この作品は、オーストラリア国立保健医療研究評議会（NHMRC＃559007）と若年性糖尿病研究財団（JDRF 4-2006-1025）とビクトリア州政府の業務インフラスキームからの補助金によってサポートされています。我々は、ヒト組織を提供するためのトムマンデル膵島移植プログラムの膵島分離チームのメンバーに感謝。ヒトの組織は、ローカル倫理承認（聖ビンセント病院HREC-011/04とセント·ビンセント健康HREC-135/08）で収集され、使用されていました。

1。脾臓組織の準備<ol><li>注 - すべての人間の材料は、感染の危険として扱われるべきであり、すべての手続きは、クラスII層流内閣で実施すべきである。滅菌ハサミとピンセットを用いて、脾臓切片（サイズは〜1-2 CM）から脂肪や繊維組織を除去し、可能な限り外側のカプセル材料の限りを切り落とす。 </li><li>脾臓組織の小片（1〜2 cm 3）をカットし、滅菌した50mlファルコンチューブに各ピースを置きます。 </li><li>液体N 2中に浸漬することにより、組織の断片をスナップインの凍結。 </li><li> -80℃で保存同様のプロトコルは、他の組織（複数可）に適しています。 </li></ol> 2。ストレージ用ヒト膵島の準備<ol><li> CMRL培地で培養膵島。 10ミリリットルコニカルチューブに小島を収集し、5分間1,500 rpmで遠心分離することにより、PBSで2回洗浄する。 PBSを捨て、ペーパータオルの上に簡単に反転管を配置することによって、残った液を排水します。ないように注意する膵島を取り除きます。 </li><li>一度-80℃で液体窒素や店舗内にチューブとスナップ凍結℃に再キャップ、排水</li></ol> 3。抽出液を調製<ol><li> 4℃のBAWミックス（10:30:60％v / v）およびストアを準備℃に</li><li> -80℃からチューブを取り外し室温で解凍する。 </li><li>組織片をカバーするのに十分な氷のように冷たいBAWを追加します。小島が3-5 mlを使用しています。脾臓組織のための組織片の大きさに応じて10〜20ミリリットルを使用しています。 </li><li>組織ホモジナイザーを組み立てる。 70％エタノール/水の10〜20 mlを &quot;均質化&quot;によって清掃してください。 </li><li>組織とBAW溶液をチューブにホモジナイザーのプローブを配置した後、複数のバーストで組織をホモジナイズする。その後氷バケツにチューブを保持します。 </li><li>徹底的に10から20まで、70％エタノール/ mlの水とその後のBAWバッファを均質化することにより、サンプル間のホモジナイザーを清掃してください。これは、私たちの後に70％エタノール/水でsamples.Dismantleandクリーンとの間の組織の交差汚染を防止電子。 </li><li>唯一の水溶性物質を含有する抽出物が必要な場合は、RTで10分間4,000 rpmで均質化された組織抽出液を遠心分離します。より多くの粗抽出液が必要な場合は、室温で5分間1,000 rpmでスピン。 BAWの不溶性タンパク質を抽出するための最も適切な手法は、タンパク質の下流分析に依存します。機能的な免疫学的ア ​​ッセイで使用するために我々は以前に、これは6忍容性が良好であることが判明しているように、8 M尿素で不溶性画分を溶解しようとお勧めします。 </li><li>きれいなチューブに上清移し、氷の上に置いた。 </li><li> BCAアッセイまたは類似を使用して抽出液中のタンパク質の濃度を決定する。 </li></ol> 4。乾燥抽出物を凍結<ol><li>必要なタンパク質の質量（ すなわち 、チューブあたり100μg）に応じて、それに応じてホモジネートを希釈し、ラベルの付いた5.0ミリリットル滅菌、ファルコン（12x75 mm）のチューブにアリコートを分注する。私たちは頻繁には100μg/チューブを使用してください。 </li><li> 1を使用します各チューブのキャップに3つの穴を作るために8から20ゲージ滅菌注射針。 </li><li> 〜10分間ドライアイス上または&gt; 1時間-80℃の冷凍庫に入れて、どちらかのチューブを凍結。 -80℃で保存凍結乾燥機を置くために準備ができるまで。 </li><li>凍結乾燥機のスイッチを入れ、（-100℃）で平衡化させます。これは、約30分かかります。 </li><li>ボリュームに応じて、凍結乾燥を3時間以内に完了しますが、我々は日常的に一晩私たちのサンプルを残すことができます。 </li><li>乾燥サイクルが完了した後、真空ポンプのスイッチを切り、ゆっくりチャンバに圧力を許す。ラックを取り外します。 </li><li>無菌フードでは、チューブから穴あきキャップを外し、新しいもの（ファルコン352032）と交換してください。 </li><li> -20℃で保存して管サンプルは培養培地、または他の緩衝液中で再構成し、機能的または生化学的アッセイに使用することができる。 </li></ol> 5。代表的な結果 図1は、タンパク質の染色を示すゲルは脾臓および膵島枯渇膵臓組織（腺房のラベルが付いている）からの抽出物が搭載されており、ヒト膵島（ラベル付き小島）精製した。結果は、各組織ごとに異なる​​分子量のタンパク質の良い表現を示しています。 ヒトT細胞増殖を刺激する組織抽出物の容量はCFSEベースの増殖アッセイ7（ 図2）を用いて試験した。このアッセイにおいて使用PBMCは1型糖尿病を持つ個体から単離された。応答の大きさは、83.1 5000、CD4 +、CFSE明るい細胞あたりCFSE 薄暗い細胞数の比として表される：5000 CD4当たりCFSE 薄暗い細胞の+、三連の試料7からの抗原を持つ細胞のCFSE 明るい 。結果は、弱者を示すが、腺房に応じて検出可能な、増殖（CD1 = 3.5）および膵島エキス（6.8）への強い応答。不活化インフルエンザウイルス（CDI = 142.6）は次のように含まれていますポジティブコントロール。 <img alt="図1" src="/files/ftp_upload/4230/4230fig1.jpg" /> 図1タンパク質ゲル。 <img alt="図2" src="/files/ftp_upload/4230/4230fig2.jpg" /> 図2房と膵島エキスに対してCFSEベースの増殖アッセイの結果は。 <a href="http://www.jove.com/files/ftp_upload/4230/4230fig2large.jpg" target="_blank">拡大図を表示するにはここをクリック</a> 。

<ol>
	<li>Mannering, S. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Current+approaches+to+measuring+human+islet-antigen+specific+T+cell+function+in+type+1+diabetes.">Current approaches to measuring human islet-antigen specific T cell function in type 1 diabetes.</a> Clin. Exp. Immunol. 162, 197-209 (2010).</li><li>Beckhove, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+T+cell-based+identification+of+human+tumor+tissue+antigens+by+automated+two-dimensional+protein+fractionation.">Rapid T cell-based identification of human tumor tissue antigens by automated two-dimensional protein fractionation.</a> J. Clin. Invest. 120, 2230-2242 (2010).</li><li>Mannering, S. I., Brodnicki, T. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recent+insights+into+CD4++T-cell+specificity+and+function+in+Type+1+diabetes.">Recent insights into CD4+ T-cell specificity and function in Type 1 diabetes.</a> Expert Review of Clinical Immunology. 3, 557-564 (2007).</li><li>Mannering, S. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+A-chain+of+insulin+is+a+hot-spot+for+CD4++T+cell+epitopes+in+human+type+1+diabetes.">The A-chain of insulin is a hot-spot for CD4+ T cell epitopes in human type 1 diabetes.</a> Clin. Exp. Immunol. 156, 226-231 (2009).</li><li>Mannering, S. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+insulin+A-chain+epitope+recognized+by+human+T+cells+is+posttranslationally+modified.">The insulin A-chain epitope recognized by human T cells is posttranslationally modified.</a> J. Exp. Med. 202, 1191-1197 (2005).</li><li>Moon, H. C., Joffe, M., Thomas, H. E., Kay, T. W. H., Mannering, S. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+method+for+extracting+tissue+proteins+for+use+in+lymphocyte+function+assays.">A method for extracting tissue proteins for use in lymphocyte function assays.</a> Journal of Immunological Methods. 359, 56-60 (2010).</li><li>Mannering, S. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+sensitive+method+for+detecting+proliferation+of+rare+autoantigen-specific+human+T+cells.">A sensitive method for detecting proliferation of rare autoantigen-specific human T cells.</a> J. Immunol. Methods. 283, 173-183 (2003).</li><li>Mannering, S. I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CD4++T+Cell+Proliferation+in+Response+to+GAD+and+Proinsulin+in+Healthy,+Pre-diabetic,+and+Diabetic+Donors.">CD4+ T Cell Proliferation in Response to GAD and Proinsulin in Healthy, Pre-diabetic, and Diabetic Donors.</a> Ann. N.Y. Acad. Sci. 1037, 16-21 (2004).</li><li>Mannering, S. I., Purcell, A. W., Honeyman, M. C., McCluskey, J., Harrison, L. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+T-cells+recognise+N-terminally+Fmoc-modified+peptide.">Human T-cells recognise N-terminally Fmoc-modified peptide.</a> Vaccine. 21, 3638-3646 (2003).</li><li>Peakman, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+preparations+of+GAD65,+proinsulin,+and+the+islet+tyrosine+phosphatase+IA-2+for+use+in+detection+of+autoreactive+T-cells+in+type+1+diabetes:+report+of+phase+II+of+the+Second+International+Immunology+of+Diabetes+Society+Workshop+for+Standardization+of+T-cell+assays+in+type+1+diabetes.">Characterization of preparations of GAD65, proinsulin, and the islet tyrosine phosphatase IA-2 for use in detection of autoreactive T-cells in type 1 diabetes: report of phase II of the Second International Immunology of Diabetes Society Workshop for Standardization of T-cell assays in type 1 diabetes.</a> Diabetes. 50, 1749-1754 (2001).</li><li>Honey, K., Rudensky, A. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lysosomal+cysteine+proteases+regulate+antigen+presentation.">Lysosomal cysteine proteases regulate antigen presentation.</a> Nat. Rev. Immunol. 3, 472-482 (2003).</li></ol>

特別な利害関係は宣言されません。

我々はこのような界面活性剤などの有害な化学物質から自由であったヒト組織からの抽出物を生成したかったので、このプロトコルが開発されました。具体的に我々は、in vitroでのヒト免疫機能のアッセイに使用することができるヒト組織の抽出物を調製し、それを使用している。このプロトコルを使用して調製した抽出液を均等に任意のバッファで再構成し、そのようなウェスタン?...

<table border="1"><tbody><tr><td> 試薬の名称 </td><td> 会社 </td><td> カタログ番号 </td><td> 注釈 </td></tr><tr><td> 5ミリリットル12×75ミリメートル無菌ポリスチレンチューブ</td><td> BDファルコン</td><td> 352054 </td><td></td></tr><tr><td>チューブのポリスチレンチューブ用キャップ（上） </td><td> BDファルコン</td><td> 352032 </td><td></td></tr><tr><td> 50ミリリットル滅菌チューブ</td><td>ベクトン·ディッキンソン</td><td> 352070 </td><td></td></tr><tr><td>アセトニトリル</td><td> Mallinckradtケミカル</td><td> 2856から10 </td><td></td></tr><tr><td>ブタン-1 - オール</td><td>シグマアルドリッチ</td><td> 537993-IL </td><td></td></tr><tr><td>ホモジナイザー：PRO200 </td><td>バイオ戦略</td><td> 01-01200 </td><td> 10×115ミリメートルのこぎりジェネレータ</td></tr><tr><td>凍結乾燥機</td><td></td><td></td><td> VIRTIS、ベンチ4K </td></tr><tr><td>滅菌針18から20ゲージ</td><td>ベクトン·ディッキンソン</td><td> REF 302032 </td><td></td></tr><tr><td> CMRL-1066ミディアム</td><td>シグマ</td><td> C0422 </td><td></td></tr><tr><td> PBS </td><td>シグマ</td><td> D8537 </td><td></td></tr></tbody></table> 表1に特異的な試薬や機器。

extraction of tissue antigens for functional assays

A、BおよびT細胞によって認識される、適応免疫応答の抗原標的の多くは1に定義されていない。これは、自己免疫疾患や癌2に特に当てはまります。私たちの目的は、自己免疫疾患の1型糖尿病1,3,4,5にヒトT細胞により認識される抗原を調べることである。 T細胞によって認識される抗原が同定されていない組織に対してヒトT細胞応答を分析するために、我々は機能的アッセイ6と互換性のあるフォーマットでヒト組織からタンパク質抗原を抽出する手法を開発しました。抽出方法は、ヒト末梢血単核細胞に有毒であった洗剤が含まれていることをライセートをもたらすので、以前は、未精製の組織抽出物に対するT細胞応答を測定することができなかった。ここでは、ヒトT細胞に有毒ではない形式でヒト組織からタンパク質を抽出するためのプロトコルを記述します。組織はブタン-1 - オール、アセトニトリル、ワットの混合物中で均質化されるER（BAW）。組織抽出液中のタンパク質濃度が測定され、タンパク質の既知の質量をチューブに等分されています。抽出後、有機溶媒は凍結乾燥によって除去される。必要になるまで凍結乾燥組織抽出物を保存することができます。免疫機能、免疫細胞の懸濁液のアッセイに使用するためには、適切な培養培地中で、凍結乾燥した抽出液に直接添加することができる。 PBMCによるサイトカイン産生と増殖は、この方法を用いて調製した抽出物に応じて、容易に測定した。したがって、我々の方法は、T細胞応答の解析における抗原のソースとして使用することができ、人間の組織ライセートの急速な製造を可能にする。我々は、この方法は移植、がんや自己免疫の組織への適応免疫応答の解析を容易にするであろうことを示唆している。

Watch this Scientific Journal Video about Extraction of Tissue Antigens for Functional Assays at JoVE.com

Extraction of Tissue Antigens for Functional Assays

機能的なT細胞アッセイにおける抗原のソースとして使用するヒト組織の抽出物を調製するための単純なプロトコルが記載されている。この方法は、組織由来の抗原に対するT細胞の反応を測定することができる<em&gt; in vitroで</em&gt;。

機能アッセイのための組織抗原の抽出

Many of the antigen targets of adaptive immune response, recognized by B and T cells, have not been defined 1. This is particularly true in autoimmune ...

extraction-of-tissue-antigens-for-functional-assays

Research

JoVE Journal

Biology

10.8K ビュー.  St. Vincent's Institute of Medical Research. 機能的なT細胞アッセイにおける抗原のソースとして使用するヒト組織の抽出物を調製するための単純なプロトコルが記載されている。この方法は、組織由来の抗原に対するT細胞の反応を測定することができる in vitroで。

ビデオ: Extraction of Tissue Antigens for Functional Assays

Light/dark Transition Test for Mice

Although all of the mouse genome sequences have been determined, we do not yet know the functions of most of these genes. Gene-targeting techniques, however, can be used to delete or manipulate a specific gene in mice. The influence of a given gene on a specific behavior can then be determined by conducting behavioral analyses of the mutant mice. As a test for behavioral phenotyping of mutant mice, the light/dark transition test is one of the most widely used tests to measure anxiety-like behavior in mice. The test is based on the natural aversion of mice to brightly illuminated areas and on their spontaneous exploratory behavior in novel environments. The test is sensitive to anxiolytic drug treatment. The apparatus consists of a dark chamber and a brightly illuminated chamber. Mice are allowed to move freely between the two chambers. The number of entries into the bright chamber and the duration of time spent there are indices of bright-space anxiety in mice. To obtain phenotyping results of a strain of mutant mice that can be readily reproduced and compared with those of other mutants, the behavioral test methods should be as identical as possible between laboratories. The procedural differences that exist between laboratories, however, make it difficult to replicate or compare the results among laboratories. Here, we present our protocol for the light/dark transition test as a movie so that the details of the protocol can be demonstrated. In our laboratory, we have assessed more than 60 strains of mutant mice using the protocol shown in the movie. Those data will be disclosed as a part of a public database that we are now constructing.

Visualization of the protocol will facilitate understanding of the details of the entire experimental procedure, allowing for standardization of the protocols used across laboratories and comparisons of the behavioral phenotypes of various strains of mutant mice assessed using this test.

The light/dark transition test is one of the most widely used tests to measure anxiety-like behavior in mice. Here, we present a movie that shows detailed procedures on how we conduct the test.

マウス用ダーク/ライト遷移テスト

Although all of the mouse genome sequences have been determined, we do not yet know the functions of most of these genes. Gene-targeting techniques, ...

生物学

Actin Co-Sedimentation Assay; for the Analysis of Protein Binding to F-Actin

The actin cytoskeleton within the cell is a network of actin filaments that allows the movement of cells and cellular processes, and that generates tension and helps maintains cellular shape.  Although the actin cytoskeleton is a rigid structure, it is a dynamic structure that is constantly remodeling.  A number of proteins can bind to the actin cytoskeleton.  The binding of a particular protein to F-actin is often desired to support cell biological observations or to further understand dynamic processes due to remodeling of the actin cytoskeleton. The actin co-sedimentation assay is an in vitro assay routinely used to analyze the binding of specific proteins or protein domains with F-actin.  The basic principles of the assay involve an incubation of the protein of interest (full length or domain of) with F-actin, ultracentrifugation step to pellet F-actin and analysis of the protein co-sedimenting with F-actin.  Actin co-sedimentation assays can be designed accordingly to measure actin binding affinities and in competition assays.

Proteins bind to filamentous actin (F-actin) through distinct actin binding modules. In this video we demonstrate the procedure of actin co-sedimentation, which is an in vitro assay routinely used to analyze proteins or specific domains that bind F-actin.

アクチン共沈降アッセイ、F -アクチンへの結合タンパク質の解析のための

The actin cytoskeleton within the cell is a network of actin filaments that allows the movement of cells and cellular processes, and that generates ...

Crystallizing Membrane Proteins for Structure Determination using Lipidic Mesophases

A detailed protocol for crystallizing membrane proteins by using lipidic mesophases is described. This method has variously been referred to as the lipidic cubic phase or in meso method. The method has been shown to be quite versatile in that it has been used to solve X-ray crystallographic structures of prokaryotic and eukaryotic proteins, proteins that are monomeric, homo- and hetero-multimeric, chromophore-containing and chromophore-free, and alpha-helical and beta-barrel proteins. Recent successes using in meso crystallization are the human engineered beta2-adrenergic and adenosine A2a G protein-coupled receptors. Protocols are presented for reconstituting the membrane protein into the monoolein-based mesophase, and for setting up crystallizations in the manual mode. Additional steps in the overall process, such as crystal harvesting, are to be addressed in future video articles. The time required to prepare the protein-loaded mesophase and to set up a crystallization plate manually is about one hour.

Herein is described the procedure implemented in the Caffrey Membrane Structural and Functional Biology Group to set up manually crystallization trials of membrane proteins in lipidic mesophases.

脂質中間相を用いた構造決定のための膜タンパク質の結晶化

A detailed protocol for crystallizing membrane proteins by using lipidic mesophases is described. This method has variously been referred to as the ...

Pharmacological and Functional Genetic Assays to Manipulate Regeneration of the Planarian Dugesia japonica

Free-living planarian flatworms have a long history of experimental usage owing to their remarkable regenerative abilities1. Small fragments excised from these animals reform the original body plan following regeneration of missing body structures. For example if a 'trunk' fragment is cut from an intact worm, a new 'head' will regenerate anteriorly and a 'tail' will regenerate posteriorly restoring the original 'head-to-tail' polarity of body structures prior to amputation (Figure 1A).
Regeneration is driven by planarian stem cells, known as 'neoblasts' which differentiate into ~30 different cell types during normal body homeostasis and enforced tissue regeneration. This regenerative process is robust and easy to demonstrate. Owing to the dedication of several pioneering labs, many tools and functional genetic methods have now been optimized for this model system. Consequently, considerable recent progress has been made in understanding and manipulating the molecular events underpinning planarian developmental plasticity2-9.
The planarian model system will be of interest to a broad range of scientists. For neuroscientists, the model affords the opportunity to study the regeneration of an entire nervous system, rather than simply the regrowth/repair of single nerve cell process that typically are the focus of study in many established models. Planarians express a plethora of neurotransmitters10, represent an important system for studying evolution of the central nervous system11, 12 and have behavioral screening potential13, 14. 
Regenerative outcomes are amenable to manipulation by pharmacological and genetic apparoaches. For example, drugs can be screened for effects on regeneration simply by placing body fragments in drug-containing solutions at different time points after amputation. The role of individual genes can be studied using knockdown methods (in vivo RNAi), which can be achieved either through cycles of microinjection or by feeding bacterially-expressed dsRNA constructs8, 9, 15. Both approaches can produce visually striking phenotypes at high penetrance- for example, regeneration of bipolar animals16-21. To facilitate adoption of this model and implementation of such methods, we showcase in this video article protocols for pharmacological and genetic assays (in vivo RNAi by feeding) using the planarian Dugesia japonica.

Pharmacological and Functional Genetic Assays to Manipulate Regeneration of the Planarian Dugesia japonica

An attractive model for studying stem cell differentiation within a live animal is the planarian flatworm. Regeneration is studied by simple amputation experiments that are easily performed in a basic laboratory and are amenable to pharmacological and genetic (in vivo RNAi) manipulation as detailed by protocols in this article.

プラナリアの再生を操作するために薬理学的および機能的遺伝学的アッセイ<emジャポニカ> Dugesia</em

Free-living planarian flatworms have a long history of experimental usage owing to their remarkable regenerative abilities1. Small fragments excised from ...

Use of a Robot for High-throughput Crystallization of Membrane Proteins in Lipidic Mesophases

Structure-function studies of membrane proteins greatly benefit from having available high-resolution 3-D structures of the type provided through macromolecular X-ray crystallography (MX). An essential ingredient of MX is a steady supply of ideally diffraction-quality crystals. The in meso or lipidic cubic phase (LCP) method for crystallizing membrane proteins is one of several methods available for crystallizing membrane proteins. It makes use of a bicontinuous mesophase in which to grow crystals. As a method, it has had some spectacular successes of late and has attracted much attention with many research groups now interested in using it. One of the challenges associated with the method is that the hosting mesophase is extremely viscous and sticky, reminiscent of a thick toothpaste. Thus, dispensing it manually in a reproducible manner in small volumes into crystallization wells requires skill, patience and a steady hand. A protocol for doing just that was developed in the Membrane Structural &amp; Functional Biology (MS&amp;FB) Group1-3. JoVE video articles describing the method are available1,4. 
The manual approach for setting up in meso trials has distinct advantages with specialty applications, such as crystal optimization and derivatization. It does however suffer from being a low throughput method. Here, we demonstrate a protocol for performing in meso crystallization trials robotically. A robot offers the advantages of speed, accuracy, precision, miniaturization and being able to work continuously for extended periods under what could be regarded as hostile conditions such as in the dark, in a reducing atmosphere or at low or high temperatures. An in meso robot, when used properly, can greatly improve the productivity of membrane protein structure and function research by facilitating crystallization which is one of the slow steps in the overall structure determination pipeline. 
In this video article, we demonstrate the use of three commercially available robots that can dispense the viscous and sticky mesophase integral to in meso crystallogenesis. The first robot was developed in the MS&amp;FB Group5,6. The other two have recently become available and are included here for completeness.	
An overview of the protocol covered in this article is presented in Figure 1. All manipulations were performed at room temperature (~20 &deg;C) under ambient conditions.

Herein is described a robotic approach to high-throughput crystallization of membrane proteins in lipidic mesophases for use in structure determination using macromolecular X-ray crystallography. Three robots capable of handling the viscous and sticky protein-laden mesophase integral to the method are introduced.

脂質中間相における膜タンパク質のハイスループット結晶化のためのロボットの使用

Structure-function studies of membrane proteins greatly benefit from having available high-resolution 3-D structures of the type provided through ...

Small-scale Nuclear Extracts for Functional Assays of Gene-expression Machineries

A great deal of progress in understanding gene expression has been made using in vitro systems. For most studies, functional assays are carried out using extracts that are prepared in bulk from 10-50 or more liters of cells grown in suspension. However, these large-scale preparations are not amenable to rapidly testing in vitro effects that result from a variety of in vivo cellular treatments or conditions. This journal video article shows a method for preparing functional small-scale nuclear extracts, using HeLa cells as an example. This method is carried out using as few as three 150 mm plates of cells grown as adherent monolayers. To illustrate the efficiency of the small-scale extracts, we show that they are as active as bulk nuclear extracts for coupled RNA Polymerase II transcription/splicing reactions. To demonstrate the utility of the extract protocol, we show that splicing is abolished in extracts prepared from HeLa cells treated with the splicing inhibitor drug E7107. The small-scale protocol should be generally applicable to any process or cell type that can be investigated in vitro using cellular extracts. These include patient cells that are only available in limited quantities or cells exposed to numerous agents such as drugs, DNA damaging agents, RNAi, or transfection, which require the use of small cell populations. In addition, small amounts of freshly grown cells are convenient and/or required for some applications.

A protocol for preparation of robust, small-scale HeLa nuclear extracts is described. This protocol is valuable for assays that require use of small populations of cells, such as cells treated with drugs or RNAi. The method should be applicable to a wide variety of gene expression assays and other cell types, including patient cells.

遺伝子発現用機械の機能的アッセイのための小規模の核抽出物

A great deal of progress in understanding gene expression has been made using in vitro systems.  For most studies, functional assays are carried out using ...

Viability Assays for Cells in Culture

Manual cell counts on a microscope are a sensitive means of assessing cellular viability but are time-consuming and therefore expensive. Computerized viability assays are expensive in terms of equipment but can be faster and more objective than manual cell counts. The present report describes the use of three such viability assays. Two of these assays are infrared and one is luminescent. Both infrared assays rely on a 16&#160;bit Odyssey Imager. One infrared assay uses the DRAQ5 stain for nuclei combined with the Sapphire stain for cytosol and is visualized in the 700 nm channel. The other infrared assay, an In-Cell Western, uses antibodies against cytoskeletal proteins (&#945;-tubulin or microtubule associated protein 2) and labels them in the 800 nm channel. The third viability assay is a commonly used luminescent assay for ATP, but we use a quarter of the recommended volume to save on cost. These measurements are all linear and correlate with the number of cells plated, but vary in sensitivity. All three assays circumvent time-consuming microscopy and sample the entire well, thereby reducing sampling error. Finally, all of the assays can easily be completed within one day of the end of the experiment, allowing greater numbers of experiments to be performed within short timeframes. However, they all rely on the assumption that cell numbers remain in proportion to signal strength after treatments, an assumption that is sometimes not met, especially for cellular ATP. Furthermore, if cells increase or decrease in size after treatment, this might affect signal strength without affecting cell number. We conclude that all viability assays, including manual counts, suffer from a number of caveats, but that computerized viability assays are well worth the initial investment. Using all three assays together yields a comprehensive view of cellular structure and function.

Therapeutic compounds are often first examined in vitro with viability assays. Blind cell counts by a human observer can be highly sensitive to small changes in cell number but do not assess function. Computerized viability assays, as described here, can assess both structure and function in an objective manner.

培養中の細胞のための生存率アッセイ

Manual cell counts on a microscope are a sensitive means of assessing cellular viability but are time-consuming and therefore expensive. Computerized ...

Isolation and Functional Analysis of Mitochondria from Cultured Cells and Mouse Tissue

Comparison between two or more distinct groups, such as healthy vs. disease, is necessary to determine cellular status. Mitochondria are at the nexus of cell heath due to their role in both cell metabolism and energy production as well as control of apoptosis. Therefore, direct evaluation of isolated mitochondria and mitochondrial perturbation offers the ability to determine if organelle-specific (dys)function is occurring. The methods described in this protocol include isolation of intact, functional mitochondria from HEK cultured cells and mouse liver and spinal cord, but can be easily adapted for use with other cultured cells or animal tissues. Mitochondrial function assessed by TMRE and the use of common mitochondrial uncouplers and inhibitors in conjunction with a fluorescent plate reader allow this protocol not only to be versatile and accessible to most research laboratories, but also offers high throughput.

Comparison of mitochondrial membrane potential between samples yields valuable information about cellular status. Detailed steps for isolating mitochondria and assessing response to inhibitors and uncouplers using fluorescence are described. The method and utility of this protocol are illustrated by use of a cell culture and animal model of cellular stress.

培養細胞およびマウス組織から単離とミトコンドリアの機能解析

Comparison between two or more distinct groups, such as healthy vs. disease, is necessary to determine cellular status. Mitochondria are at the nexus of ...

Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction

Formalin-fixed paraffin embedded tissue (FFPET) represents a valuable, well-annotated substrate for molecular investigations. The utility of FFPET in molecular analysis is complicated both by heterogeneous tissue composition and low yields when extracting nucleic acids. A literature search revealed a paucity of protocols addressing these issues, and none that showed a validated method for simultaneous extraction of RNA and DNA from regions of interest in FFPET. This method addresses both issues. Tissue specificity was achieved by mapping cancer areas of interest on microscope slides and transferring annotations onto FFPET blocks. Tissue cores were harvested from areas of interest using 0.6 mm microarray punches. Nucleic acid extraction was performed using a commercial FFPET extraction system, with modifications to homogenization, deparaffinization, and Proteinase K digestion steps to improve tissue digestion and increase nucleic acid yields. The modified protocol yields sufficient quantity and quality of nucleic acids for use in a number of downstream analyses, including a multi-analyte gene expression platform, as well as reverse transcriptase coupled real time PCR analysis of mRNA expression, and methylation-specific PCR (MSP) analysis of DNA methylation.

This modified extraction protocol improves RNA and DNA yields from more precisely targeted regions of interest in histopathologic tissue blocks.

RNA及びDNA抽出の両方のためのホルマリン固定パラフィン包埋組織コアの調製

Formalin-fixed paraffin embedded tissue (FFPET) represents a valuable, well-annotated substrate for molecular investigations. The utility of FFPET in ...

Study of Protein-protein Interactions in Autophagy Research

Protein-protein interactions are important for understanding cellular signaling cascades and identifying novel pathway components and protein dynamics. The majority of cellular activities require physical interactions between proteins. To analyze and map these interactions, various experimental techniques as well as bioinformatics tools were developed. Autophagy is a cellular recycling mechanism that allows the cells to cope with different stressors, including nutrient deprivation, chemicals, and hypoxia. In order to better understand autophagy-related signaling events and to discover novel factors that regulate protein complexes in autophagy, we performed protein-protein interaction screens. Validation of these screening results requires the use of immunofluorescence and immunoprecipitation techniques. In this system, specific autophagy-related protein-protein interactions that we discovered were tested in Neuro2A (N2A) and HEK293T cell lines. Details of the technical procedures used are explained in this visualized experiment paper.

Presented here are two antibody-based protein-protein interaction research techniques: immunofluorescence and immunoprecipitation. These techniques are suitable for studying physical interactions between proteins for the discovery of novel components of cellular signaling pathways and for understanding protein dynamics.

オートファジー研究でタンパク質間相互作用の研究

Protein-protein interactions are important for understanding cellular signaling cascades and identifying novel pathway components and protein dynamics. ...

Methods Article

機能アッセイのための組織抗原の抽出