These experiments have been supported by research grants from Merck and Co. and Summit, PLC.

異なる環境または臨床源からC.ディフィシルを単離する<ol><li>環境分離物：0.85％NaClで軽く濡らした滅菌済み綿ゲージを使用して、関心領域（床、ドア、ハンドル、棚など ）の表面を拭きます。 8滅菌手袋を着用し、綿棒を滅菌済みのチューブに入れてください。 </li><li>臨床分離株（便）：接種ループを使用してセフォキシチン - サイクロセリン - フルクトース寒天（CCFA）上に10〜100mgの臨床便検体をプレートし、厳重な嫌気条件下で48〜72時間インキュベートする。さらなる分析のために、 CryovialsにC.difficileストックの分離したコロニーを-80℃で保存する。 7,9,10 </li><li> 0.05％タウロコール酸ナトリウムを含むブレインハートインフュージョン（BHI）ブロスの環境スワブサンプルを濃縮し、37℃の嫌気性チャンバーに入れます5日間。 10,000×gで1mLの培養液を遠心分離し、100μLのエタノールにペレットを再懸濁する。 </li><li>再懸濁した細胞（50μL）をシクロセリン・エキシチン・フルクトース寒天（CCFA）プレート上にプレートし、37℃で40〜48時間嫌気性チャンバーでインキュベートする。さらなる分析のために、 CryovialsにC.difficileストックの分離したコロニーを-80℃で保存する。 </li><li>ラテックス凝集試薬またはPCRを用いて疑わしいクロストリジウム・ディフィシル（C.difficile）コロニーを試験する。 </li></ol> C.ディフィシルの培養およびキネティクス手順の殺傷<ol><li> 37℃で48時間、嫌気性チャンバー内の血液寒天プレート上の精製された環境的または臨床的C.ディフィシレ株を増殖させる。 </li><li>接種ループで1つの単離コロニーをとり、15 mLチューブで5 mL BHI培地に移し、37℃の嫌気性チャンバーで24時間増殖させます。 </li><li>前培養1：100を約10 6コロニー形成単位0.1％タウロコール酸ナトリウムおよび適切な濃度の抗生物質（T0）を補充した新鮮な予備還元BHIS（BHI + 5g / L酵母抽出物および1％L-システイン）中でのs（CFU）/ mL。 </li><li>各時点（T0、T6、T24、T48）でピペットを用いて1mLのサンプルを採取し、少量（100μLを連続希釈したもの）を血液寒天プレート上に撒き散布する。細胞を37℃の嫌気性チャンバー内で48時間血液寒天プレート上で増殖させ、得られたコロニー数をカウントしてCFUを決定する。 </li></ol>走査型電子顕微鏡のための試料の準備<ol><li>マイクロ遠心チューブの各時点から1 mLの細胞を集め、10,000 xgで10分間遠心分離します。上清を捨て、PBSで細胞を洗浄する。 </li><li> 10,000xgで10分間再度サンプルを遠心分離し、上清を捨てる。 1mLの4％パラホルムアルデヒドで細胞を再希釈し、室温で1時間インキュベートする。 </li><li>サンプルを再び1分間10分間遠心分離する。0,000xgで上清を捨てる。細胞を蒸留水で2回洗浄し、100μLの蒸留水で再希釈する。溶液の濁度に応じて容量を調整する。 注：複数の連続希釈を行うことは良い考えです。 </li><li>カバースリップにラベルを貼り、40μLのサンプルを加えます。フローフード内で15分間インキュベートして液体を蒸発させ、細胞をカバーグラスに接着させる。液体がまだ残っている場合は、ブロワーを使用して液体を取り除いてください。 </li><li>机上のスパッタリング装置に細胞をラベルしたカバースリップを置き、テープを剥がします。スパッタリング装置に純金を固定します。機械をオンにし、低圧（50mTorr）でスパッタリングを開始する。 80nmで30秒間被覆し、20nmの金コーティングとなる。 </li><li>コーティングされた細胞を走査電子顕微鏡に移す。 </li></ol> 4.走査電子顕微鏡上のC.ディフィシレ細胞の画像化<ol><li>走査電子顕微鏡（SEM）を適切に通気するコンピュータソフトウェアのベントボタンを押す。 </li><li>カーボンテープを使用して、コーティングされたカバーガラスを金属ステージに固定します。 SEMが通気されると、ドアは容易に開くはずです。金属ステージをねじ込むことでSEMチャンバーに固定します。 </li><li>コンピュータソフトウェアのPUMPボタンをクリックします。 SEMが &quot;Vac OK&quot;と表示されているときにSEMを使用できます。 </li><li> DetectorタブのSE検出器をクリックします。電圧を表示するボタンをクリックしてビームをオンにします。電圧を上げる前に、より低い電圧（5 kV）でイメージングを開始します（最大15 kV）。ビームがオンになった後に画像が表示されます。 </li><li>トラッキング機能を使用して、コーティングされたカバースリップの画像を描く領域を見つけます。領域を拡大し、棒状の構造を見つける。これらはクロストリジウム・ディフィシルである。 </li><li>システムを較正するために、画像を拡大して焦点を合わせる。これは、複数の作業距離（15,9および5 mm）で行う必要があります。 5mmの作動距離で画像。 </li><li>あなたのスイッチを入れて高解像度のイメージングモードを開始し、非点収差の焦点合わせと最適化を開始します。 </li><li>高倍率でピントを合わせ始める。これを行うには、粗くて細かいフォーカストグルを使用します。非点収差も同様に調整して、より鮮明な画像を得る。 <ol><li>高倍率で非点収差を調整する。これを行うには、非点収差トグル（微妙な/粗いフォーカストグルに似ています）を調整し、コンピュータソフトウェアをデジタルズームして画像を明瞭に確認します。 </li></ol></li><li>スロースキャン機能を使用して高品質の画像を収集します。収集した画像を解析に使用する.TIFFファイルとして保存します。分析中に測定が行われる場合は、データバーが選択されていることを確認してください。 </li><li>角度を変えて画像を収集する（手動で角度をSEMで直接回転させることで最大52°まで）角度のついた画像はより深い情報を示す傾向があります。 </li><li>撮影されている細胞に応じてビーム電圧を変更します。これは、ほとんどの場合、5〜15 kVの間で行います。 </li&gt; <li>イメージングが完了したら、ビームをオフにし、作動距離を20 mmに上げます。その後、チャンバを通気することができ、ステージを取り外すことができる。さらに分析するために、すべての画像をドライブにコピーします。 </li></ol> 5.画像処理と解析<ol><li>自由に利用できるソフトウェアFIJI（http://fiji.sc）をコンピュータにダウンロードしてインストールします。 </li><li> FIJIで画像ファイルを開きます。 </li><li>ライン機能を使用して、スケールバーを正確にトレースします。 </li><li> FIJIプログラムのAnalyzeタブをクリックし、最後にSelect Scaleを選択します。スケールバーに基づいて既知の距離の設定が必要なウィンドウが表示されます。長さの単位も変更し、[OK]をクリックします。 </li><li>プログラムが距離に対して校正されたので、ライン関数を使用してセルの長さを測定します。長さを取得するには、line関数を使用して、セル全体をトレースします。 [分析]タブを再度選択し、[測定]をクリックします。長さはappでなければならない以前に示されたユニットの耳。 </li></ol>

<ol>
	<li>Lessa, F. 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=Burden+of+Clostridium+difficile+infection+in+the+United+States.">Burden of Clostridium difficile infection in the United States.</a> N Engl J Med. 372 (9), 825-834 (2015).</li><li>Vickers, R. 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G., 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=New+EMA+guideline+for+antimicrobial+development.">New EMA guideline for antimicrobial development.</a> Lancet Infect Dis. 12 (4), 265-266 (2012).</li><li>Bass&#232;res, E., 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=Impact+on+toxin+production+and+cell+morphology+in+Clostridium+difficile+by+ridinilazole+(SMT19969),+a+novel+treatment+for+C.+difficile+infection.">Impact on toxin production and cell morphology in Clostridium difficile by ridinilazole (SMT19969), a novel treatment for C. difficile infection.</a> J Antimicrob Chemother. 71 (5), 1245-1251 (2016).</li><li>Endres, B. T., 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=A+novel+method+for+imaging+the+pharmacological+effects+of+antibiotic+treatment+on+Clostridium+difficile.">A novel method for imaging the pharmacological effects of antibiotic treatment on Clostridium difficile.</a> Anaerobe. 40, 10-14 (2016).</li><li>Endres, B. T., 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=Evaluating+the+Effects+of+Surotomycin+Treatment+on+Clostridium+difficile+Toxin+A+and+B+Production,+Immune+Response,+and+Morphological+Changes.">Evaluating the Effects of Surotomycin Treatment on Clostridium difficile Toxin A and B Production, Immune Response, and Morphological Changes.</a> Antimicrob Agents Chemother. 60 (6), 3519-3523 (2016).</li><li>Alam, M. J., Anu, A., Walk, S. T., Garey, K. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Investigation+of+potentially+pathogenic+Clostridium+difficile+contamination+in+household+environs.">Investigation of potentially pathogenic Clostridium difficile contamination in household environs.</a> Anaerobe. 27, 31-33 (2014).</li><li>Aitken, S. L., 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=In+the+Endemic+Setting,+Clostridium+difficile+Ribotype+027+Is+Virulent+But+Not+Hypervirulent.">In the Endemic Setting, Clostridium difficile Ribotype 027 Is Virulent But Not Hypervirulent.</a> Infect Control Hosp Epidemiol. , 1-6 (2015).</li><li>Basseres, E., 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=Impact+on+toxin+production+and+cell+morphology+in+Clostridium+difficile+by+ridinilazole+(SMT19969),+a+novel+treatment+for+C.+difficile+infection.">Impact on toxin production and cell morphology in Clostridium difficile by ridinilazole (SMT19969), a novel treatment for C. difficile infection.</a> J Antimicrob Chemother. 71 (5), 1245-1251 (2016).</li><li>Walters, B. A., Roberts, R., Stafford, R., Seneviratne, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relapse+of+antibiotic+associated+colitis:+endogenous+persistence+of+Clostridium+difficile+during+vancomycin+therapy.">Relapse of antibiotic associated colitis: endogenous persistence of Clostridium difficile during vancomycin therapy.</a> Gut. 24 (3), 206-212 (1983).</li><li>Chilton, C. H., 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=Evaluation+of+the+effect+of+oritavancin+on+Clostridium+difficile+spore+germination,+outgrowth+and+recovery.">Evaluation of the effect of oritavancin on Clostridium difficile spore germination, outgrowth and recovery.</a> J Antimicrob Chemother. 68 (9), 2078-2082 (2013).</li><li>Ofosu, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clostridium+difficile+infection:+a+review+of+current+and+emerging+therapies.">Clostridium difficile infection: a review of current and emerging therapies.</a> Ann Gastroenterol. 29 (2), 147-154 (2016).</li><li>McDonald, L. 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=An+epidemic,+toxin+gene-variant+strain+of+Clostridium+difficile.">An epidemic, toxin gene-variant strain of Clostridium difficile.</a> New Eng J Med. 353 (23), 2433-2441 (2005).</li></ol>

KWG has received past and current research support from Merck &amp; Co. and Summit, PLC.

現在の研究の目的は、C.difficileを単離し、抗生物質の薬理学的作用のより完全な特徴付けのための手段として走査型電子顕微鏡（SEM）を用いて抗生物質感受性を試験するためのハイスループット法を作製することであった。本明細書で概説したプロトコールを用いて、抗生物質治療に対する細胞の表現型応答を画像化することにより、薬物の薬理学的作用についての洞察を明らかにすること?...

Clostridium difficileはグラム陽性の胞子形成細菌であり、米国では毎年約50万の感染を引き起こし、最高レベルのリスクである疾病防除センター（CDC）による脅威レベルの緊急の病原体と考えられています。 1過去10年間に、クロストリジウム・ディフィシレ（C.difficile）に対する抗菌剤の開発が著しかった。 インビトロ研究は、薬物開発プロセスの必要な要素です。伝統的に、 インビトロ感受性および時間殺滅試験は、将来の動物および他のインビボ研究を検証するために使用される。 これらの方法は殺傷作用を評価するために重要な役割を果たすが、薬理学的治療に対する細胞の表現型応答を捕捉しない。スタンドで走査型電子顕微鏡（SEM）を組み込むことにより動力学研究を殺すと、抗生物質の直接的効果のより完全な特徴付けが可能である。ここでは、SEMを抗生物質治療の有効性をプロファイルする手段として使用する方法を提示する。

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>cotton gauze&#160;</td>
			<td>Caring</td>
			<td>PRM21408C</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Macron</td>
			<td>7532</td>
			<td></td>
		</tr>
		<tr>
			<td>50mL tubes</td>
			<td>Falcon</td>
			<td>352098</td>
			<td></td>
		</tr>
		<tr>
			<td>Brain Heart Infusion (BHI)&#160;</td>
			<td>Criterion</td>
			<td>C5141</td>
			<td></td>
		</tr>
		<tr>
			<td>L-cysteine</td>
			<td>Alfa Aesar</td>
			<td>A10389</td>
			<td></td>
		</tr>
		<tr>
			<td>yeast extract</td>
			<td>Criterion</td>
			<td>C741</td>
			<td></td>
		</tr>
		<tr>
			<td>sodium taurocholate</td>
			<td>Alfa Aesar</td>
			<td>A18346</td>
			<td></td>
		</tr>
		<tr>
			<td>anaerobic chamber</td>
			<td>Coy</td>
			<td></td>
			<td>vinyl anaerobic chamber</td>
		</tr>
		<tr>
			<td>cycloserinecefoxitin fructose agar (CCFA) plates</td>
			<td>Anaerobe systems</td>
			<td>AS-213</td>
			<td></td>
		</tr>
		<tr>
			<td>blood agar plates</td>
			<td>Hardy diagnostics</td>
			<td>A-10</td>
			<td></td>
		</tr>
		<tr>
			<td>latex agglutination reagent</td>
			<td>Oxoid</td>
			<td>DR1107A</td>
			<td>C. diff test kit</td>
		</tr>
		<tr>
			<td>microcentrifuge tubes</td>
			<td>Eppendorf</td>
			<td>222363204</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>Gibco</td>
			<td>10010-031</td>
			<td></td>
		</tr>
		<tr>
			<td>4% paraformaldehyde</td>
			<td>Fisher Scientific</td>
			<td>50-259-98</td>
			<td></td>
		</tr>
		<tr>
			<td>microscope slides</td>
			<td>J. Melvin freed brand</td>
			<td>7525M</td>
			<td>75x25mm</td>
		</tr>
		<tr>
			<td>flow hood</td>
			<td>Labconco</td>
			<td>Class II type A2&#160;</td>
			<td>biosafety cabinet</td>
		</tr>
		<tr>
			<td>desk sputtering machine</td>
			<td>Denton Vacuum</td>
			<td>Desk II</td>
			<td></td>
		</tr>
		<tr>
			<td>tape</td>
			<td>Plastic Core</td>
			<td>05072-AB</td>
			<td>SPI Double Sided Adhesive Carbon Tape</td>
		</tr>
		<tr>
			<td>gold</td>
			<td>Denton Vacuum</td>
			<td>TAR001-0158</td>
			<td>2.375&#8221; Diameter x .002&#8221; Thick Gold foil</td>
		</tr>
		<tr>
			<td>scanning electron microscope</td>
			<td>FEI</td>
			<td>XL-30</td>
			<td></td>
		</tr>
	</tbody>
</table>

a protocol to characterize the morphological changes of clostridium difficile in response to antibiotic treatment

嫌気性細菌に向けられた新薬開発による抗生物質作用の評価は困難で技術的に要求される。可能なMOAについての洞察を得るために、抗生物質曝露に伴う形態学的変化を走査型電子顕微鏡（SEM）を用いて視覚化することができる。 SEMイメージングを伝統的なキル曲線と統合することで、薬物行動への洞察が向上し、医薬品開発プロセスが進歩する可能性があります。この前提を試験するために、既知の異なるMOA（バンコマイシンおよびメトロニダゾール）を有する薬物を用いて、曲線を殺し、SEM研究を行った。 C. difficile細胞（R20291）を抗生物質の存在下または非存在下で48時間まで増殖させた。 48時間間隔で、複数の時点で細胞を収集して、抗生物質の有効性を判定し、SEMで画像化した。以前の報告と一致して、バンコマイシンおよびメトロニダゾールは、コロニー形成単位（CFU）カウンターによって測定して、24時間の処理後に有意な殺菌活性を有したティン。 SEMイメージングを用いて、メトロニダゾールは、対照およびバンコマイシンと比較して、細胞長（各抗生物質について細胞長の&gt; 50％の減少; P &lt;0.05）に有意な効果を有することが判明した。薬物治療に対する表現型応答はこれまでにこのように報告されていないが、イメージングおよび測定の汎用性および信頼性ならびに他の実験化合物に対するこの技術の適用を実証する薬物のMOAと一致する。

クロストリジウム・ディフィシル（Clostridium difficile）は胞子形成細菌であるため、機能的分析の前に栄養細胞と胞子細胞との形態学的相違を決定することが不可欠である。 図1は、増殖曲線および胞子細胞の指数期の間に捕捉された栄養細胞の代表的な画像を示す。図示のように、栄養細胞は長くて滑らかな棒状の構造であるのに対し、胞子は粗?...

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A Protocol to Characterize the Morphological Changes of Clostridium difficile in Response to Antibiotic Treatment

Antibiotic efficacy is most commonly determined by conducting killing kinetic studies and measuring colony forming units (CFUs). By integrating scanning electron microscopy (SEM) with these standard methods, we can distinguish the pharmacological effects of treatment between different antibiotics.

形態変化を特徴付けるプロトコル<em&gt;クロストリジウム・ディフィシル</em&gt;抗生物質治療に対する反応

Assessment of antibiotic action with new drug development directed towards anaerobic bacteria is difficult and technically demanding. To gain insight into ...

a-protocol-to-characterize-morphological-changes-clostridium

Research

JoVE Journal

Immunology and Infection

A Protocol to Characterize the Morphological Changes of Clostridium difficile in Response to Antibiotic Treatment

8.9K ビュー.  University of Houston College of Pharmacy. Antibiotic efficacy is most commonly determined by conducting killing kinetic studies and measuring colony forming units (CFUs). By integrating scanning electron microscopy (SEM) with these standard methods, we can distinguish the pharmacological effects of treatment between different antibiotics.

ビデオ: A Protocol to Characterize the Morphological Changes of Clostridium difficile in Response to Antibiotic Treatment

Use of Artificial Sputum Medium to Test Antibiotic Efficacy Against Pseudomonas aeruginosa in Conditions More Relevant to the Cystic Fibrosis Lung

There is growing concern about the relevance of in vitro antimicrobial susceptibility tests when applied to isolates of P. aeruginosa from cystic fibrosis (CF) patients. Existing methods rely on single or a few isolates grown aerobically and planktonically. Predetermined cut-offs are used to define whether the bacteria are sensitive or resistant to any given antibiotic1. However, during chronic lung infections in CF, P. aeruginosa populations exist in biofilms and there is evidence that the environment is largely microaerophilic2. The stark difference in conditions between bacteria in the lung and those during diagnostic testing has called into question the reliability and even relevance of these tests3.
 Artificial sputum medium (ASM) is a culture medium containing the components of CF patient sputum, including amino acids, mucin and free DNA. P. aeruginosa growth in ASM mimics growth during CF infections, with the formation of self-aggregating biofilm structures and population divergence4,5,6. The aim of this study was to develop a microtitre-plate assay to study antimicrobial susceptibility of P. aeruginosa based on growth in ASM, which is applicable to both microaerophilic and aerobic conditions.
 An ASM assay was developed in a microtitre plate format. P. aeruginosa biofilms were allowed to develop for 3 days prior to incubation with antimicrobial agents at different concentrations for 24 hours. After biofilm disruption, cell viability was measured by staining with resazurin. This assay was used to ascertain the sessile cell minimum inhibitory concentration (SMIC) of tobramycin for 15 different P. aeruginosa isolates under aerobic and microaerophilic conditions and SMIC values were compared to those obtained with standard broth growth. Whilst there was some evidence for increased MIC values for isolates grown in ASM when compared to their planktonic counterparts, the biggest differences were found with bacteria tested in microaerophilic conditions, which showed a much increased resistance up to a &gt;128 fold, towards tobramycin in the ASM system when compared to assays carried out in aerobic conditions.
 The lack of association between current susceptibility testing methods and clinical outcome has questioned the validity of current methods3. Several in vitro models have been used previously to study P. aeruginosa biofilms7, 8. However, these methods rely on surface attached biofilms, whereas the ASM biofilms resemble those observed in the CF lung9 . In addition, reduced oxygen concentration in the mucus has been shown to alter the behavior of P. aeruginosa2 and affect antibiotic susceptibility10. Therefore using ASM under microaerophilic conditions may provide a more realistic environment in which to study antimicrobial susceptibility.

Use of Artificial Sputum Medium to Test Antibiotic Efficacy Against Pseudomonas aeruginosa in Conditions More Relevant to the Cystic Fibrosis Lung

Current diagnostic antimicrobial susceptibility testing relies on the planktonic growth of isolates in nutrient rich, aerobic conditions. Here, we employ an alternative artificial sputum medium to study antimicrobial susceptibility of Pseudomonas aeruginosa biofilms under both aerobic and microaerophilic conditions more representative of the cystic fibrosis lung.

に対する抗生物質の有効性をテストするための人工痰培地の使用<em&gt;緑膿菌（Pseudomonas aeruginosa）</em&gt;肺嚢胞性線維症へのより適切な条件で

There  is growing concern about the relevance of in vitro antimicrobial  susceptibility tests when applied to isolates of P. aeruginosa from  cystic ...

免疫・感染学

A Comparative Approach to Characterize the Landscape of Host-Pathogen Protein-Protein Interactions

Significant efforts were gathered to generate large-scale comprehensive protein-protein interaction network maps. This is instrumental to understand the pathogen-host relationships and was essentially performed by genetic screenings in yeast two-hybrid systems. The recent improvement of protein-protein interaction detection by a Gaussia luciferase-based fragment complementation assay now offers the opportunity to develop integrative comparative interactomic approaches necessary to rigorously compare interaction profiles of proteins from different pathogen strain variants against a common set of cellular factors.
This paper specifically focuses on the utility of combining two orthogonal methods to generate protein-protein interaction datasets: yeast two-hybrid (Y2H) and a new assay, high-throughput Gaussia princeps protein complementation assay (HT-GPCA) performed in mammalian cells.
A large-scale identification of cellular partners of a pathogen protein is performed by mating-based yeast two-hybrid screenings of cDNA libraries using multiple pathogen strain variants. A subset of interacting partners selected on a high-confidence statistical scoring is further validated in mammalian cells for pair-wise interactions with the whole set of pathogen variants proteins using HT-GPCA. This combination of two complementary methods improves the robustness of the interaction dataset, and allows the performance of a stringent comparative interaction analysis. Such comparative interactomics constitute a reliable and powerful strategy to decipher any pathogen-host interplays.

This article focuses on the identification of high-confident interaction datasets between host and pathogen proteins using a combination of two orthogonal methods: yeast two-hybrid followed by a high-throughput interaction assay in mammalian cells called HT-GPCA.

ホスト病原体のタンパク質 - タンパク質相互作用の風景を特徴づけるために比較的アプローチ

Significant efforts were gathered to generate  large-scale comprehensive protein-protein interaction network maps. This is  instrumental to understand the ...

Culturing and Maintaining Clostridium difficile in an Anaerobic Environment

Clostridium difficile is a Gram-positive, anaerobic, sporogenic bacterium that is primarily responsible for antibiotic associated diarrhea (AAD) and is a significant nosocomial pathogen. C. difficile is notoriously difficult to isolate and cultivate and is extremely sensitive to even low levels of oxygen in the environment. Here, methods for isolating C. difficile from fecal samples and subsequently culturing C. difficile for preparation of glycerol stocks for long-term storage are presented. Techniques for preparing and enumerating spore stocks in the laboratory for a variety of downstream applications including microscopy and animal studies are also described. These techniques necessitate an anaerobic chamber, which maintains a consistent anaerobic environment to ensure proper conditions for optimal C. difficile growth. We provide protocols for transferring materials in and out of the chamber without causing significant oxygen contamination along with suggestions for regular maintenance required to sustain the appropriate anaerobic environment for efficient and consistent C. difficile cultivation.

Culturing and Maintaining Clostridium difficile in an Anaerobic Environment

Clostridium difficile is a pathogenic bacterium that is a strict anaerobe and causes antibiotic associated diarrhea (AAD). Here, methods for isolating, culturing and maintaining C. difficile vegetative cells and spores are described. These techniques necessitate an anaerobic chamber, which requires regular maintenance to ensure proper conditions for optimal C. difficile cultivation.

培養およびメンテナンス<em&gt;クロストリジウム·ディフィシル</em&gt;嫌気性環境での

Clostridium  difficile is a Gram-positive, anaerobic, sporogenic bacterium  that is primarily responsible for antibiotic associated diarrhea (AAD) and is ...

In Vitro Analysis of Myd88-mediated Cellular Immune Response to West Nile Virus Mutant Strain Infection

An attenuated West Nile virus (WNV), a nonstructural (NS) 4B-P38G mutant, induced higher innate cytokine and T cell responses than the wild-type WNV in mice. Recently, myeloid differentiation factor 88 (MyD88) signaling was shown to be important for initial T cell priming and memory T cell development during WNV NS4B-P38G mutant infection. In this study, two flow cytometry-based methods &#8211; an in vitro T cell priming assay and an intracellular cytokine staining (ICS) &#8211; were utilized to assess dendritic cells (DCs) and T cell functions. In the T cell priming assay, cell proliferation was analyzed by flow cytometry following co-culture of DCs from both groups of mice with carboxyfluorescein succinimidyl ester (CFSE) - labeled CD4+ T cells of OTII transgenic mice. This approach provided an accurate determination of the percentage of proliferating CD4+ T cells with significantly improved overall sensitivity than the traditional assays with radioactive reagents. A microcentrifuge tube system was used in both cell culture and cytokine staining procedures of the ICS protocol. Compared to the traditional tissue culture plate-based system, this modified procedure was easier to perform at biosafety level (BL) 3 facilities. Moreover, WNV- infected cells were treated with paraformaldehyde in both assays, which enabled further analysis outside BL3 facilities. Overall, these in vitro immunological assays can be used to efficiently assess cell-mediated immune responses during WNV infection.

In Vitro Analysis of Myd88-mediated Cellular Immune Response to West Nile Virus Mutant Strain Infection

Two flow cytometry-based methods &#8211; an in vitro T cell priming assay and intracellular cytokine staining were utilized to measure antigen presenting capacity of dendritic cells and antigen-specific T cell responses to a West Nile virus mutant infection in mice.

西ナイルウイルス変異株の感染に対するMyD88非介在細胞性免疫応答のインビトロ分析

An attenuated West Nile virus (WNV), a nonstructural (NS) 4B-P38G mutant, induced higher innate cytokine and T cell responses than the wild-type WNV in ...

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysis by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.

Here, we present phenomic approaches for the functional characterization of putative phage genes. Techniques include a developed assay capable of monitoring host anabolic metabolism, the Multi-phenotype Assay Plates (MAPs), in addition to the established method of metabolomics, capable of measuring effects to catabolic metabolism.

ファージフェノミクス：小説のウイルスタンパク質を特徴づけるために、生理的アプローチ

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage ...

Biomimetic Materials to Characterize Bacteria-host Interactions

Bacterial attachment to host cells is one of the earliest events during bacterial colonization of host tissues and thus a key step during infection. The biochemical and functional characterization of adhesins mediating these initial bacteria-host interactions is often compromised by the presence of other bacterial factors, such as cell wall components or secreted molecules, which interfere with the analysis. This protocol describes the production and use of biomimetic materials, consisting of pure recombinant adhesins chemically coupled to commercially available, functionalized polystyrene beads, which have been used successfully to dissect the biochemical and functional interactions between individual bacterial adhesins and host cell receptors. Protocols for different coupling chemistries, allowing directional immobilization of recombinant adhesins on polymer scaffolds, and for assessment of the coupling efficiency of the resulting &#8220;bacteriomimetic&#8221; materials are also discussed. We further describe how these materials can be used as a tool to inhibit pathogen mediated cytotoxicity and discuss scope, limitations and further applications of this approach in studying bacterial - host interactions.

Bacterial attachment to host cells is a key step during host colonization and infection. This protocol describes the generation of polymer-coupled recombinant adhesins as biomimetic materials which allow analysis of the contribution of individual adhesins to these processes, independent of other bacterial factors.

細菌 - 宿主相互作用を特徴づけるために、バイオミメティック材料

Bacterial attachment to host cells is one of the earliest events during bacterial colonization of host tissues and thus a key step during infection. The ...

Cefoperazone-treated Mouse Model of Clinically-relevant Clostridium difficile Strain R20291

Clostridium difficile is an anaerobic, gram-positive, spore-forming enteric pathogen that is associated with increasing morbidity and mortality and consequently poses an urgent threat to public health. Recurrence of a C. difficile infection (CDI) after successful treatment with antibiotics is high, occurring in 20-30% of patients, thus necessitating the discovery of novel therapeutics against this pathogen. Current animal models of CDI result in high mortality rates and thus do not approximate the chronic, insidious disease manifestations seen in humans with CDI. To evaluate therapeutics against C. difficile, a mouse model approximating human disease utilizing a clinically-relevant strain is needed. This protocol outlines the cefoperazone mouse model of CDI using a clinically-relevant and genetically-tractable strain, R20291. Techniques for clinical disease monitoring, C. difficile bacterial enumeration, toxin cytotoxicity, and histopathological changes throughout CDI in a mouse model are detailed in the protocol. Compared to other mouse models of CDI, this model is not uniformly lethal at the dose administered, allowing for the observation of a prolonged clinical course of infection concordant with the human disease. Therefore, this cefoperazone mouse model of CDI proves a valuable experimental platform to assess the effects of novel therapeutics on the amelioration of clinical disease and on the restoration of colonization resistance against C. difficile.

Cefoperazone-treated Mouse Model of Clinically-relevant Clostridium difficile Strain R20291

This protocol outlines the cefoperazone mouse model of Clostridium difficile infection (CDI) using a clinically-relevant and genetically-tractable strain, R20291. Emphasis on clinical disease monitoring, C. difficile bacterial enumeration, toxin cytotoxicity, and histopathological changes throughout CDI in a mouse model are detailed in the protocol.

臨床的に関連のセフォペラゾン処理されたマウスモデル<em&gt;クロストリジウム・ディフィシル</em&gt;ひずみR20291

Clostridium difficile is an anaerobic, gram-positive, spore-forming enteric pathogen that is associated with increasing morbidity and mortality and ...

Examination of Host Phenotypes in Gambusia affinis Following Antibiotic Treatment

The commonality of antibiotic usage in medicine means that understanding the resulting consequences to the host is vital. Antibiotics often decrease host microbiome community diversity and alter the microbial community composition. Many diseases such as antibiotic-associated enterocolitis, inflammatory bowel disease, and metabolic disorders have been linked to a disrupted microbiota. The complex interplay between host, microbiome, and antibiotics needs a tractable model for studying host-microbiome interactions. Our freshwater vertebrate fish serves as a useful model for investigating the universal aspects of mucosal microbiome structure and function as well as analyzing consequential host effects from altering the microbial community. Methods include host challenges such as infection by a known fish pathogen, exposure to fecal or soil microbes, osmotic stress, nitrate toxicity, growth analysis, and measurement of gut motility. These techniques demonstrate a flexible and useful model system for rapid determination of host phenotypes.

Examination of Host Phenotypes in Gambusia affinis Following Antibiotic Treatment

This study involves methods to reveal effects on a model fish host following alteration of the skin and gut microbiome communities&#160;composition by an antibiotic.

ホスト表現型の検討で<em&gt;カダヤシアフィニス</em&gt;続き抗生物質治療

The commonality of antibiotic usage in medicine means that understanding the resulting consequences to the host is vital. Antibiotics often decrease host ...

Screening Assays to Characterize Novel Endothelial Regulators Involved in the Inflammatory Response

The endothelial layer is essential for maintaining homeostasis in the body by controlling many different functions. Regulation of the inflammatory response by the endothelial layer is crucial to efficiently fight against harmful inputs and aid in the recovery of damaged areas. When the endothelial cells are exposed to an inflammatory environment, such as the outer component of gram-negative bacteria membrane, lipopolysaccharide (LPS), they express soluble pro-inflammatory cytokines, such as Ccl5, Cxcl1 and Cxcl10, and trigger the activation of circulating leukocytes. In addition, the expression of adhesion molecules E-selectin, VCAM-1 and ICAM-1 on the endothelial surface enables the interaction and adhesion of the activated leukocytes to the endothelial layer, and eventually the extravasation towards the inflamed tissue. In this scenario, the endothelial function must be tightly regulated because excessive or defective activation in the leukocyte recruitment could lead to inflammatory-related disorders. Since many of these disorders do not have an effective treatment, novel strategies with a focus on the vascular layer must be investigated. We propose comprehensive assays that are useful to the search of novel endothelial regulators that modify leukocyte function. We analyze endothelial activation by using specific expression targets involved in leukocyte recruitment (such as, cytokines, chemokines, and adhesion molecules) with several techniques, including: real-time quantitative polymerase chain reaction (RT-qPCR), western-blot, flow cytometry and adhesion assays. These approaches determine endothelial function in the inflammatory context and are very useful to perform screening assays to characterize novel endothelial inflammatory regulators that are potentially valuable for designing new therapeutic strategies.

Vascular endothelium tightly controls leukocyte recruitment. Inadequate leukocyte extravasation contributes to human inflammatory diseases. Therefore, searching for novel regulatory elements of endothelial activation is necessary to design improved therapies for inflammatory disorders. Here, we describe a comprehensive methodology to characterize novel endothelial regulators that can modify leukocyte trafficking during inflammation.

炎症反応に関与する新規血管内皮レギュレータを特徴付けるための試金をスクリーニング

The endothelial layer is essential for maintaining homeostasis in the body by controlling many different functions. Regulation of the inflammatory ...

Overexpression and Purification of Human Cis-prenyltransferase in Escherichia coli

Prenyltransferases (PT) are a group of enzymes that catalyze chain elongation of allylic diphosphate using isopentenyl diphosphate (IPP) via multiple condensation reactions. DHDDS (dehydrodolichyl diphosphate synthase) is a eukaryotic long-chain cis-PT (forming cis double bonds from the condensation reaction) that catalyzes chain elongation of farnesyl diphosphate (FPP, an allylic diphosphate) via multiple condensations with isopentenyl diphosphate (IPP). DHDDS is of biomedical importance, as a non-conservative mutation (K42E) in the enzyme results in retinitis pigmentosa, ultimately leading to blindness. Therefore, the present protocol was developed in order to acquire large quantities of purified DHDDS, suitable for mechanistic studies. Here, the usage of protein fusion, optimized culture conditions and codon-optimization were used to allow the overexpression and purification of functionally active human DHDDS in E. coli. The described protocol is simple, cost-effective and time sparing. The homology of cis-PT among different species suggests that this protocol may be applied for other eukaryotic cis-PT as well, such as those involved in natural rubber synthesis.

Overexpression and Purification of Human Cis-prenyltransferase in Escherichia coli

A simple protocol for overexpression and purification of codon-optimized, human cis-prenyltransferase, under non-denaturing conditions, from Escherichia coli, is described, along with an enzymatic activity assay. This protocol can be generalized for production of other cis- prenyltransferase proteins in quantity and quality suitable for mechanistic studies.

ヒトの過剰発現と精製<em&gt;シス</em&gt; - プレニルトランスフェラーゼ<em&gt;大腸菌</em

Prenyltransferases (PT) are a group of enzymes that catalyze chain elongation of allylic diphosphate using isopentenyl diphosphate (IPP) via multiple ...