr>
<td>Tris</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1321-01</td>
<td>&nbsp;</td>
<tr>
<td>Sodium Dodecylsulfate (SDS)</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1313-01</td>
<td>&nbsp;</td>
<tr>
<td>PlusOne Glycerol 87%</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1325-01</td>
<td>&nbsp;</td>
<tr>
<td>PlusOne ReadySol IEF 40% T, 3% C</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1310-01</td>
<td>&nbsp;</td>
<tr>
<td>PlusOne TEMED</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1312-01</td>
<td>&nbsp;</td>
<tr>
<td>PlusOne Ammonium Persulfate</td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1311-01</td>
<td>&nbsp;</td>
<tr>
<td>PlusOne Glycine </td>
<td>Reagent</td>
<td>GE Healthcare</td>
<td>17-1323-01</td>
<td>&nbsp;</td>
<tr>
<td>2-D Sample Prep for membrane proteins</td>
<td>Reagent</td>
<td>Pierce</td>
<td>89864</td>
<td>&nbsp;</td>
<tr>
<td>Streptomycin sulphate</td>
<td>Reagent</td>
<td>Invitrogen</td>
<td>15140-122</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>

selective labelling of cell-surface proteins using cydye dige fluor minimal dyes

表面タンパク質は、その環境に反応すると、隣接細胞と相互作用する細胞の能力の中心となっています。彼らはほとんどすべての細胞内シグナル伝達の誘導剤であることが知られている。また、彼らは環境適応や薬物治療で重要な役割を果たしており、しばしば疾患の病因と病理学（1）に関与している。タンパク質 - タンパク質相互作用は、シグナル伝達経路に固有であり、これらの複雑な生物学的プロセスのより多くの洞察を得るために、高感度かつ信頼性の高い方法は、細胞表面のタンパク質を研究するために必要とされる。二次元（2 - D）電気泳動は、差動の変化を研究するために複雑なタンパク質サンプルのバイオマーカーや他の標的の検出のために広範に使用されます。彼らの低濃度（細胞タンパク質の1 2％）が部分的に原因の細胞表面タンパク質は、分画もしくは濃縮のいくつかの他のタイプなしで2 - Dゲルで検出するのは困難である。彼らはまた、しばしば不十分な彼らの疎水性の性質と高分子量（2）による2 - Dゲルで表されます。本研究では、我々はタンパク質のこの重要なグループの特定のラベリングと検出のためのCyDye DIGEフルーア最小限の染料を使用して完全な細胞のための新しいプロトコルを提示する。結果は、細胞内タンパク質の最小限のラベルを持つ細胞表面タンパク質の大量の特定のラベルを示した。このプロトコルは、使用するために、迅速に簡単です、そしてすべての3つのCyDye DIGEフルーア最小限の色素（CY 2、サイ3、Cyの5）の細胞表面タンパク質を標識するために使用することができます。これらの機能は、DeCyder 2次元差分解析ソフトウェアを用いてタンパク質発現の変化のEttan DIGE技術と解析との2次元蛍光差ゲル電気泳動（2 - D DIGE）を用いて多重化することができます。細胞表面タンパク質のレベルは、時間の種々の長さのためのCHO細胞（表1参照）の血清飢餓の間に続いた。存在量の小さな変化を高精度に検出され、その結果は定義されている統計的手法によってサポートされています。

Watch this Scientific Journal Video about Selective Labelling of Cell-surface Proteins using CyDye DIGE Fluor Minimal Dyes at JoVE.com

Selective Labelling of Cell-surface Proteins using CyDye DIGE Fluor Minimal Dyes

シンプルで具体的な方法は、分別工程なしで蛍光標識し、細胞表面タンパク質の拡張検出用に実証された。細胞表面タンパク質の差の存在量は、（2 - D）二次元電気泳動とEttan™DIGE技術を用いて解析した。

CyDye DIGEフルーア最小限の色素を用いた細胞表面タンパク質の選択的ラベリング

Surface  proteins are central to the cell's ability to react to its environment and to interact with neighboring cells. They are known to be inducers of ...

selective-labelling-cell-surface-proteins-using-cydye-dige-fluor

Research

JoVE Journal

Biology

15.1K ビュー.  GE Healthcare Bio-Sciences AB. シンプルで具体的な方法は、分別工程なしで蛍光標識し、細胞表面タンパク質の拡張検出用に実証された。細胞表面タンパク質の差の存在量は、（2 - D）二次元電気泳動とEttan™DIGE技術を用いて解析した。

ビデオ: Selective Labelling of Cell-surface Proteins using CyDye DIGE Fluor Minimal Dyes

Optical Recording of Electrical Activity in Guinea-pig Enteric Networks using Voltage-sensitive Dyes

The enteric nervous system (ENS) is a self-contained network with identified functions, capable of performing complex behaviors in isolation. Its neurons (10 to 25 &mu;m in diameter) are arranged in plexuses that are confined to distinct planes of the gut wall 1; the myenteric plexus can be found between the longitudinal and circular muscle layers, and the submucous plexus between the circular muscle layer and the mucosa. Since the effector systems for these plexuses (transporting epithelium, endocrine cells, immune elements, blood vessels and smooth muscle) are also contained within the gut wall, semi-intact preparations can be dissected that preserve individual components of different reflex pathways. The behavior of the effector systems is controlled by the submucous and myenteric plexuses acting in concert. Therefore, detailed knowledge of synaptic interactions within and between ganglia, and of communication between the plexuses, is essential for understanding normal gastrointestinal function. The ENS, as an intact nervous system, is a unique experimental model in which one can correlate molecular and cellular events with the electrical behavior of the neuronal network and its physiological outputs. Because of the quasi-two-dimensional organization of its plexuses, the ENS is particularly well suited for the study of neural networks using multiple site optical recording techniques that employ voltage-sensitive dyes 2,7,8,9. We will illustrate here the use of a relatively new naphthylstyryl-pyridinium dye (di-4-ANEPPDHQ) 3 that offers multiple advantages over its predecessors, including very low phototoxicity, slow rate of internalization, and remarkable chemical stability. When used in conjunction with a camera that permits sub-millisecond time resolution, this dye allows us to monitor the electrical activity of all the neurons in the field of view with a maximal spatial resolution of ~ 2.5 &mu;m at 100X magnification. At lower magnification (10X or 20X), the sacrifice of single-cell resolution is compensated by a gain in perspective, revealing the intricacies of the inter-ganglionic circuitry.

This protocol illustrates how voltage-sensitive dyes enable optical recording of electrical activity from intact neural networks such as the plexuses of the guinea-pig enteric nervous system, with an adjustable resolution that ranges from single-cells to multi-ganglionic circuitry.

電位感受性色素を用いてモルモット腸ネットワークにおける電気活動の光学的記録

The enteric nervous system (ENS) is a self-contained network with identified functions, capable of performing complex behaviors in isolation. Its neurons ...

生物学

Avidity-based Extracellular Interaction Screening (AVEXIS) for the Scalable Detection of Low-affinity Extracellular Receptor-Ligand Interactions

Extracellular protein:protein interactions between secreted or membrane-tethered proteins are critical for both initiating intercellular communication and ensuring cohesion within multicellular organisms. Proteins predicted to form extracellular interactions are encoded by approximately a quarter of human genes1, but despite their importance and abundance, the majority of these proteins have no documented binding partner. Primarily, this is due to their biochemical intractability: membrane-embedded proteins are difficult to solubilise in their native conformation and contain structurally-important posttranslational modifications. Also, the interaction affinities between receptor proteins are often characterised by extremely low interaction strengths (half-lives &lt; 1 second) precluding their detection with many commonly-used high throughput methods2. 
Here, we describe an assay, AVEXIS (AVidity-based EXtracellular Interaction Screen) that overcomes these technical challenges enabling the detection of very weak protein interactions (t1/2 &le; 0.1 sec) with a low false positive rate3. The assay is usually implemented in a high throughput format to enable the systematic screening of many thousands of interactions in a convenient microtitre plate format (Fig. 1). It relies on the production of soluble recombinant protein libraries that contain the ectodomain fragments of cell surface receptors or secreted proteins within which to screen for interactions; therefore, this approach is suitable for type I, type II, GPI-linked cell surface receptors and secreted proteins but not for multipass membrane proteins such as ion channels or transporters.
The recombinant protein libraries are produced using a convenient and high-level mammalian expression system4, to ensure that important posttranslational modifications such as glycosylation and disulphide bonds are added. Expressed recombinant proteins are secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (&beta;-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA (Fig. 1). The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, we have shown that interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates3.

Avidity-based Extracellular Interaction Screening AVEXIS for the Scalable Detection of Low-affinity Extracellular Receptor-Ligand Interactions

AVEXIS is a high throughput protein interaction assay developed to systematically screen for novel extracellular receptor-ligand pairs involved in cellular recognition processes. It is specifically designed to detect transient protein interactions that are difficult to identify using other high throughput approaches.

低親和性細胞外受容体 - リガンド相互作用の検出のためのスケーラブルな親和性ベースの細胞外相互作用のスクリーニング（AVEXIS）

Extracellular protein:protein interactions between secreted or membrane-tethered proteins are critical for both initiating intercellular communication and ...

Optimized Staining and Proliferation Modeling Methods for Cell Division Monitoring using Cell Tracking Dyes

Fluorescent cell tracking dyes, in combination with flow and image cytometry, are powerful tools with which to study the interactions and fates of different cell types in vitro and in vivo.1-5 Although there are literally thousands of publications using such dyes, some of the most commonly encountered cell tracking applications include monitoring of:
<ol>
	<li>stem and progenitor cell quiescence, proliferation and/or differentiation6-8</li>
	<li>antigen-driven membrane transfer9 and/or precursor cell proliferation3,4,10-18 and</li>
	<li>immune regulatory and effector cell function1,18-21.</li>
</ol>
Commercially available cell tracking dyes vary widely in their chemistries and fluorescence properties but the great majority fall into one of two classes based on their mechanism of cell labeling. "Membrane dyes", typified by PKH26, are highly lipophilic dyes that partition stably but non-covalently into cell membranes1,2,11. "Protein dyes", typified by CFSE, are amino-reactive dyes that form stable covalent bonds with cell proteins4,16,18. Each class has its own advantages and limitations. The key to their successful use, particularly in multicolor studies where multiple dyes are used to track different cell types, is therefore to understand the critical issues enabling optimal use of each class2-4,16,18,24.
The protocols included here highlight three common causes of poor or variable results when using cell-tracking dyes. These are:
<ol>
	<li>Failure to achieve bright, uniform, reproducible labeling. This is a necessary starting point for any cell tracking study but requires attention to different variables when using membrane dyes than when using protein dyes or equilibrium binding reagents such as antibodies.</li>
	<li>Suboptimal fluorochrome combinations and/or failure to include critical compensation controls. Tracking dye fluorescence is typically 102 - 103 times brighter than antibody fluorescence. It is therefore essential to verify that the presence of tracking dye does not compromise the ability to detect other probes being used.</li>
	<li>Failure to obtain a good fit with peak modeling software. Such software allows quantitative comparison of proliferative responses across different populations or stimuli based on precursor frequency or other metrics. Obtaining a good fit, however, requires exclusion of dead/dying cells that can distort dye dilution profiles and matching of the assumptions underlying the model with characteristics of the observed dye dilution profile.</li>
</ol>
Examples given here illustrate how these variables can affect results when using membrane and/or protein dyes to monitor cell proliferation.

Successful use of cell tracking dyes to monitor immune cell function and proliferation involves several critical steps. We describe methods for: 1) obtaining bright, uniform, reproducible label-ing with membrane dyes; 2) selecting fluorochromes and data acquisition conditions; and 3) choosing a model to quantify cell proliferation based on dye dilution.

細胞トラッキング染料を使用して細胞分裂監視のための最適化された染色と増殖モデリング方法

Fluorescent cell tracking dyes, in combination with flow and image cytometry, are powerful tools with which to study the interactions and fates of ...

Selective Capture of 5-hydroxymethylcytosine from Genomic DNA

5-methylcytosine (5-mC) constitutes ~2-8% of the total cytosines in human genomic DNA and impacts a broad range of biological functions, including gene expression, maintenance of genome integrity, parental imprinting, X-chromosome inactivation, regulation of development, aging, and cancer1. Recently, the presence of an oxidized 5-mC, 5-hydroxymethylcytosine (5-hmC), was discovered in mammalian cells, in particular in embryonic stem (ES) cells and neuronal cells2-4. 5-hmC is generated by oxidation of 5-mC catalyzed by TET family iron (II)/&alpha;-ketoglutarate-dependent dioxygenases2, 3. 5-hmC is proposed to be involved in the maintenance of embryonic stem (mES) cell, normal hematopoiesis and malignancies, and zygote development2, 5-10. To better understand the function of 5-hmC, a reliable and straightforward sequencing system is essential. Traditional bisulfite sequencing cannot distinguish 5-hmC from 5-mC11. To unravel the biology of 5-hmC, we have developed a highly efficient and selective chemical approach to label and capture 5-hmC, taking advantage of a bacteriophage enzyme that adds a glucose moiety to 5-hmC specifically12.
Here we describe a straightforward two-step procedure for selective chemical labeling of 5-hmC. In the first labeling step, 5-hmC in genomic DNA is labeled with a 6-azide-glucose catalyzed by &beta;-GT, a glucosyltransferase from T4 bacteriophage, in a way that transfers the 6-azide-glucose to 5-hmC from the modified cofactor, UDP-6-N3-Glc (6-N3UDPG). In the second step, biotinylation, a disulfide biotin linker is attached to the azide group by click chemistry. Both steps are highly specific and efficient, leading to complete labeling regardless of the abundance of 5-hmC in genomic regions and giving extremely low background. Following biotinylation of 5-hmC, the 5-hmC-containing DNA fragments are then selectively captured using streptavidin beads in a density-independent manner. The resulting 5-hmC-enriched DNA fragments could be used for downstream analyses, including next-generation sequencing.
Our selective labeling and capture protocol confers high sensitivity, applicable to any source of genomic DNA with variable/diverse 5-hmC abundances. Although the main purpose of this protocol is its downstream application (i.e., next-generation sequencing to map out the 5-hmC distribution in genome), it is compatible with single-molecule, real-time SMRT (DNA) sequencing, which is capable of delivering single-base resolution sequencing of 5-hmC.

Described is a two-step labeling process using &beta;-glucosyltransferase (&beta;-GT) to transfer an azide-glucose to 5-hmC, followed by click chemistry to transfer a biotin linker for easy and density-independent enrichment. This efficient and specific labeling method enables enrichment of 5-hmC with extremely low background and high-throughput epigenomic mapping via next-generation sequencing.

ゲノムDNAから5  - ヒドロキシの選択的捕獲

5-methylcytosine (5-mC) constitutes ~2-8% of the total cytosines in human genomic DNA and impacts a broad range of biological functions, including gene ...

Glycopeptide Capture for Cell Surface Proteomics

Cell surface proteins, including extracellular matrix proteins, participate in all major cellular processes and functions, such as growth, differentiation, and proliferation. A comprehensive characterization of these proteins provides rich information for biomarker discovery, cell-type identification, and drug-target selection, as well as helping to advance our understanding of cellular biology and physiology. Surface proteins, however, pose significant analytical challenges, because of their inherently low abundance, high hydrophobicity, and heavy post-translational modifications. Taking advantage of the prevalent glycosylation on surface proteins, we introduce here a high-throughput glycopeptide-capture approach that integrates the advantages of several existing N-glycoproteomics means. Our method can enrich the glycopeptides derived from surface proteins and remove their glycans for facile proteomics using LC-MS. The resolved N-glycoproteome comprises the information of protein identity and quantity as well as their sites of glycosylation. This method has been applied to a series of studies in areas including cancer, stem cells, and drug toxicity. The limitation of the method lies in the low abundance of surface membrane proteins, such that a relatively large quantity of samples is required for this analysis compared to studies centered on cytosolic proteins.

Cell surface proteins are biologically important and widely glycosylated. We introduce here a glycopeptide-capture approach to solubilize, enrich, and deglycosylate these proteins for facile LC-MS based proteomic analyses.

細胞表面プロテオミクスのための糖ペプチドキャプチャ

Cell surface proteins, including extracellular matrix proteins, participate in all major cellular processes and functions, such as growth, ...

Measurement of Extracellular Ion Fluxes Using the Ion-selective Self-referencing Microelectrode Technique

Cells from animals, plants and single cells are enclosed by a barrier called the cell membrane that separates the cytoplasm from the outside. Cell layers such as epithelia also form a barrier that separates the inside from the outside or different compartments of multicellular organisms. A key feature of these barriers is the differential distribution of ions across cell membranes or cell layers. Two properties allow this distribution: 1) membranes and epithelia display selective permeability to specific ions; 2) ions are transported through pumps across cell membranes and cell layers. These properties play crucial roles in maintaining tissue physiology and act as signaling cues after damage, during repair, or under pathological condition. The ion-selective self-referencing microelectrode allows measurements of specific fluxes of ions such as calcium, potassium or sodium at single cell and tissue levels. The microelectrode contains an ionophore cocktail which is selectively permeable to a specific ion. The internal filling solution contains a set concentration of the ion of interest. The electric potential of the microelectrode is determined by the outside concentration of the ion. As the ion concentration varies, the potential of the microelectrode changes as a function of the log of the ion activity. When moved back and forth near a source or sink of the ion (i.e. in a concentration gradient due to ion flux) the microelectrode potential fluctuates at an amplitude proportional to the ion flux/gradient. The amplifier amplifies the microelectrode signal and the output is recorded on computer. The ion flux can then be calculated by Fick&#8217;s law of diffusion using the electrode potential fluctuation, the excursion of microelectrode, and other parameters such as the specific ion mobility. In this paper, we describe in detail the methodology to measure extracellular ion fluxes using the ion-selective self-referencing microelectrode and present some representative results.

Transporters in cell membranes allow differential segregation of ions across cell membranes or cell layers and play crucial roles during tissue physiology, repair and pathology. We describe the ion-selective self-referencing microelectrode that allows the measurement of specific ion fluxes at single cells and tissues in vivo.

イオン選択自己参照微小電極法を用いた細胞外イオンフラックスの測定

Cells from animals, plants and single cells are enclosed by a barrier called the cell membrane that separates the cytoplasm from the outside. Cell layers ...

Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes

In this protocol, we demonstrate a method for the synthesis of 2&#39;-alkyne modified deoxyribonucleic acid (DNA) strands by automated solid phase synthesis using standard phosphoramidite chemistry. Oligonucleotides are post-synthetically labeled by two new photostable cyanine dyes using copper-catalyzed click-chemistry. The synthesis of both donor and acceptor dye is described and is performed in three consecutive steps. With the DNA as the surrounding architecture, these two dyes undergo an energy transfer when they are brought into close proximity by hybridization. Therefore, annealing of two single stranded DNA strands is visualized by a change of fluorescence color. This color change is characterized by fluorescence spectroscopy but can also be directly observed by using a handheld ultraviolet (UV) lamp. The concept of a dual fluorescence color readout makes these oligonucleotide probes excellent tools for molecular imaging especially when the described photostable dyes are used. Thereby, photobleaching of the imaging probes is prevented, and biological processes can be observed in real time for a longer time period.

Photostable cyanine dyes are attached to oligonucleotides to monitor hybridization by energy transfer.

光安定シアニン色素を用いた波長シフトDNAハイブリダイゼーションプローブの合成

In this protocol, we demonstrate a method for the synthesis of 2&#39;-alkyne modified deoxyribonucleic acid (DNA) strands by automated solid phase ...

Determination of the Relative Cell Surface and Total Expression of Recombinant Ion Channels Using Flow Cytometry

Inherited or de novo mutations in cation-selective channels may lead to sudden cardiac death. Alteration in the plasma membrane trafficking of these multi-spanning transmembrane proteins, with or without change in channel gating, is often postulated to contribute significantly in this process. It has thus become critical to develop a method to quantify the change of the relative cell surface expression of cardiac ion channels on a large scale. Herein, a detailed protocol is provided to determine the relative total and cell surface expression of cardiac L-type calcium channels CaV1.2 and membrane-associated subunits in tsA-201 cells using two-color fluorescent cytometry assays. Compared with other microscopy-based or immunoblotting-based qualitative methods, flow cytometry experiments are fast, reproducible, and large-volume assays that deliver quantifiable end-points on large samples of live cells (ranging from 104 to 106 cells) with similar cellular characteristics in a single flow. Constructs were designed to constitutively express mCherry at the intracellular C-terminus (thus allowing a rapid assessment of the total protein expression) and express an extracellular-facing hemagglutinin (HA) epitope to estimate the cell surface expression of membrane proteins using an anti-HA fluorescence conjugated antibody. To avoid false negative, experiments were also conducted in permeabilized cells to confirm the accessibility and proper expression of the HA epitope. The detailed procedure provides: (1) design of tagged DNA (deoxyribonucleic acid) constructs, (2) lipid-mediated transfection of constructs in tsA-201 cells, (3) culture, harvest, and staining of non-permeabilized and permeabilized cells, and (4) acquisition and analysis of fluorescent signals. Additionally, the basic principles of flow cytometry are explained and the experimental design, including the choice of fluorophores, titration of the HA antibody and control experiments, is thoroughly discussed. This specific approach offers objective relative quantification of the total and cell surface expression of ion channels that can be extended to study ion pumps and plasma membrane transporters.

Inherited cardiac arrhythmias are often caused by mutations that alter the surface delivery of one or more ion channels. Here, we adapt flow cytometry assays to provide a quantification of the relative total and cell surface protein expression of recombinant ion channels expressed in tsA-201 cells.

フローサイトメトリーを用いた組換えイオンチャネルの相対的な細胞表面および合計式の決意

Inherited or de novo mutations in cation-selective channels may lead to sudden cardiac death. Alteration in the plasma membrane trafficking of these ...

Analyzing Cell Surface Adhesion Remodeling in Response to Mechanical Tension Using Magnetic Beads

Mechanosensitive cell surface adhesion complexes allow cells to sense the mechanical properties of their surroundings. Recent studies have identified both force-sensing molecules at adhesion sites, and force-dependent transcription factors that regulate lineage-specific gene expression and drive phenotypic outputs. However, the signaling networks converting mechanical tension into biochemical pathways have remained elusive. To explore the signaling pathways engaged upon mechanical tension applied to cell surface receptor, superparamagnetic microbeads can be used. Here we present a protocol for using magnetic beads to apply forces to cell surface adhesion proteins. Using this approach, it is possible to investigate not only force-dependent cytoplasmic signaling pathways by various biochemical approaches, but also adhesion remodeling by magnetic isolation of adhesion complexes attached to the ligand-coated beads. This protocol includes the preparation of ligand-coated superparamagnetic beads, and the application of define tensile forces followed by biochemical analyses. Additionally, we provide a representative sample of data demonstrating that tension applied to integrin-based adhesion triggers adhesion remodeling and alters protein tyrosine phosphorylation.

Cell surface adhesions are central in mechanotransduction, as they transmit mechanical tension and initiate the signaling pathways involved in tissue homeostasis and development. Here, we present a protocol for dissecting the biochemical pathways that are activated in response to tension, using ligand-coated magnetic microbeads and force application to adhesion receptors.

磁気ビーズを使用した機械的張力に応答して細胞表面接着リフォームの分析

Mechanosensitive cell surface adhesion complexes allow cells to sense the mechanical properties of their surroundings. Recent studies have identified both ...

Application of Membrane and Cell Wall Selective Fluorescent Dyes for Live-Cell Imaging of Filamentous Fungi

The application of membrane and cell wall selective fluorescent dyes for live-cell imaging analyses of organelle dynamics in fungal cells started two decades ago and since then continues to contribute greatly to our understanding of the filamentous fungal lifestyle. This paper provides a practical guide for the utilization of the two membrane dyes FM 1-43 and FM 4-64 and the four cell wall stains Calcofluor White M2R, Solophenyl Flavine 7GFE 500, Pontamine Fast Scarlet 48 and Congo Red. The focus is on their low-dose application to ascertain artefact-free staining, their co-imaging properties, and their quantitative evaluation. The presented methods are applicable to all filamentous fungal samples that can be prepared in the described ways. The fundamental staining approaches can serve as starting points for adaptations to species that might require different cultivation conditions. First, biophysical and biochemical properties are reviewed as their understanding is essential for using these dyes as truly vital fluorescent stains. Secondly, step-by-step protocols are presented that detail the preparation of various fungal sample types for fluorescent live-cell imaging. Finally, example experiments illustrate different approaches to: (1) identify defects in the spatio-temporal organization of endocytosis in genetic mutants, (2) comparatively characterize shared and distinct co-localization of GFP-labeled target proteins in the endocytic pathway, (3) identify morphogenetic cell wall defects in a genetic mutant, and (4) monitor cell wall biogenesis in real time.

Vital fluorescent dyes are essential tools for live-cell imaging analyses in modern fungal cell biology. This paper details the application of established and lesser-known fluorescent dyes for tracking plasma membrane dynamics, endo-/exocytosis and cell wall morphogenesis in filamentous fungi.

糸状菌の生細胞イメージングのための膜および細胞壁選択的蛍光色素の応用

The application of membrane and cell wall selective fluorescent dyes for live-cell imaging analyses of organelle dynamics in fungal cells started two ...