我々は、RNAPとMFDタンパク質および発現ベクターを提供するためのセスダーストに特に感謝しています。我々はまた、技術サポートのためにGreBとダン張を提供するためのセルゲイBorukhovに感謝している。この作品は、国立衛生研究所（MOD）からの助成金によって、ロックフェラー大学（RTP）でマリー=ジョゼとヘンリークラビスフェローシップでサポートされていました。

このメソッドは、で報告された研究で使用され<a href="http://www.sciencemag.org/cgi/content-nw/full/327/5965/590/F3">ポメランツとオドネル、科学327、590〜592（2010） 。</a> 1。停止RNAPの伸長複合体のアセンブリは、以下のように行った： E.の500nMの最終濃度大腸菌の RNAポリメラーゼは、HEがバッファー100μl中T7A1プロモーター（20mMのトリス- Cl（pH7.5）中、8 mMのMgCl 2、0.5mMのEDTA、5を含むビオチン化3.6キロバイトのDNAテンプレートの5nMの最終濃度と混合された70、σ 37℃で10分のためmMのDTT、10％グリセロール） APUの100μMおよび40μMGTP、ATP、およびCTPのそれぞれが37℃でさらに10分間添加した℃、 2。ストレプトアビジンビーズ上に停止したRNAポリメラーゼの伸長複合体の固定化は、以下のように行った： ストレプトアビジン磁気コーティングされたビーズ（Invitrogen社）を200μl室温で10分間、上記の反応に加えた。 3。固定化停止RNAPの伸長複合体の精製は以下のように行った： ビーズ（上記から）、次のバッファ0.9 mLで含む、0.75MのNaCl、200μg/ mlのヘパリン、および20μg/ mlのssDNAを（上清を磁気分離することにより、各洗浄ステップの後に削除されました。）5回洗浄し、ビーズを緩衝液Aの0.9 mlで2回洗浄し、 4。 ：に正面からRNAP次のように実行された下流の相対的な複製フォークの形成ビーズ（上記から）ニューイングランドバイオラボバッファ4と樹液私の10ユニット（New England Biolabs社）100μlに再懸濁し37℃で10分間追加されました℃にビーズをバッファー0.9 mLで3回洗浄し、次にクイックT4ライゲーション反応バッファー（New England Biolabs社）を50μlに再懸濁した。クイックT4リガーゼ（New England Biolabs）2μlを室温で10分間プレアニーリングしたフォークDNAの6nmの最終濃度（RP10、RP22、RP25）と一緒に追加されました。ビーズを緩衝液Aの0.9 mlで3回洗浄し、 5。複製フォークでreplisomeとリーディング鎖合成の開始のアセンブリは、以下のように行った： DnaB 448 pmolのは（量体として）30秒のバッファを150μl（20mMのトリス- Cl（pH7.5）中、8 mMのMgCl 2、0.5mMのEDTA、5mMのDTT、10％グリセロール）でビーズとインキュベートした23℃ポリメラーゼIIIの4.9 pmolの*（はPol III HEマイナスβ）、βの15 pmolの、2mMのATP、60μMdGTP及びdATPのそれぞれを200μlの体積に添加し、37でさらに5分間℃にインキュベートした。レプリケーションは、と一緒に10μgのSSBと24μMのdATPとdTTPの各々を加えることにより開始された[α- 32 P] dTTPのと[α- 32 P] dCTPを（特定の活動、3,000〜5,000 CPM / pmol）を250の最終容量にμL。反応は、500mMのEDTA 12μLを加える時に10分後に終了した。 6。放射性標識DNA産物の精製および濃縮は次のように行った： 反応は、ビーズからDNAを除去するために終了した後、ビーズを（上から）煮沸した。ビーズに接続されている残っている残存DNAを50℃で30分間、10 ulのボリュームでプロテイナーゼKとビーズを処理することにより削除されました℃にビーズを沸騰させ、上清を磁気分離により除去した。 DNAを含む組み合わせて上清をQiagen PCRクリーンアップキットを用いて精製した。精製された放射性標識DNA産物をアルカリアガロースゲルで分析した。 ヘッドオンRNAP伸長複合体が上記のように実行された停止、しかし、σ70の存在下で*レプリケーションが省略されていました。 代表的な結果： とreplisomeの正面衝突でRNAP通常2.5 kbおよび長さは3.6 kbの二つの製品につながる。 2.5キロバイトの製品は、フォークから停止RNAPとRNAポリメラーゼとの衝突時に失速replisomeから結果へのDNAの長さを表します。 3.6キロバイトの製品は、不完全なRNAPによるプロモーターの占有または部分的replisomeヘッドオンRNAPのリードスルーのどちらかから完全長のDNAとの結果を表しています。いいや、正確な結果が約50％の完全長DNAが生成されていることを示しています。ただし、場合によっては、RNAPによるプロモーターの少ない占有が発生し、replisomesの大きい人口がヘッドオンRNAPが発生しないので、完全長のDNAの割合が高いが観察される。唯一の完全長DNA（3.6 KB）の停止RNAPの結果がない場合に複製。 <img src="/files/ftp_upload/1919/1919fig1.jpg" alt="図1" /> 図。 1 replisomeは、ヘッドオンRNAPによって妨げられている。 （A）実験のセットアップ。 E.コル私は停止伸長複合体は、前述のようにT7A1プロモーターを含むビオチン化DNA（9）にアセンブルされたRNAP。簡単に言えば、停止伸長複合体は、さらに10分間APU、GTP、ATP、およびCTPを加えて10分間、ビオチン化DNAとRNAポリメラーゼホロ酵素をインキュベートすることにより、プロモーターから20 bpsの下流に形成された。ストレプトアビジンビーズは、ビーズをバッファー0.9 mlのは、不安定なRNAP - DNA複合体と過剰のNTP削除するには、0.75MのNaCl、200 mg / mlのヘパリン、および100nMの一本鎖DNAを含むで5回それぞれ洗浄し、さらに10分間追加されました。 DNAを洗浄し、SAPIで消化し、プレアニーリングしたフォークDNAに連結した。ビーズをreplisomeの組み立て前に再度洗浄した。プロモーターは、フォークから2.5 kbの位置とフォークに向かって直接転写を指向しているさ。DnaBが追加された（B）その後replisomeがアセンブルされ、複製が存在する（レーン2）または非存在下（レーン1）のいずれかで開始されたヘッドオンRNAP。

<ol>
	<li>Rudolph, C. J., Dhillon, P., Moore, T., Lloyd, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Avoiding+and+resolving+conflicts+between+DNA+replication+and+transcription.">Avoiding and resolving conflicts between DNA replication and transcription.</a> DNA Repair (Amst). 6, 981-98 (2007).</li><li>Vilette, D., Ehrlich, S. D., Michel, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcription-induced+deletions+in+plasmid+vectors:+M13+DNA+replication+as+a+source+of+instability.">Transcription-induced deletions in plasmid vectors: M13 DNA replication as a source of instability.</a> Mol Gen Genet. 252, 398-398 (1996).</li><li>Trautinger, B. W., Jaktaji, R. P., Rusakova, E., Lloyd, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+polymerase+modulators+and+DNA+repair+activities+resolve+conflicts+between+DNA+replication+and+transcription.">RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription.</a> Mol Cell. 19, 247-247 (2005).</li><li>McGlynn, P., Lloyd, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modulation+of+RNA+Polymerase+by+(p)ppGpp+Reveals+a+RecG-Dependent+Mechanism+for+Replication+Fork+Progression.">Modulation of RNA Polymerase by (p)ppGpp Reveals a RecG-Dependent Mechanism for Replication Fork Progression.</a> Cell. 101, 35-35 (2000).</li><li>McGlynn, P., Guy, C. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication+forks+blocked+by+protein-DNA+complexes+have+limited+stability+in+vitro.">Replication forks blocked by protein-DNA complexes have limited stability in vitro.</a> J Mol Biol. 381, 249-249 (2008).</li><li>Labib, K., Hodgson, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication+fork+barriers:+pausing+for+a+break+or+stalling+for+time.">Replication fork barriers: pausing for a break or stalling for time.</a> EMBO Rep. 8, 346-346 (2007).</li><li>Bidnenko, V., Ehrlich, S. D., Michel, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication+fork+collapse+at+replication+terminator+sequences.">Replication fork collapse at replication terminator sequences.</a> Embo J. 21, 3898-3898 (2002).</li><li>Pomerantz, R. T., O'Donnell, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replisome+mechanics:+insights+into+a+twin+DNA+polymerase+machine.">Replisome mechanics: insights into a twin DNA polymerase machine.</a> Trends Microbiol. 15, 156-156 (2007).</li><li>Pomerantz, R. T., O'Donnell, 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+replisome+uses+mRNA+as+a+primer+after+colliding+with+RNA+polymerase.">The replisome uses mRNA as a primer after colliding with RNA polymerase.</a> Nature. 456, 762-762 (2008).</li><li>Heller, R. C., Marians, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication+fork+reactivation+downstream+of+a+blocked+nascent+leading+strand.">Replication fork reactivation downstream of a blocked nascent leading strand.</a> Nature. 439, 557-557 (2006).</li><li>Yuzhakov, A., Turner, J., O'Donnell, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication+fork+reactivation+downstream+of+a+blocked+nascent+leading+strand.">Replication fork reactivation downstream of a blocked nascent leading strand.</a> Cell. 86, 557-557 (1996).</li><li>Hinkle, D. C., Ring, J., Chamberlin, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replisome+assembly+reveals+the+basis+for+asymmetric+function+in+leading+and+lagging+strand+replication.">Replisome assembly reveals the basis for asymmetric function in leading and lagging strand replication.</a> J Mol Biol. 70, 197-197 (1972).</li><li>Kaplan, D. L., O'Donnell, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Studies+of+the+binding+of+Escherichia+coli+RNA+polymerase+to+DNA.+V.+T7+RNA+chain+initiation+by+enzyme-DNA+complexes.">Studies of the binding of Escherichia coli RNA polymerase to DNA. V. T7 RNA chain initiation by enzyme-DNA complexes.</a> Mol Cell. 15, 453-453 (2004).</li><li>Park, J. S., Marr, M. T., Roberts, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Twin+DNA+pumps+of+a+hexameric+helicase+provide+power+to+simultaneously+melt+two+duplexes.">Twin DNA pumps of a hexameric helicase provide power to simultaneously melt two duplexes.</a> Cell. 109, 757-757 (2002).</li><li>Hanawalt, P. C., Spivak, G. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=coli+Transcription+repair+coupling+factor+(Mfd+protein)+rescues+arrested+complexes+by+promoting+forward+translocation.">coli Transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation.</a> Nat Rev Mol Cell Biol. 9, 958-958 (2008).</li><li>Hanawalt, P. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcription-coupled+DNA+repair:+two+decades+of+progress+and+surprises.">Transcription-coupled DNA repair: two decades of progress and surprises.</a> Science. 266, 1957-1957 (1994).</li><li>Selby, C. P., Sancar, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcription-coupled+repair+and+human+disease.">Transcription-coupled repair and human disease.</a> J Biol Chem. 270, 4882-4882 (1995).</li><li>Liu, B., Alberts, B. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+and+function+of+transcription-repair+coupling+factor.+I.+Structural+domains+and+binding+properties.+Head-on+collision+between+a+DNA+replication+apparatus+and+RNA+polymerase+transcription+complex.">Structure and function of transcription-repair coupling factor. I. Structural domains and binding properties. Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex.</a> Science. 267, 1131-1131 (1995).</li><li>George, D. L., Witkin, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Slow+excision+repair+in+an+mfd+mutant+of+Escherichia+coli+B/r.">Slow excision repair in an mfd mutant of Escherichia coli B/r.</a> Mol Gen Genet. 133, 283-283 (1974).</li></ol>

高塩濃度でビーズに結合した停止伸長複合体を洗濯しても不安定になったり、非特異的に結合したRNAポリメラーゼの分子を除去するために重要です。 RNAPは、プライマーとテンプレートの型のDNA構造のための非常に高い親和性を持っています。したがって、プライマーテンプレートから複製を実行するために、そのような非特異的RNAP - DNA複合体を除去する必要がある。キアゲンPCR精製キットを用いて放射性標識DNA産物を集中するとゲルで観察することができる十分に高い放射性シグナルを得るためにも重要です。

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<td>Dynabeads M-270</td>
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direct restart of a replication fork stalled by a head-on rna polymerase

in vivo試験で複製フォークが原因でヘッドオン転写複合体との遭遇に逮捕されていることを示唆している。まだ、正面衝突に続くreplisomeとRNAポリメラーゼ（RNAP）の運命は不明である。ここで、我々は見つけることE.大腸菌ヘッドオン転写複合体ではなく、崩壊のとの衝突時にreplisome屋台は、複製フォークでは非常に安定していると最終的にDNAからRNAポリメラーゼを置換した後、伸長を再開します。我々は、転写修復カップリング係数、MFDが、RNAPの変位を容易にすることによって衝突の後のフォークの直接の再起動を促進することをも見つける。これらの知見は、複製装置の固有の安定性とRNAPのブロックを越えて複製を促進する転写共役修復経路のための新たな役割を示しています。

Watch this Scientific Journal Video about Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase at JoVE.com

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

ヘッドオンRNAポリメラーゼ（RNAP）との衝突に続くreplisomeの運命は不明である。我々は、DNAからRNAポリメラーゼを置換した後、伸長をreplisomeヘッドオンRNAPとの衝突時に屋台が、再開することを見つける。 MFDは、衝突後のRNAPの変位を容易にすることによって、レプリケーションの再起動を促進する。

ヘッドオンRNAポリメラーゼによって停止した複製フォークの再起動を指示する

In vivo studies suggest that replication forks are arrested due to encounters with head-on transcription complexes. Yet, the fate of the replisome and RNA ...

direct-restart-replication-fork-stalled-head-on-rna

Research

JoVE Journal

Biology

13.5K ビュー.  Rockefeller University. ヘッドオンRNAポリメラーゼ（RNAP）との衝突に続くreplisomeの運命は不明である。我々は、DNAからRNAポリメラーゼを置換した後、伸長をreplisomeヘッドオンRNAPとの衝突時に屋台が、再開することを見つける。 MFDは、衝突後のRNAPの変位を容易にすることによって、レプリケーションの再起動を促進する。

ビデオ: Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

Production of Replication-Defective Retrovirus by Transient Transfection of 293T cells

Our lab studies human myeloproliferative diseases induced by such oncogenes as Bcr-Abl or growth factor receptor-derived oncogenes (ZNF198-FGFR1, Bcr-PDGFR&#945;, etc.). We are able to model and study a human-like disease in our mouse model, by transplanting bone marrow cells previously infected with a retrovirus expressing the oncogene of interest. Replication-defective retrovirus encoding a human oncogene and a marker (GFP, RFP, antibiotic resistance gene, etc.) is produced by a transient transfection protocol using 293T cells, a human renal epithelial cell line transformed by the adenovirus E1A gene product. 293 cells have the unusual property of being highly transfectable by calcium phosphate (CaPO4), with up to 50-80% transfection efficiency readily attainable. Here, we co-transfect 293 cells with a retroviral vector expressing the oncogene of interest and a plasmid that expresses the gag-pol-env packaging functions, such as the single-genome packaging constructs kat or pCL, in this case the EcoPak plasmid. The initial transfection is further improved by use of chloroquine. Stocks of ecotropic virus, collected as culture supernatant 48 hrs. post-transfection, can be stored at -80&deg;C and used for infection of cell-lines in view of transformation and in vitro studies, or primary cells such as mouse bone marrow cells, that can then be used for transplant in our mouse model.

This technique demonstrates an efficient way to prepare replication-defective retroviral stocks encoding a human oncogene, and subsequently used for induction of myeloproliferative disease in the mouse model.

293T細胞の一過性トランスフェクションにより、複製欠損レトロウイルスの生産

Our lab studies human myeloproliferative diseases induced by such oncogenes as Bcr-Abl or growth factor receptor-derived oncogenes (ZNF198-FGFR1, ...

生物学

Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides (Figure 1). The growing product double-strand DNA (dsDNA) is extended with laminar flow and visualized by using an intercalating dye. Measuring the position of the growing DNA end in real time allows precise determination of replication rate (Figure 2). Furthermore, the length of completed DNA products reports on the processivity of replication. This experiment can be performed very easily and rapidly and requires only a fluorescence microscope with a reasonably sensitive camera.


This protocol demonstrates a simple single-molecule fluorescence microscopy technique for visualizing DNA replication by individual replisomes in real time.

蛍光顕微鏡による可視化単分子のDNAの複製

We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA ...

Direct Observation of Enzymes Replicating DNA Using a Single-molecule DNA Stretching Assay

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system. Linearized &lambda; DNA is modified to have a biotin on the end of one strand, and a digoxigenin moiety on the other end of the same strand. The biotinylated end is attached to a functionalized glass coverslip and the digoxigeninated end to a small bead. The assembly of these DNA-bead tethers on the surface of a flow cell allows a laminar flow to be applied to exert a drag force on the bead. As a result, the DNA is stretched close to and parallel to the surface of the coverslip at a force that is determined by the flow rate (Figure 1). The length of the DNA is measured by monitoring the position of the bead. Length differences between single- and double-stranded DNA are utilized to obtain real-time information on the activity of the replication proteins at the fork. Measuring the position of the bead allows precise determination of the rates and processivities of DNA unwinding and polymerization (Figure 2).

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system.

アッセイをストレッチ単一分子のDNAを用いて酵素の複製DNAの直接観察

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system. ...

Visualizing RNA Localization in Xenopus Oocytes

RNA localization is a conserved mechanism of establishing cell polarity. Vg1 mRNA localizes to the vegetal pole of Xenopus laevis oocytes and acts to spatially restrict gene expression of Vg1 protein. Tight control of Vg1 distribution in this manner is required for proper germ layer specification in the developing embryo. RNA sequence elements in the 3' UTR of the mRNA, the Vg1 localization element (VLE) are required and sufficient to direct transport. To study the recognition and transport of Vg1 mRNA in vivo, we have developed an imaging technique that allows extensive analysis of trans-factor directed transport mechanisms via a simple visual readout. 
To visualize RNA localization, we synthesize fluorescently labeled VLE RNA and microinject this transcript into individual oocytes. After oocyte culture to allow transport of the injected RNA, oocytes are fixed and dehydrated prior to imaging by confocal microscopy. Visualization of mRNA localization patterns provides a readout for monitoring the complete pathway of RNA transport and for identifying roles in directing RNA transport for cis-acting elements within the transcript and trans-acting factors that bind to the VLE (Lewis et al., 2008, Messitt et al., 2008). We have extended this technique through co-localization with additional RNAs and proteins (Gagnon and Mowry, 2009, Messitt et al., 2008), and in combination with disruption of motor proteins and the cytoskeleton (Messitt et al., 2008) to probe mechanisms underlying mRNA localization.

Visualizing RNA Localization in Xenopus Oocytes

Visualization of in vivo RNA transport is accomplished by microinjection of fluorescently labeled RNA transcripts into Xenopus oocytes, followed by confocal microscopy.

可視化RNAの局在にアフリカツメガエル卵母細胞

RNA localization is a conserved mechanism of establishing cell polarity.  Vg1 mRNA localizes to the vegetal pole of Xenopus laevis oocytes and acts to ...

Direct Delivery of MIF Morpholinos Into the Zebrafish Otocyst by Injection and Electroporation Affects Inner Ear Development

In recent years, electroporation has become a popular technique for in vivo transfection of DNA, RNA, and morpholinos into various tissues, including the eye, brain, and somites of zebrafish. The advantage of electroporation over other methods of genetic manipulation is that specific tissues can be targeted, both spatially and temporally, for the introduction of macromolecules by the application of electrical current. Here we describe the use of electroporation for transfecting mif and mif-like morpholinos into the tissues of the developing inner ear of the zebrafish. In past studies, mif morpholino injected into embryos at the 1- to 8-cell stage resulted in widespread morphological changes in the nervous system and eye, as well as the ear. By targeting the tissues of the inner ear at later stages in development, we can determine the primary effects of MIF in the developing inner ear, as opposed to secondary effects that may result from the influence of other tissues. By using phalloidin and acetylated tubulin staining to study the morphology of neurons, neuronal processes, and hair cells associated with the posterior macula, we were able to assess the efficacy of electroporation as a method for targeted transfection in the zebrafish inner ear. The otic vesicles of 24hpf embryos were injected with morpholinos and electroporated and were then compared to embryos that had received no treatment or had been only injected or electroporated. Embryos that were injected and electroporated showed a decrease in hair cell numbers, decreased innervation by the statoacoustic ganglion (SAG) and fewer SAG neurons compared with control groups. Our results showed that direct delivery of morpholinos into otocysts at later stages avoids the non-specific nervous system and neural crest effects of morpholinos delivered at the 1-8 cell stage. It also allows examination of effects that are directed to the inner ear and not secondary effects on the ear from primary effects on the brain, neural crest or periotic mesenchyme.

A method to deliver morpholinos directly into the zebrafish otocyst at 24hpf has been developed. Using microinjection of morpholinos into the lumen of otic vesicle and electroporation to effect penetration, we were able to bypass the effect of morpholinos on the brain and obtain effects specific to the inner ear.

注射とエレクトロポレーションによりゼブラフィッシュ耳胞イントゥMIFモルフォの直接配信は、内耳の開発に影響を与える

In recent years, electroporation has become a popular technique for in vivo transfection of DNA, RNA, and morpholinos into various tissues, including the ...

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence (T7, T3, SP6) and the gene to be transcribed (Figure 1A). A typical transcription reaction consists of the template DNA, RNA polymerase, ribonucleotide triphosphates, RNase inhibitor and buffer containing Mg2+ ions.
Large amounts of high quality RNA are often required for a variety of applications. Use of in vitro transcription has been reported for RNA structure and function studies such as splicing1, RNAi experiments in mammalian cells2, antisense RNA amplification by the "Eberwine method"3, microarray analysis4 and for RNA vaccine studies5. The technique can also be used for producing radiolabeled and dye labeled probes6. Warren, et al. recently reported reprogramming of human cells by transfection with in vitro transcribed capped RNA7. The T7 High Yield RNA Synthesis Kit from New England Biolabs has been designed to synthesize up to 180 &mu;g RNA per 20 &mu;l reaction. RNA of length up to 10kb has been successfully transcribed using this kit. Linearized plasmid DNA, PCR products and synthetic DNA oligonucleotides can be used as templates for transcription as long as they have the T7 promoter sequence upstream of the gene to be transcribed.
Addition of a 5' end cap structure to the RNA is an important process in eukaryotes. It is essential for RNA stability8, efficient translation9, nuclear transport10 and splicing11. The process involves addition of a 7-methylguanosine cap at the 5' triphosphate end of the RNA. RNA capping can be carried out post-transcriptionally using capping enzymes or co-transcriptionally using cap analogs. In the enzymatic method, the mRNA is capped using the Vaccinia virus capping enzyme12,13. The enzyme adds on a 7-methylguanosine cap at the 5' end of the RNA using GTP and S-adenosyl methionine as donors (cap 0 structure). Both methods yield functionally active capped RNA suitable for transfection or other applications14 such as generating viral genomic RNA for reverse-genetic systems15 and crystallographic studies of cap binding proteins such as eIF4E16.
In the method described below, the T7 High Yield RNA Synthesis Kit from NEB is used to synthesize capped and uncapped RNA transcripts of Gaussia luciferase (GLuc) and Cypridina luciferase (CLuc). A portion of the uncapped GLuc RNA is capped using the Vaccinia Capping System (NEB). A linearized plasmid containing the GLuc or CLuc gene and T7 promoter is used as the template DNA. The transcribed RNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity. Capped CLuc RNA is used as the internal control to normalize GLuc expression.

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

This method describes high yield in vitro synthesis of both capped and uncapped mRNA from a linearized plasmid containing the Gaussia luciferase (GLuc) gene. The RNA is purified and a fraction of the uncapped RNA is enzymatically capped using the Vaccinia virus capping enzyme. In the final step, the mRNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity.

HeLa細胞のトランスフェクションに続いてGaussiaルシフェラーゼmRNA のインビトロ転写とキャッピングの

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence ...

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

Marine elasmobranchs are valued animal models for biomedical and genomic studies as they are the most primitive vertebrates to have adaptive immunity and have unique mechanisms for osmoregulation 1-3. As the most primitive living jawed-vertebrates with paired appendages, elasmobranchs are an evolutionarily important model, especially for studies in evolution and development. Marine elasmobranchs have also been used to study aquatic toxicology and stress physiology in relationship to climate change 4. Thus, development and adaptation of methodologies is needed to facilitate and expand the use of these primitive vertebrates to multiple biological disciplines. Here I present the successful adaptation of RNA whole mount in situ hybridization and histological techniques to study gene expression and cell histology in elasmobranchs.
Monitoring gene expression is a hallmark tool of developmental biologists, and is widely used to investigate developmental processes 5. RNA whole mount in situ hybridization allows for the visualization and localization of specific gene transcripts in tissues of the developing embryo. The expression pattern of a gene's message can provide insight into what developmental processes and cell fate decisions a gene may control. By comparing the expression pattern of a gene at different developmental stages, insight can be gained into how the role of a gene changes during development.
While whole mount in situ's provides a means to localize gene expression to tissue, histological techniques allow for the identification of differentiated cell types and tissues. Histological stains have varied functions. General stains are used to highlight cell morphology, for example hematoxylin and eosin for general staining of nuclei and cytoplasm, respectively. Other stains can highlight specific cell types. For example, the alcian blue stain reported in this paper is a widely used cationic stain to identify mucosaccharides. Staining of the digestive tract with alcian blue can identify the distribution of goblet cells that produce mucosaccharides. Variations in mucosaccharide constituents on short peptides distinguish goblet cells by function within the digestive tract 6. By using RNA whole mount in situ's and histochemical methods concurrently, cell fate decisions can be linked to gene-specific expression.
Although RNA in situ's and histochemistry are widely used by researchers, their adaptation and use in marine elasmobranchs have met limited and varied success. Here I present protocols developed for elasmobranchs and used on a regular basis in my laboratory. Although further modification of the RNA in situ's hybridization method may be needed to adapt to different species, the protocols described here provide a strong starting point for researchers wanting to adapt the use of marine elasmobranchs to their scientific inquiries.

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

By combining methods for RNA whole mount in situ hybridization and histology, gene expression can be linked with cell fate decisions in the developing embryo. These methods have been adapted to marine elasmobranchs and facilitate the use of these animals as model organisms for biomedical, toxicology and comparative studies.

RNAを<em&gt;その場</emホールマウント胚および細胞組織学で&gt;ハイブリダイゼーションは、海洋軟骨魚類に適合した

Marine  elasmobranchs are valued animal models for biomedical and genomic studies as  they are the most primitive vertebrates to have adaptive immunity ...

RNA Isolation from Mouse Pancreas: A Ribonuclease-rich Tissue

Isolation of high-quality RNA from ribonuclease-rich tissue such as mouse pancreas presents a challenge. As a primary function of the pancreas is to aid in digestion, mouse pancreas may contain as much a 75 mg of ribonuclease. We report modifications of standard phenol/guanidine thiocyanate lysis reagent protocols to isolate RNA from mouse pancreas. Guanidine thiocyanate is a strong protein denaturant and will effectively disrupt the activity of ribonuclease under most conditions. However, critical modifications to standard protocols are necessary to successfully isolate RNA from ribonuclease-rich tissues. Key steps include a high lysis reagent to tissue ratio, removal of undigested tissue prior to phase separation and inclusion of a ribonuclease inhibitor to the RNA solution. Using these and other modifications, we routinely isolate RNA with RNA Integrity Number (RIN) greater than 7. The isolated RNA is of suitable quality for routine gene expression analysis. Adaptation of this protocol to isolate RNA from ribonuclease rich tissues besides the pancreas should be readily achievable.

We report a procedure to isolate RNA with high integrity from the ribonuclease rich mouse pancreas.

マウス膵臓からのRNAの単離：リボヌクレアーゼが豊富な組織

Isolation of high-quality RNA from ribonuclease-rich tissue such as mouse pancreas presents a challenge.  As a primary function of the pancreas is to aid ...

Development of a Quantitative Recombinase Polymerase Amplification Assay with an Internal Positive Control

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to quantify DNA sample concentration using a standard curve. In this manuscript, a detailed protocol for developing and implementing a real-time quantitative recombinase polymerase amplification assay (qRPA assay) is provided. Using HIV-1 DNA quantification as an example, the assembly of real-time RPA reactions, the design of an internal positive control (IPC) sequence, and co-amplification of the IPC and target of interest are all described. Instructions and data processing scripts for the construction of a standard curve using data from multiple experiments are provided, which may be used to predict the concentration of unknown samples or assess the performance of the assay. Finally, an alternative method for collecting real-time fluorescence data with a microscope and a stage heater as a step towards developing a point-of-care qRPA assay is described. The protocol and scripts provided may be used for the development of a qRPA assay for any DNA target of interest.

Provided is a protocol for developing a real-time recombinase polymerase amplification assay to quantify initial concentration of DNA samples using either a thermal cycler or a microscope and stage heater. Also described is the development of an internal positive control. Scripts are provided for processing raw real-time fluorescence data.

内部陽性対照との定量的リコンビナーゼポリメラーゼ増幅アッセイの開発

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to ...

Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System

Obstacles present on DNA, including tightly-bound proteins and various lesions, can severely inhibit the progression of the cell&#39;s replication machinery. The stalling of a replisome can lead to its dissociation from the chromosome, either in part or its entirety, leading to the collapse of the replication fork. The recovery from this collapse is a necessity for the cell to accurately complete chromosomal duplication and subsequently divide. Therefore, when the collapse occurs, the cell has evolved diverse mechanisms that take place to restore the DNA fork and allow replication to be completed with high fidelity. Previously, these replication repair pathways in bacteria have been studied using UV damage, which has the disadvantage of not being localized to a known site. This manuscript describes a system utilizing a Fluorescence Repressor Operator System (FROS) to create a site-specific protein block that can induce the stalling and collapse of replication forks in Escherichia coli. Protocols detail how the status of replication can be visualized in single living cells using fluorescence microscopy and DNA replication intermediates can be analyzed by 2-dimensional agarose gel electrophoresis. Temperature sensitive mutants of replisome components (e.g. DnaBts) can be incorporated into the system to induce a synchronous collapse of the replication forks. Furthermore, the roles of the recombination proteins and helicases that are involved in these processes can be studied using genetic knockouts within this system.

Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System

We describe here a system utilizing a site-specific, reversible in vivo protein block to stall and collapse replication forks in Escherichia coli. The establishment of the replication block is evaluated by fluorescence microscopy and neutral-neutral 2-dimensional agarose gel electrophoresis is used to visualize replication intermediates.