この研究は、SHにドイツ学術振興GraKo1121、Hu1011/2-1とSFB940の補助金によって支えられて

注意：プロトコルに示されたバッファに関する詳細な情報は、 表1で提供されています。 1。生細胞におけるホルムアルデヒド架橋によってタンパク質 - タンパク質相互作用の固定<ol><li>増殖培地、ストック溶液とバッファP1の準備を開始するには<ol><li>培地500ミリリットルを準備します。媒体が膜baitタンパク質と獲物タンパク質間の相互作用をサポートする条件を提供する必要があります。さらに、1つの実験は、（ 例えば、架橋せず）の相互作用が期待されない条件下で行われるべきである。 注意：我々は強調し、非ストレス細菌中のタンパク質 - タンパク質相互作用を比較する。そのため、私たちは、2Lの三角フラスコ中のストレス誘導剤（ 例えば 、0.5M NaCl）で補完する500ミリリットルルリアベルターニ（LB）培地（ 表1）を準備します。制御のために、我々は0.17のNaCl（pH7.0）で、通常のLB培地を使用しています。 </li><li>トリス緩衝液を調製し（20mMのTris-HClでpHを8.0）および0.1 Mエチレンジアミン四酢酸（EDTA）、pH8.0の原液（ 表1）。 </li><li>バッファP1を準備します。トリス緩衝液中の0.5 Mの最終濃度になるようにスクロースを溶解させる。濾過によりバッファP1を滅菌し、4℃で保存し</li></ol></li><li>ベクターからC-末端のStrep-tag融合有する膜ベイトタンパク質を発現する細胞を成長させる。十分な時間のための膜ベイトタンパク質の発現を誘導する。 注：我々 500 mlの培地を250μlの1 Mイソプロピル-β-D-チオガラクトピラノシド（IPTG）の添加により早期対数増殖期（A 600 = 0.3）で（最終濃度：0.5mMの）を細菌膜のベイトタンパク質の発現を誘導する。十分な発現を可能にするために、我々は対数期後期（600 = 1.2）まで、細菌を培養する。 </li><li> 300ミリリットルそれぞれの最小​​容積と各培養用の2遠心ビーカーを用意し、氷の上に置きます。 </li><li>ホルムアルデヒド架橋を行う。 CAUTION：ホルムアルデヒドは毒性が強く私たちは、安全性のヒュームフードの下で働いてお勧めします。 <ol><li>安全ヒュームフードの下で培養容器を移す。 （ - X）と架橋ホルムアルデヒド（+ X）を含む一つのサンプルは、架橋を省略一つに各サンプルを分割。 0.6％の最終濃度に達するように250mlの培養物に4ミリリットルの37％ホルムアルデヒド溶液を添加する。 </li></ol></li><li>バック培養容器を転送し、以前のように、さらに20分間細胞を増殖。 </li><li>安全ヒュームフードの下の遠心管にあなたの文化を記入してください。 30分間3000×gの遠心分離によって細胞を収集します。 </li><li>慎重に安全ヒュームフードの下でそれをピペッティングにより上清を捨てる。有毒なホルムアルデヒド含有上清を収集し、適切に廃棄してください。 </li><li>膜タンパク質の調製中に最適な収率を達成するために、第一のスフェロプラストを調製する。ここでは、グラム陰性細菌のスフェロプラスト形成のためのプロトコルを提供する。 <ol><li>た準備凍結乾燥粉末から電子バッファP2（ 表1）。穏やかに1.5mlチューブに、0.1 M EDTA、pHを8に2mgのリゾチームを溶解する。常に実験の日のために新鮮にバッファP2を準備します。 </li><li>プロテアーゼ阻害剤（バッファP3）とトリス緩衝液を準備します。トリス緩衝液10mlに、10mMの最終濃度を0.1 mlの1 Mフェニルメチルスルホニルフルオリド（PMSF）（ 表1）を加える。プロテアーゼ阻害剤PMSFとしての適切な機能を確保するために、すぐにバッファを使用する。 </li><li>プロテアーゼ阻害し、15mlのコニカルチューブに移す溶液で10mlトリス緩衝液に再懸濁した細胞ペレット。 </li><li> 1ミリリットルの緩衝P2を追加し、30分間氷上でインキュベートする。 </li><li> 30分間3000×gの遠心分離によりスフェロプラストを収集し、慎重に上清を捨てる。 </li></ol></li><li> -20℃で一晩フェロプラストペレットをインキュベート</li></ol> 2。 Strepタグの膜タンパク質の精製（ベイト） <ol><li>氷上でフェロプラストペレットを配置します。&lt;/李&gt; <li>フェロプラストペレットを氷上で解凍時間の間に、それぞれのスフェロプラストを調製するための10ミリリットルバッファP3を準備します。静かに10ミリリットルトリス緩衝液中で1mgのDNアーゼIを溶かす。使用直前に0.1ミリリットルの1M PMSFを追加します。 </li><li> 6ミリリットルの新たに調製し、P3でペレットを再懸濁します。スフェロプラストを破壊するために、各バーストの間に1分間の休止と氷上で1分間、連続的に試料を4回超音波処理する。 </li><li>収穫細胞細片を10分間、10,000×gで試料を遠心分離する。超遠心管にピペットを用いて上清を転送します。 </li><li> 30分、100,000×gで膜画分をペレット化。それを溶解することなく、トリス緩衝液中で慎重にペレットを洗浄。紙の組織（ 例えばクリネックス）でチューブを乾燥させます。いつでもペレットを乱さないようにしてください。 </li><li>丁寧に1ミリリットルのトリス緩衝液（=膜）ペレットを再懸濁。 例えば、BCAアッセイによりタンパク質濃度を決定するために、20μlのアリコートを使用する。このステップでは、膜は、リチウムでショック凍結することができる頭の良い窒素と-80℃で保存</li></ol> 3。 Strepタグメンブレンbaitタンパク質とSDS-PAGEの精製<ol><li>トリスバッファーで5 mg / mlの、膜画分のタンパク質濃度を正規化する。超遠心分離管に2.5ミリリットルの膜画分（5 mg / mlの）を取り、膜タンパク質を可溶化するために、2％の最終濃度に達するように、20％トリトンX-100 0.25mlの投稿。マイクロ磁気棒を加え、氷上で1時間撹拌する。 注：一般に、我々は洗浄剤としてトリトンX-100を使用して良い結果を持っていますが、最適化のための界面活性剤を変更することが役に立つかもしれません。この点において、我々は、それぞれの膜ベイトタンパク質の機能的な精製の ​​ために使用されるもの清浄剤で最良の結果を有している。 </li><li>ステップ3.1を実行している間、（ 表1）から50ミリリットル液Wと5ミリリットル緩衝液Eを準備します。 10ミリリットルの5×50ミリリットルにW濃縮液をバッファリングし、150μlの20％トリトンX-100を追加埋める。 <ol><li> 1ミリリットル5X buffeを埋めるR E 10ミリリットルに集中し、30μlの20％トリトンX-100を追加します。 8ミリリットルバッファーWに1ミリリットルのStrep-Tactinのスーパーフロー自然落下カラムを平衡化 注：これは、精製手順の間の任意の緩衝液中の臨界ミセル濃度（CMC）以上の濃度の10倍で可溶化に使用される界面活性剤を添加することが必須である。 </li></ol></li><li>不溶性膜画分をペレット化し、30分間、100,000×gで可溶化サンプルと超遠心機からマイクロ磁気棒を取り外します。さらに精製するためにピペットを用いて上清を取り除きます。 </li><li>カラムに上清をロードします。唯一の重力流でカラムを実行します。 W.この洗浄工程を5回繰り返して、5ミリリットル緩衝液でカラムを洗浄します。 </li><li>この溶出ステップ4Xを繰り返して1ミリリットルバッファーEで膜ベイトタンパク質を溶出。 </li><li>遠心式フィルターユニットで溶出画分2,3、および4から300μLを濃縮する。 </li><li> 50μlの5倍のSDS-PAGで各サンプルを200μlを混ぜてEローディングダイ。 125μlを各準備を分割します。ホルムアルデヒド架橋を逆にする、95℃で20分間の各製剤の1アリコートを沸かす。サンプルは作業台の上に、少なくとも10分間、室温まで冷却してみましょう。 </li><li>免疫ブロッティングに適しポリアクリルアミドゲルの単一のレーンに負荷各サンプルから30μlの。最良の方向について予め染色した分子量マーカーを使用し、SDS-PAGE 10を実行します。 </li></ol> 4。相互作用パートナーを確認するためのイムノブロット分析<ol><li>一旦3.8は、例えばセミドライによりニトロセルロース膜に転写タンパク質を終了するステップ。 </li><li>非特異的な標識を防ぐための膜をブロックします。 0.05％のTween-20（TBS-T）の最終濃度を補充したトリス緩衝食塩水で体積当たり3％の重量を達成するために、ウシ血清アルブミン（BSA）を秤量して、ブロッキング緩衝液調製する。メンブレンをカバーするために、ブロッキング緩衝液の十分なボリュームを使用。室温で1時間、膜をブロックします。 </li><li>希薄NDいつものように獲物タンパク質特異的一次抗体をインキュベートする。二次抗体としてHRP結合抗体を使用してください。 </li><li>高感度化学発光検出キットを用いたイムノブロットを開発。古典映画の処理手順やデジタルイメージング機器を用いて信号を監視します。 </li></ol> 5。相互作用パートナーを識別するためにNanoLC-ESI-MS/MS高解像度実験<ol><li>識別されるべきである特定の抗体が獲物タンパク質または未知の相互作用パートナーのために提供されていない場合には、識別のために質量分析（MS）を使用します。ケラチン汚染を防止するために、使用は、タンパク質分離のためにゲルをプレキャスト。 </li><li>銀は、製造業者のプロトコルに従ってMS適合性染色キットを用いてSDS-PAGEを染色する。ガラスタンク内のすべての染色および洗浄の手順を実行します。 </li><li>消費税各バンドと高分解能LC / MS 9でこれらを分析します。 </li></ol>

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	<li>Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E. L. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Predicting+transmembrane+protein+topology+with+a+hidden+markov+model:+application+to+complete+genomes.">Predicting transmembrane protein topology with a hidden markov model: application to complete genomes.</a> J. Mol. Biol. 305, 567-580 (2001).</li><li>Bakheet, T. M., Doig, A. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Properties+and+identification+of+human+protein+drug+targets.">Properties and identification of human protein drug targets.</a> Bioinformatics. 25, 451-457 (2009).</li><li>Yildirim, M. A., Goh, K. I., Cusick, M. E., Barabasi, A. L., Vidal, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Drug-target+network.">Drug-target network.</a> Nat. Biotechnol. 25, (2007).</li><li>Daley, D. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+assembly+of+membrane+proteins+into+complexes.">The assembly of membrane proteins into complexes.</a> Curr. Opin. Struct. Biol. 18, 420-424 (2008).</li><li>Jung, K., Fried, L., Behr, S., Heermann, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Histidine+kinases+and+response+regulators+in+networks.">Histidine kinases and response regulators in networks.</a> Curr. Opin. Microbiol. 15, 118-124 (2012).</li><li>M&#252;ller, V. S., Jungblut, P. R., Meyer, T. F., Hunke, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Membrane-SPINE:+An+improved+method+to+identify+protein-protein+interaction+partners+of+membrane+proteins+in+vivo.">Membrane-SPINE: An improved method to identify protein-protein interaction partners of membrane proteins in vivo.</a> Proteomics. 11, 2124-2128 (2011).</li><li>Herzberg, C., 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=SPINE:+A+method+for+the+rapid+detection+and+analysis+of+protein-protein+interactions+in+vivo.">SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo.</a> Proteomics. 7, 4032-4035 (2007).</li><li>Sutherland, B. W., Toews, J., Kast, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Utility+of+formaldehyde+cross-linking+and+mass+spectrometry+in+the+study+of+protein-protein+interactions.">Utility of formaldehyde cross-linking and mass spectrometry in the study of protein-protein interactions.</a> J. Mass Spectrom. 43, 699-715 (2008).</li><li>Hernandez, P., M&#252;ller, M., Appel, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Automated+protein+identification+by+tandem+mass+spectrometry:+Issues+and+strategies.">Automated protein identification by tandem mass spectrometry: Issues and strategies.</a> Mass Spectrom. Rev. 25, 235-254 (2006).</li><li>Laemmli, U. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cleavage+of+structural+proteins+during+the+assembly+of+the+head+of+bacteriophage+T4.">Cleavage of structural proteins during the assembly of the head of bacteriophage T4.</a> Nature. 227, 680-685 (1970).</li><li>Hunke, S., Keller, R., M&#252;ller, V. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Signal+integration+by+the+Cpx-envelope+stress+system.">Signal integration by the Cpx-envelope stress system.</a> FEMS Microbiol. Lett. 326, 12-22 (2012).</li><li>Weber, R. F., Silverman, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Cpx+proteins+of+Escherichia+coli+K12+:+Structure+of+the+CpxA+polypeptide+as+an+inner+membrane+component.">The Cpx proteins of Escherichia coli K12 : Structure of the CpxA polypeptide as an inner membrane component.</a> J. Mol. Biol. 203, 467-478 (1988).</li></ol>

我々は、開示することは何もありません。

膜脊椎分析は1を確認し、この時点まで膜タンパク質の未知の相互作用パートナーを識別でき、生化学的なアプローチである。メンブレン背骨がStrep-tag IIタグの膜ベイトタンパク質の精製をホルムアルデヒドによって生体内架橋を兼ね備えています。免疫ブロット法との併用は、予測された相互作用パートナー（ 図2）の確認を容易にする。さらに、MS解析との組み合...

タンパク質の機能を理解するためには、その相互作用パートナーを知ることが不可欠である。いくつかの古典的な手法は、可溶性タンパク質の相互作用パートナーの同定のために用意されています。しかし、これらの技術は、簡単に自分の疎水性の性質4による膜タンパク質に譲渡することはできません。この制限を克服するために、我々は、膜のStrep-タンパク質相互作用実験（膜- SPINE）6を開発した。これは、可溶性タンパク質7にのみ適した脊椎法に基づいています。 架橋剤のホルムアルデヒドの二つの利点から、膜-背骨の利点は：まず、ホルムアルデヒドは簡単に膜を透過し、そのため生細胞8のインタラクトームの正確なスナップショットを生成することができます。第二に、ホルムアルデヒド架橋が9を沸騰させることによって逆転させることができる。ここで、これらの二つの利点は、膜proteの永久的でなく、過渡のPPIだけを識別するために使用されプラグ6。 要するに、Strepタグは内在性膜ベイトタンパク質のC末端に融合される。膜ベイトタンパク質を発現する細胞は、架橋は、膜ベイトタンパク質にタンパク質を捕食ホルムアルデヒド（ 図1）とともにインキュベートする。獲物タンパク質の修正は必要ありません。次に、膜画分を調製する。したがって、膜タンパク質は、治療およびベイトタンパク質は、アフィニティー精製を使用して、その獲物タンパク質と同時精製される界面活性剤によって可溶化される。続いて、架橋を沸騰させることによって反転され、餌及びその共溶出獲物タンパク質は、SDS-PAGEによって分離されている。最後に、獲物タンパク質は、イムノブロット分析または質量分析によって同定することができる。

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		<tr height="21">
			<td height="21" style="height:21px;width:343px;">37% Formaldehyde</td>
			<td style="width:128px;">Roth</td>
			<td style="width:137px;">4979.1</td>
			<td style="width:271px;">Should not be older than one year</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">DNaseI</td>
			<td style="width:128px;">Sigma</td>
			<td style="width:137px;">DN25</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">BCA protein assay kit</td>
			<td style="width:128px;">Pierce</td>
			<td style="width:137px;">23225</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">Micromagnetic rod</td>
			<td style="width:128px;">Roth</td>
			<td style="width:137px;">0955.2</td>
			<td style="width:271px;">5 mm in length, 2 mm in diameter</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">Triton X-100</td>
			<td style="width:128px;">Roth</td>
			<td style="width:137px;">6683.1</td>
			<td style="width:271px;">standard detergent for solubilization</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">n-Dodecyl-&#946;-maltoside</td>
			<td style="width:128px;">Glycon</td>
			<td style="width:137px;">D97002-C</td>
			<td style="width:271px;">the best detergent to solubilze CpxA</td>
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		<tr height="21">
			<td height="21" style="height:21px;width:343px;">1 ml Strep-Tactin superflow gravity flow column</td>
			<td style="width:128px;">IBA</td>
			<td style="width:137px;">2-1207-050</td>
			<td style="width:271px;"></td>
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		<tr height="21">
			<td height="21" style="height:21px;width:343px;">Strep-tag protein purification buffer set</td>
			<td style="width:128px;">IBA</td>
			<td style="width:137px;">2-1002-001</td>
			<td style="width:271px;">Contains buffer W and buffer E</td>
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		<tr height="21">
			<td height="21" style="height:21px;width:343px;">Amicon Ultra-4 centrifugal filter</td>
			<td style="width:128px;">Millipore</td>
			<td style="width:137px;">UFC803024</td>
			<td style="width:271px;"></td>
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		<tr height="42">
			<td height="42" style="height:42px;width:343px;">SuperSignal West Pico Chemiluminescent substrate</td>
			<td style="width:128px;">Pierce</td>
			<td style="width:137px;">34080</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">SilverQuest Silverstaining kit</td>
			<td style="width:128px;">Invitrogen</td>
			<td style="width:137px;">LC6070</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">FireSilver Staining Kit</td>
			<td style="width:128px;">Proteome Factory</td>
			<td style="width:137px;">P-S-2001</td>
			<td style="width:271px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:343px;">Ultracentrifuge</td>
			<td style="width:128px;"></td>
			<td style="width:137px;"></td>
			<td style="width:271px;"></td>
		</tr>
	</tbody>
</table>

membrane-spine: a biochemical tool to identify protein-protein interactions of membrane proteins in vivo

膜タンパク質は、細胞の生存に必須であり、したがって、重要な治療標的である1-3。これらは複合体4で機能するので、それらの相互作用を同定し、特徴付けるための方法が5必要です。この目的のために、我々は、膜- SPINE 6と呼ばれる膜のStrep-タンパク質相互作用実験を、開発した。この技術は、 インビボ Strepタグ膜ベイトタンパク質のアフィニティー精製の ​​可逆架橋剤ホルムアルデヒドを用いて架橋で組み合わせる。処置中に、架橋された獲物タンパク質は、膜ベイトタンパク質と共精製し、続いて沸騰させることによって分離される。イムノブロッティングによって提案された相互作用パートナーの第一、確認、および質量分析による新たな相互作用パートナーの第2の識別：膜 - SPINEを用いた膜タンパク質のタンパク質 - タンパク質相互作用薬（PPI）を分析するとき、したがって、二つの主要なタスクを実行することができる。また、あってもLOW親和性、一過性のPPIは、この技術によって検出可能である。最後に、膜 - SPINEは、膜タンパク質の同定のPPIをスクリーニングするための強力なツールとして、適用すること、ほぼすべての細胞型に適用可能である。

膜SPINE分析は、膜タンパク質の同時精製および一過性の相互作用タンパク質パートナーを可能にする。共精製は、架橋剤、ホルムアルデヒドを使用することによって達成される。ホルムアルデヒド濃度および架橋時間：2つのパラメータは、非特異的な架橋を防止するために重要である。ホルムアルデヒドのに十分ではなく、過度の使用を容易にイムノブロッティングによって制御することが?...

Watch this Scientific Journal Video about Membrane-SPINE: A Biochemical Tool to Identify Protein-protein Interactions of Membrane Proteins In Vivo at JoVE.com

Membrane-SPINE: A Biochemical Tool to Identify Protein-protein Interactions of Membrane Proteins In Vivo

生化学的ア ​​プローチは、膜タンパク質のin vivoでのタンパク質-タンパク質相互作用（PPI）を識別するために記載されている。この方法は、タンパク質架橋、アフィニティー精製および質量分析を組み合わせて、ほぼすべての細胞型または生物に適用可能である。このアプローチでは、一過性のPPIのさえ識別が可能となる。

膜脊柱：膜タンパク質のタンパク質 - タンパク質相互作用を識別するために、生化学的ツール<em&gt;インビボ</em

Membrane proteins are essential for cell viability and are therefore important therapeutic targets1-3. Since they function in complexes4, methods to ...

membrane-spine-biochemical-tool-to-identify-protein-protein

Research

JoVE Journal

Bioengineering

Membrane-SPINE: A Biochemical Tool to Identify Protein-protein Interactions of Membrane Proteins In Vivo

13.6K ビュー.  Universität Osnabrück. 生化学的ア ​​プローチは、膜タンパク質のin vivoでのタンパク質-タンパク質相互作用（PPI）を識別するために記載されている。この方法は、タンパク質架橋、アフィニティー精製および質量分析を組み合わせて、ほぼすべての細胞型または生物に適用可能である。このアプローチでは、一過性のPPIのさえ識別が可能となる。 

ビデオ: Membrane-SPINE: A Biochemical Tool to Identify Protein-protein Interactions of Membrane Proteins In Vivo

Fabrication of Electrochemical-DNA Biosensors for the Reagentless Detection of Nucleic Acids, Proteins and Small Molecules

As medicine is currently practiced, doctors send specimens to a central laboratory for testing and thus must wait hours or days to 
receive the results. Many patients would be better served by rapid, bedside tests. To this end our laboratory and others have developed a versatile, reagentless 
biosensor platform that supports the quantitative, reagentless, electrochemical detection of nucleic acids (DNA, RNA), proteins (including antibodies) and small 
molecules analytes directly in unprocessed clinical and environmental samples. In this video, we demonstrate the preparation and use of several biosensors in this 
"E-DNA" class. In particular, we fabricate and demonstrate sensors for the detection of a target DNA sequence in a polymerase chain reaction mixture, an HIV-specific antibody and the drug cocaine. The preparation procedure requires only three hours of hands-on effort followed by an overnight incubation, and their use requires only minutes.

"E-DNA" sensors, reagentless, electrochemical biosensors that perform well even when challenged directly in blood and other complex matrices, have been adapted to the detection of a wide range of nucleic acid, protein and small molecule analytes. Here we present a general procedure for the fabrication and use of such sensors.

核酸、タンパク質と低分子のReagentless検出用電気化学DNAバイオセンサーの作製

As medicine is currently practiced, doctors send specimens to a central laboratory for testing and thus must wait hours or days to 
receive the results. ...

生物工学

Visualizing Proteins and Macromolecular Complexes by Negative Stain EM: from Grid Preparation to Image Acquisition

Single particle electron microscopy (EM), of both negative stained or frozen hydrated biological samples, has become a versatile tool in structural biology 1. In recent years, this method has achieved great success in studying structures of proteins and macromolecular complexes 2, 3. Compared with electron cryomicroscopy (cryoEM), in which frozen hydrated protein samples are embedded in a thin layer of vitreous ice 4, negative staining is a simpler sample preparation method in which protein samples are embedded in a thin layer of dried heavy metal salt to increase specimen contrast 5. The enhanced contrast of negative stain EM allows examination of relatively small biological samples. In addition to determining three-dimensional (3D) structure of purified proteins or protein complexes 6, this method can be used for much broader purposes. For example, negative stain EM can be easily used to visualize purified protein samples, obtaining information such as homogeneity/heterogeneity of the sample, formation of protein complexes or large assemblies, or simply to evaluate the quality of a protein preparation.
In this video article, we present a complete protocol for using an EM to observe negatively stained protein sample, from preparing carbon coated grids for negative stain EM to acquiring images of negatively stained sample in an electron microscope operated at 120kV accelerating voltage. These protocols have been used in our laboratory routinely and can be easily followed by novice users.

Visualizing protein samples by negative stain electron microscopy (EM) has become a popular structural analysis method. It is useful for quantitative structural analysis, such as calculating a 3D reconstruction of the molecules being studied, and also for qualitative examination of the quality of protein preparations. In this article we present detailed protocols for preparing the EM grids, staining the sample and visualizing the sample in an electron microscope. Novice users can follow these protocols easily and to utilize negative stain EM as a routine assay, in addition to other biochemical assays, for evaluating their protein samples.

ネガティブステインEMによるタンパク質と高分子複合体の可視化：グリッドの準備から画像取り込みに

Single particle electron microscopy (EM), of both negative stained or frozen hydrated biological samples, has become a versatile tool in structural ...

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic valve leaflets are composed of interstitial cells suspended within an extracellular matrix (ECM) and are lined with an endothelial cell monolayer. The valve withstands a harsh, dynamic environment and is constantly exposed to shear, flexion, tension, and compression. Research has shown calcific lesions in diseased valves occur in areas of high mechanical stress as a result of endothelial disruption or interstitial matrix damage1-3. Hence, it is not surprising that epidemiological studies have shown high blood pressure to be a leading risk factor in the onset of aortic valve disease4. 
The only treatment option currently available for valve disease is surgical replacement of the diseased valve with a bioprosthetic or mechanical valve5. Improved understanding of valve biology in response to physical stresses would help elucidate the mechanisms of valve pathogenesis. In turn, this could help in the development of non-invasive therapies such as pharmaceutical intervention or prevention. Several bioreactors have been previously developed to study the mechanobiology of native or engineered heart valves6-9. Pulsatile bioreactors have also been developed to study a range of tissues including cartilage10, bone11 and bladder12. The aim of this work was to develop a cyclic pressure system that could be used to elucidate the biological response of aortic valve leaflets to increased pressure loads. 
The system consisted of an acrylic chamber in which to place samples and produce cyclic pressure, viton diaphragm solenoid valves to control the timing of the pressure cycle, and a computer to control electrical devices. The pressure was monitored using a pressure transducer, and the signal was conditioned using a load cell conditioner. A LabVIEW program regulated the pressure using an analog device to pump compressed air into the system at the appropriate rate. The system mimicked the dynamic transvalvular pressure levels associated with the aortic valve; a saw tooth wave produced a gradual increase in pressure, typical of the transvalvular pressure gradient that is present across the valve during diastole, followed by a sharp pressure drop depicting valve opening in systole. The LabVIEW program allowed users to control the magnitude and frequency of cyclic pressure. The system was able to subject tissue samples to physiological and pathological pressure conditions. This device can be used to increase our understanding of how heart valves respond to changes in the local mechanical environment.

Design of a Cyclic Pressure Bioreactor for the Ex Vivo Study of Aortic Heart Valves

A cyclic pressure bioreactor capable of subjecting heart valve tissue to physiological and pathological pressure conditions has been designed. A LabVIEW program allows users to control pressure magnitude, amplitude and frequency. This device can be used to study the mechanobiology of heart valve tissue or isolated cells.

のための周期的圧力のバイオリアクターの設計生体外で</em大動脈心臓弁の>研究

The aortic valve, located between the left ventricle and the aorta, allows for unidirectional blood flow, preventing backflow into the ventricle. Aortic ...

Determination of the Transport Rate of Xenobiotics and Nanomaterials Across the Placenta using the ex vivo Human Placental Perfusion Model

Decades ago the human placenta was thought to be an impenetrable barrier between mother and unborn child. However, the discovery of thalidomide-induced birth defects and many later studies afterwards proved the opposite. Today several harmful xenobiotics like nicotine, heroin, methadone or drugs as well as environmental pollutants were described to overcome this barrier. With the growing use of nanotechnology, the placenta is likely to come into contact with novel nanoparticles either accidentally through exposure or intentionally in the case of potential nanomedical applications. Data from animal experiments cannot be extrapolated to humans because the placenta is the most species-specific mammalian organ 1. Therefore, the ex vivo dual recirculating human placental perfusion, developed by Panigel et al. in 1967 2 and continuously modified by Schneider et al. in 1972 3, can serve as an excellent model to study the transfer of xenobiotics or particles.
Here, we focus on the ex vivo dual recirculating human placental perfusion protocol and its further development to acquire reproducible results.
The placentae were obtained after informed consent of the mothers from uncomplicated term pregnancies undergoing caesarean delivery. The fetal and maternal vessels of an intact cotyledon were cannulated and perfused at least for five hours. As a model particle fluorescently labelled polystyrene particles with sizes of 80 and 500 nm in diameter were added to the maternal circuit. The 80 nm particles were able to cross the placental barrier and provide a perfect example for a substance which is transferred across the placenta to the fetus while the 500 nm particles were retained in the placental tissue or maternal circuit. The ex vivo human placental perfusion model is one of few models providing reliable information about the transport behavior of xenobiotics at an important tissue barrier which delivers predictive and clinical relevant data.

Determination of the Transport Rate of Xenobiotics and Nanomaterials Across the Placenta using the ex vivo Human Placental Perfusion Model

The ex vivo dual recirculating human placental perfusion model can be used to investigate the transfer of xenobiotics and nanoparticles across the human placenta. In this video protocol we describe the equipment and techniques required for a successful execution of a placenta perfusion.

使用プラ​​センタアクロス異物およびナノ材料の輸送速度の決定<em&gt; ex vivoで</em&gt;ヒト胎盤灌流モデル

Decades ago the human placenta was thought to be an impenetrable barrier between mother and unborn child. However, the discovery of thalidomide-induced ...

Isolation and Characterization Of Chimeric Human Fc-expressing Proteins Using Protein A Membrane Adsorbers And A Streamlined Workflow

Laboratory scale to industrial scale purification of biomolecules from cell culture supernatants and lysed cell solutions can be accomplished using affinity chromatography.&#160;While affinity chromatography using porous protein A agarose beads packed in columns is arguably the most common method of laboratory scale isolation of antibodies and recombinant proteins expressing Fc fragments of IgG, it can be a time consuming and expensive process.&#160;Time and financial constraints are especially daunting in small basic science labs that must recover hundreds of micrograms to milligram quantities of protein from dilute solutions, yet lack access to high pressure liquid delivery systems and/or personnel with expertise in bioseparations. Moreover, product quantification and characterization may also excessively lengthen processing time over several workdays and inflate expenses (consumables, wages, etc.).&#160;Therefore, a fast, inexpensive, yet effective protocol is needed for laboratory scale isolation and characterization of antibodies and other proteins possessing an Fc fragment.&#160;To this end, we have devised a protocol that can be completed by limited-experience technical staff in less than 9 hr (roughly one workday) and as quickly as 4 hr, as opposed to traditional methods that demand 20+ work hours. Most required equipment is readily available in standard biomedical science, biochemistry, and (bio)chemical engineering labs, and all reagents are commercially available.&#160;To demonstrate this protocol, representative results are presented in which chimeric&#160;murine galectin-1 fused to human Fc (Gal-1hFc) from cell culture supernatant was isolated using a protein A membrane adsorber.&#160;Purified Gal-1hFc was quantified using an expedited Western blotting analysis procedure and characterized using flow cytometry. The streamlined workflow can be modified for other Fc-expressing proteins, such as antibodies, and/or altered to incorporate alternative quantification and characterization methods.

Compared with traditional affinity chromatography using protein A agarose bead-packed columns, protein A membrane adsorbers can significantly speed laboratory-scale isolation of antibodies and other Fc fragment-expressing proteins.&#160;Appropriate analysis and quantification methods can further accelerate protein processing, allowing isolation/characterization to be completed in one workday, instead of 20+ work hours.

タンパク質A膜吸着体と合理化されたワークフローを用いたキメラヒトFc発現タンパク質の単離と特性評価

Laboratory scale to industrial scale purification of biomolecules from cell culture supernatants and lysed cell solutions can be accomplished using ...

Luminescence Resonance Energy Transfer to Study Conformational Changes in Membrane Proteins Expressed in Mammalian Cells

Luminescence Resonance Energy Transfer, or LRET, is a powerful technique used to measure distances between two sites in proteins within the distance range of 10-100 &#197;. By measuring the distances under various ligated conditions, conformational changes of the protein can be easily assessed. With LRET, a lanthanide, most often chelated terbium, is used as the donor fluorophore, affording advantages such as a longer donor-only emission lifetime, the flexibility to use multiple acceptor fluorophores, and the opportunity to detect sensitized acceptor emission as an easy way to measure energy transfer without the risk of also detecting donor-only signal. Here, we describe a method to use LRET on membrane proteins expressed and assayed on the surface of intact mammalian cells. We introduce a protease cleavage site between the LRET fluorophore pair. After obtaining the original LRET signal, cleavage at that site removes the specific LRET signal from the protein of interest allowing us to quantitatively subtract the background signal that remains after cleavage. This method allows for more physiologically relevant measurements to be made without the need for purification of protein.

We describe here an improved Luminescence Resonance Energy Transfer (LRET) method where we introduce a protease cleavage site between the donor and acceptor fluorophore sites. This modification allows us to obtain specific LRET signals arising from membrane proteins of interest, allowing for the study of membrane proteins without protein purification.

発光共鳴エネルギーは、哺乳動物細胞で発現膜タンパク質の立体構造変化を研究するために転送

Luminescence Resonance Energy Transfer, or LRET, is a powerful technique used to measure distances between two sites in proteins within the distance range ...

Fluorescence-quenching of a Liposomal-encapsulated Near-infrared Fluorophore as a Tool for In Vivo Optical Imaging

Optical imaging offers a wide range of diagnostic modalities and has attracted a lot of interest as a tool for biomedical imaging. Despite the enormous number of imaging techniques currently available and the progress in instrumentation, there is still a need for highly sensitive probes that are suitable for in vivo imaging. One typical problem of available preclinical fluorescent probes is their rapid clearance in vivo, which reduces their imaging sensitivity. To circumvent rapid clearance, increase number of dye molecules at the target site, and thereby reduce background autofluorescence, encapsulation of the near-infrared fluorescent dye, DY-676-COOH in liposomes and verification of its potential for in vivo imaging of inflammation was done. DY-676 is known for its ability to self-quench at high concentrations. We first determined the concentration suitable for self-quenching, and then encapsulated this quenching concentration into the aqueous interior of PEGylated liposomes. To substantiate the quenching and activation potential of the liposomes we use a harsh freezing method which leads to damage of liposomal membranes without affecting the encapsulated dye. The liposomes characterized by a high level of fluorescence quenching were termed Lip-Q. We show by experiments with different cell lines that uptake of Lip-Q is predominantly by phagocytosis which in turn enabled the characterization of its potential as a tool for in vivo imaging of inflammation in mice models. Furthermore, we use a zymosan-induced edema model in mice to substantiate the potential of Lip-Q in optical imaging of inflammation in vivo. Considering possible uptake due to inflammation-induced enhanced permeability and retention (EPR) effect, an always-on liposome formulation with low, non-quenched concentration of DY-676-COOH (termed Lip-dQ) and the free DY-676-COOH were compared with Lip-Q in animal trials.

Fluorescence-quenching of a Liposomal-encapsulated Near-infrared Fluorophore as a Tool for In Vivo Optical Imaging

The use of fluorophores for in vivo imaging can be greatly limited by opsonization, rapid clearance, low detection sensitivity and cytotoxic effects on the host. Encapsulation of fluorophores in liposomes by film hydration and extrusion leads to fluorescence quenching and protection which enables in vivo imaging with high detection sensitivity.

のためのツールと​​してのリポソームカプセル化された近赤外蛍光体の蛍光消光<em&gt;インビボ</em&gt;光学イメージング

Optical imaging offers a wide range of diagnostic modalities and has attracted a lot of interest as a tool for biomedical imaging. Despite the enormous ...

Sandwich-like Microenvironments to Harness Cell/Material Interactions

Cell culture has been traditionally carried out on bi-dimensional (2D) substrates where cells adhere using ventral receptors to the biomaterial surface. However in vivo, most of the cells are completely surrounded by the extracellular matrix (ECM), resulting in a three-dimensional (3D) distribution of receptors. This may trigger differences in the outside-in signaling pathways and thus in cell behavior.
This article shows that stimulating the dorsal receptors of cells already adhered to a 2D substrate by overlaying a film of a new material (a sandwich-like culture) triggers important changes with respect to standard 2D cultures. Furthermore, the simultaneous excitation of ventral and dorsal receptors shifts cell behavior closer to that found in 3D environments. Additionally, due to the nature of the system, a sandwich-like culture is a versatile tool that allows the study of different parameters in cell/material interactions, e.g., topography, stiffness and different protein coatings at both the ventral and dorsal sides. Finally, since sandwich-like cultures are based on 2D substrates, several analysis procedures already developed for standard 2D cultures can be used normally, overcoming more complex procedures needed for 3D systems.

The following protocol describes the procedure to assemble sandwich-like cultures to be used as an intermediate stage between bi-dimensional (2D) and three-dimensional (3D) cellular environments. The engineered systems can have applications in microscopy, biomechanics, biochemistry and cell biology assays.

サンドイッチ状の微小環境は、Cell /材料の相互作用を活用します

Cell culture has been traditionally carried out on bi-dimensional (2D) substrates where cells adhere using ventral receptors to the biomaterial surface. ...

Preparation of 3D Collagen Gels and Microchannels for the Study of 3D Interactions In Vivo

Historically, most cellular processes have been studied in only 2 dimensions. While these studies have been informative about general cell signaling mechanisms, they neglect important cellular cues received from the structural and mechanical properties of the local microenvironment and extracellular matrix (ECM). To understand how cells interact within a physiological ECM, it is important to study them in the context of 3 dimensional assays. Cell migration, cell differentiation, and cell proliferation are only a few processes that have been shown to be impacted by local changes in the mechanical properties of a 3-dimensional ECM. Collagen I, a core fibrillar component of the ECM, is more than a simple structural element of a tissue. Under normal conditions, mechanical cues from the collagen network direct morphogenesis and maintain cellular structures. In diseased microenvironments, such as the tumor microenvironment, the collagen network is often dramatically remodeled, demonstrating altered composition, enhanced deposition and altered fiber organization. In breast cancer, the degree of fiber alignment is important, as an increase in aligned fibers perpendicular to the tumor boundary has been correlated to poorer patient prognosis1. Aligned collagen matrices result in increased dissemination of tumor cells via persistent migration2,3. The following is a simple protocol for embedding cells within a 3-dimensional, fibrillar collagen hydrogel. This protocol is readily adaptable to many platforms, and can reproducibly generate both aligned and random collagen matrices for investigation of cell migration, cell division, and other cellular processes in a tunable, 3-dimensional, physiological microenvironment.

Preparation of 3D Collagen Gels and Microchannels for the Study of 3D Interactions In Vivo

Collagen is a core component of the ECM, and provides essential cues for several cellular processes ranging from migration to differentiation and proliferation. Provided here is a protocol for embedding cells within 3D collagen hydrogels, and a more advanced technique for generating randomized or aligned collagen matrices using PDMS microchannels.

3D相互作用の研究のための3Dコラーゲンゲルおよびマイクロチャネルの作製<em&gt;インビボ</em

Historically, most cellular processes have been studied in only 2 dimensions.  While these studies have been informative about general cell signaling ...

DNA Nanotubes as a Versatile Tool to Study Semiflexible Polymers

Mechanical properties of complex, polymer-based soft matter, such as cells or biopolymer networks, can be understood in neither the classical frame of flexible polymers nor of rigid rods. Underlying filaments remain outstretched due to their non-vanishing backbone stiffness, which is quantified via the persistence length (lp), but they are also subject to strong thermal fluctuations. Their finite bending stiffness leads to unique, non-trivial collective mechanics of bulk networks, enabling the formation of stable scaffolds at low volume fractions while providing large mesh sizes. This underlying principle is prevalent in nature (e.g., in cells or tissues), minimizing the high molecular content and thereby facilitating diffusive or active transport. Due to their biological implications and potential technological applications in biocompatible hydrogels, semiflexible polymers have been subject to considerable study. However, comprehensible investigations remained challenging since they relied on natural polymers, such as actin filaments, which are not freely tunable. Despite these limitations and due to the lack of synthetic, mechanically tunable, and semiflexible polymers, actin filaments were established as the common model system. A major limitation is that the central quantity lp cannot be freely tuned to study its impact on macroscopic bulk structures. This limitation was resolved by employing structurally programmable DNA nanotubes, enabling controlled alteration of the filament stiffness. They are formed through tile-based designs, where a discrete set of partially complementary strands hybridize in a ring structure with a discrete circumference. These rings feature sticky ends, enabling the effective polymerization into filaments several microns in length, and display similar polymerization kinetics as natural biopolymers. Due to their programmable mechanics, these tubes are versatile, novel tools to study the impact of lp on the single-molecule as well as the bulk scale. In contrast to actin filaments, they remain stable over weeks, without notable degeneration, and their handling is comparably straightforward.

Semiflexible polymers display unique mechanical properties that are extensively applied by living systems. However, systematic studies on biopolymers are limited since properties such as polymer rigidity are inaccessible. This manuscript describes how this limitation is circumvented by programmable DNA nanotubes, enabling experimental studies on the impact of filament rigidity.

セミフレキシブル高分子を研究する多目的ツールとして DNA ナノチューブ

Mechanical properties of complex, polymer-based soft matter, such as cells or biopolymer networks, can be understood in neither the classical frame of ...