Name: computational analysis of the caenorhabditis elegans germline to study the distribution of nuclei, proteins, and the cytoskeleton
Uploaded: 2018-04-19T12:30:00
Description: Watch this Scientific Journal Video about Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton at JoVE.com

彼らのテクニカル サポートありがとうモナッシュ マイクロ イメージング。いくつかの系統は、線虫の遺伝学センター研究インフラストラクチャ プログラム (P40 OD010440) の NIH のオフィスによって資金が供給されるによって提供されました。この作品は、モナッシュ大学生物医学発見交わり、NHMRC プロジェクト助成金 (GNT1105374)、NHMRC 上級研究員 (GNT1137645) と veski 社革新交わりによって支えられた: ロジャー ・ ポコックに VIF 23。

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<ol><li>OP50大腸菌文化: 文化ホストゲノム スープ (LB) (1% トリプトン、0.5% 酵母、0.5% の塩化ナトリウム、pH 7.0) 37 ° C 抗生物質なしで一晩で OP50 細菌。</li>
	<li>OP50 細菌線虫成長メディア (NGM) 板 (1.5 g の塩化ナトリウム、寒天、ペプトン、1 M CaCl2エタノール、1 M MgSO4</...

<ol>
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L., Suh, N., Kimble, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GLD-3+and+control+of+the+mitosis/meiosis+decision+in+the+germline+of+Caenorhabditis+elegans.">GLD-3 and control of the mitosis/meiosis decision in the germline of Caenorhabditis elegans.</a> Genetics. 168 (1), 147-160 (2004).</li><li>Schumacher, B., 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=Translational+repression+of+C.+elegans+p53+by+GLD-1+regulates+DNA+damage-induced+apoptosis.">Translational repression of C. elegans p53 by GLD-1 regulates DNA damage-induced apoptosis.</a> Cell. 120 (3), 357-368 (2005).</li><li>McMullen, P. 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R., Francis, R., Schedl, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=GLD-1,+a+cytoplasmic+protein+essential+for+oocyte+differentiation,+shows+stage-+and+sex-specific+expression+during+Caenorhabditis+elegans+germline+development.">GLD-1, a cytoplasmic protein essential for oocyte differentiation, shows stage- and sex-specific expression during Caenorhabditis elegans germline development.</a> Dev Biol. 180 (1), 165-183 (1996).</li><li>Hasegawa, E., Karashima, T., Sumiyoshi, E., Yamamoto, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=C.+elegans+CPB-3+interacts+with+DAZ-1+and+functions+in+multiple+steps+of+germline+development.">C. elegans CPB-3 interacts with DAZ-1 and functions in multiple steps of germline development.</a> Dev Biol. 295 (2), 689-699 (2006).</li><li>Austin, J., Kimble, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=glp-1+is+required+in+the+germ+line+for+regulation+of+the+decision+between+mitosis+and+meiosis+in+C.+elegans.">glp-1 is required in the germ line for regulation of the decision between mitosis and meiosis in C. elegans.</a> Cell. 51 (4), 589-599 (1987).</li><li>Berry, L. W., Westlund, B., Schedl, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Germ-line+tumor+formation+caused+by+activation+of+glp-1,+a+Caenorhabditis+elegans+member+of+the+Notch+family+of+receptors.">Germ-line tumor formation caused by activation of glp-1, a Caenorhabditis elegans member of the Notch family of receptors.</a> Development. 124 (4), 925-936 (1997).</li><li>Fox, P. M., Schedl, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+Germline+Stem+Cell+Differentiation+Following+Loss+of+GLP-1+Notch+Activity+in+Caenorhabditis+elegans.">Analysis of Germline Stem Cell Differentiation Following Loss of GLP-1 Notch Activity in Caenorhabditis elegans.</a> Genetics. 201 (1), 167-184 (2015).</li><li>Pasierbek, P., 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+Caenorhabditis+elegans+cohesion+protein+with+functions+in+meiotic+chromosome+pairing+and+disjunction.">A Caenorhabditis elegans cohesion protein with functions in meiotic chromosome pairing and disjunction.</a> Genes and Development. 15 (11), 1349-1360 (2001).</li><li>Klass, M., Wolf, N., Hirsh, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+the+male+reproductive+system+and+sexual+transformation+in+the+nematode+Caenorhabditis+elegans.">Development of the male reproductive system and sexual transformation in the nematode Caenorhabditis elegans.</a> Dev Biol. 52 (1), 1-18 (1976).</li><li>Korta, D. Z., Tuck, S., Hubbard, E. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=S6K+links+cell+fate,+cell+cycle+and+nutrient+response+in+C.+elegans+germline+stem/progenitor+cells.">S6K links cell fate, cell cycle and nutrient response in C. elegans germline stem/progenitor cells.</a> Development. 139 (5), 859-870 (2012).</li><li>Laband, K., 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=Chromosome+segregation+occurs+by+microtubule+pushing+in+oocytes.">Chromosome segregation occurs by microtubule pushing in oocytes.</a> Nat Commun. 8 (1), 1499 (2017).</li></ol>

このプロトコルの目標は、精度を向上させる・生殖細胞の解析に必要な時間を短縮することです。切り裂かれた germlines の標準的な準備の後、生殖核の三次元モデルは計算のレンダリングによって準備されます。空間における生殖核分布の観測を可能にしながら、三次元レンダリングは生殖細胞の特定の領域での核の数を計算します。本手法の重要な側面は、原子核のサイズと形状パラメー?...

シグナル伝達経路の哺乳類の保全は、複数の生物学的プロセス1,2を研究するエクセレント モデル線虫をなります。私たちの研究室では、線虫の生殖を使用して、遺伝子発現、アポトーシス、幹細胞の開発を研究します。生殖細胞は立体構造が、多くの研究は三次元解析の時間のかかり、労働集約的な性質のため二次元です。二次元解析が生殖細胞の生体内でイベントを偽ることがあります可能性が高いです。線虫 c. エレガンス大人の両性具有者がそれぞれの家は遠位生殖細胞未分化状態3,4を維持体の遠位先端細胞 (DTC)、2 つの生殖腕。これらの生殖細胞はその影響をエスケープ、DTC から離れるにつれて分化を開始して生殖細胞の近位端に達する彼らと卵子と精子になります。このプロセス中に胚細胞核は減数分裂5,6に移行する前に有糸分裂を経る。精子の生産はその後卵母細胞は成人で作成される開発の幼虫 4 (L4) によって完了です。精子は、卵子の胚を生成する肥やす交尾に格納されます。
線虫核の数, アポトーシス イベント、染色体ダイナミクスとタンパク質の発現や局在7 の番号変更を伴う生殖細胞の発生に影響を与えることができる複数の遺伝子と環境要因があります。 ,8,9,10,11。これらのイベントの分析には、核の形態と分布に基づく分化の各段階の身分証明書が必要です。大規模なサンプル サイズを手動でこれらのパラメーターを正確に分析するには、手間と時間がかかるです。カウント核、核の分布、蛋白質の表現、線虫の生殖の三次元検査のための自動方法を開発したこれらの欠点を回避するために、解析の整合性を有効にするには、細胞骨格と構造体です。三次元レンダリングと共焦点顕微鏡を用いて生殖細胞分化の各段階の身分証明書のサイズと形状パラメーターを生成されます。さらに、このメソッドは、生殖細胞の核と精子のカウントに加えて各卵母細胞における染色体数の得点できます。
生殖細胞の 1 つ重要な構造が細胞骨格、生殖細胞コンパートメント、エイズ細胞質ストリーミングと生殖核12保護に安定性を提供します。計算のレンダリングを使用すると、生殖細胞骨格の 3次元再構築を実施し、生殖細胞内の異なる細胞骨格機能を識別.ここでは、線虫の生殖の共焦点イメージングにより包括的な分析と組み合わせる方法計算の分析を説明するためにステップバイ ステップのプロトコルについて述べる。
急速な線虫の生殖 (図 1) の三次元解析法を提案します。三次元解析を使用して、セル (図 2) 生殖細胞系列の細胞骨格 (の再構築の自動化 (図 2および図 3) 生殖核の三次元分布カウントを研究することが可能です。図 3)、タンパク質 (図 4) や、交尾で精子と卵母細胞 (図 5) の染色体数を得点の分布。メソッドは、生殖細胞を簡単かつ正確な数量化できるだけでなく、生理学的に関連する表現型を識別します。

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			<td height="21" style="height:21px;width:335px;">C. elegans strains: wild type (N2, Bristol), rnp-8(tm2435) I/hT2[bli-4(e937) let-?(q782) qIs48] (I;III), cpb-3(bt17) I, glp-1 (e2141) III&#160;</td>
			<td style="width:264px;">Caenorhabditis Genetics Center (CGC)</td>
			<td style="width:168px;"></td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">OP50 Escherichia coli bacteria</td>
			<td style="width:264px;">Homemade</td>
			<td style="width:168px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nematode Growth Media (NGM) plates</td>
			<td style="width:264px;">Homemade</td>
			<td style="width:168px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">polyclonal rabbit anti-REC-8&#160;</td>
			<td>SDIX</td>
			<td>29470002</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Alexa 488 conjugated antibody raised in goat</td>
			<td>Thermofisher Scientific</td>
			<td>A-21236</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Cytoskeletal dye phalloidin&#160;</td>
			<td>Thermofisher Scientific</td>
			<td style="width:168px;">A-12380</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DAPI&#160;</td>
			<td>Thermofisher Scientific&#160;</td>
			<td>62248</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Poly-L-lysine&#160;</td>
			<td>Sigma Aldrich</td>
			<td>P5899</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Tetramisol&#160;</td>
			<td>Sigma Aldrich</td>
			<td>P5899</td>
			<td></td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;">MgSO4</td>
			<td>Sigma Aldrich</td>
			<td style="width:168px;">M7506</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">1M HEPES buffer, pH 7.4&#160;</td>
			<td>Sigma Aldrich</td>
			<td style="width:168px;">G0887</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">10X PBS pH 7.4&#160;</td>
			<td>Thermofisher Scientific</td>
			<td>AM9625</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Tween-20&#160;</td>
			<td>Sigma Aldrich</td>
			<td>P1389</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">EGTA</td>
			<td>Sigma Aldrich</td>
			<td>E3889</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">37% Paraformaldehyde solution</td>
			<td>Merck Millipore</td>
			<td>1040031000</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Normal goat serum</td>
			<td>Sigma Aldrich</td>
			<td>G9023</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Fluoroshield fixing reagent&#160;</td>
			<td>Sigma Aldrich</td>
			<td>F6182</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Ethanol&#160;</td>
			<td>Millipore&#160;</td>
			<td>1009832511</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Methanol</td>
			<td>Sigma Aldrich</td>
			<td>34860</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">20&#176;C &#38; 25&#176;CIncubator&#160;</td>
			<td>Any brand</td>
			<td style="width:168px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Light microscope</td>
			<td style="width:264px;">Any brand</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Confocal microscope&#160;&#160;</td>
			<td style="width:264px;">Any brand (Leica, Zeiss)</td>
			<td style="width:168px;"></td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">Computer equipped with Imaris suit 8.4.1 or later version, full licence to use the software and Matlab software.</td>
			<td style="width:264px;">Bitplane</td>
			<td style="width:168px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:335px;">Phospho buffered saline, pH 7.4</td>
			<td style="width:264px;">Homemade</td>
			<td style="width:168px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Teflon microscope slides&#160;</td>
			<td style="width:264px;">Tekdon&#160;</td>
			<td style="width:168px;">&#160;941-322-8288</td>
			<td></td>
		</tr>
	</tbody>
</table>

computational analysis of the caenorhabditis elegans germline to study the distribution of nuclei, proteins, and the cytoskeleton

線虫(C. elegans) 生殖細胞、幹細胞の開発、アポトーシスと染色体のダイナミクスを含むいくつかの重要な生物学的プロセスの研究に使用されます。生殖細胞はエクセレント モデルが、解析は、しばしば 2 つの時間と労力を三次元解析による寸法です。このような研究の主要な読み出しは、核と生殖細胞内のタンパク質分布の位です。生殖細胞数と生殖細胞の各地域で核の位置を決定する共焦点顕微鏡と計算のアプローチを使用しての自動解析を実行する方法を紹介します。本手法は、また異なる遺伝背景の蛋白質の表現を立体的に調べることができる生殖細胞蛋白質の分布を分析します。さらに、我々 の研究は、特定の空間発達要件に対応することができる生殖の異なる領域で細胞骨格のアーキテクチャでバリエーションを示します。最後に、提案手法は、各生殖の交尾で精子の自動カウントできます。一緒に取られて、私たちのメソッドは、線虫の生殖の迅速かつ再現性のある表現型分析できます。

図 1は、生殖細胞の三次元分析に必要な時間を示します。20 ° C で培養した L4 両性具有は、germlines を分離するために解剖、DAPI、ファロイジン、および生殖細胞のタンパク質に対する抗体で染色しました。共焦点顕微鏡を用いた Germlines が作成されます。完全な生殖核の位置と数をカウント、特定蛋白質の分布、細胞骨格構造やスコア分析に 10-15 ...

Watch this Scientific Journal Video about Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton at JoVE.com

Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton

核の分布、蛋白質および細胞骨格を研究する線虫生殖細胞の解析

線虫生殖.の三次元再構成のための自動化手法を提案します。本手法は、数と生殖と生殖細胞蛋白質の分布の解析と細胞骨格構造内にある各核の位置を決定します。

The Caenorhabditis elegans (C. elegans) germline is used to study several biologically important processes including stem cell development, apoptosis, and ...

The overall goal of this method is to automate the analysis of a Caenorhabditis elegans germline to study its nuclei, protein, and cytoskeletal distribution. This method can help answer the key questions in the C.Elegans field about the number of nuclei and sperm, nuclear distribution, and cytoskeletal structure of the germline. The main advantages of this technique are it reduces the analysis time, increases the sample size, and eliminate the human error associated with the manual analysis.To image the samples, place slides with stained germlines into the slide holder above the 63X objective of a confocal microscope, and locate a germline. Focus on the top of the germline, and mark it with the confocal microscope software. When the total germline thickness has been established, define the thickness of each slice up to 0.5 micrometers, and mark the complete germline.Then, start the acquisition, scanning each slice eight times and averaging the values to improve the image quality. When all of the images have been obtained, import the images to an appropriate image analysis software program, and use the surface function tool to select the mitotic region. An image of the distal end of the germline will appear.Cancel the automatic surface creation wizard, and manually draw a region of interest around the mitotic region at the first and last slices of the image from the three-dimensional stack. Click Create Surface, followed by Mask Channel, to mask all of the channels except the DAPI channel. Using the spot function tool, define the size parameters of the mitotic region with an XY diameter of two micrometers and with the Z diameter undefined.Click subtract background to subtract the background. To define the minimum threshold, increase the minimum 3D rendering threshold on a DAPI-stained wild-type germline until the first spot appears outside of the germline, and generate a 3D model for each region. After saving the images, click table to view the number of nuclei, as generated automatically by the software, and export the images as TIFF files.For the transition zone, create surface as explained before. Then, click Mask Channel to mask all the channels except the DAPI channel. Using spot function, define an XY diameter of two micrometers and Z diameter of 1.5 micrometers, and click subtract background to subtract the background.To define the minimum threshold, increase the minimum 3D rendering threshold on a DAPI-stained wild-type germline until the first spot appears outside of the germline, and generate a 3D model for each region. After saving the images, click table to view the number of nuclei, as generated automatically by the software, and export the images as TIFF files. For scoring the sperm number, select the spermatheca as the region of interest, as demonstrated for the nuclei regions, and use the spot function tool to define the XY diameter between 0.75 and one micrometers with an undefined Z diameter to detect each sperm.Select the Background Subtract box, and use the background correction values calculated by the software to subtract the background. Then, adjust the 3D rendering threshold to detect all of the DAPI-stained sperm in the spermatheca. For chromosome counting in the oocytes, select the oocytes and define the XY diameter as less than 0.75 micrometers, and define the threshold before developing the 3D models.Then, save the images for export as TIFF files. For cytoskeletal germline reconstruction, identify the mitotic region of interest in the germline and create a surface mask as previously demonstrated. Click Mask Channels to mask all of the channels except the phalloidin channel, and use the surface function tool to define a surface detail of 0.25 micrometers.After subtracting the background, adjust the 3D rendering threshold to save the developed 3D image for export as a TIFF file. The nuclei distribution is dependent on the stage of differentiation. For example, at the mitotic region, the inner actin appears as a solid mass upon which the nuclei are organized.In a wild-type germline, the mitotic region contains approximately 250 nuclei and is tightly packed with nuclei compared to the rest of the germline. As the nuclei move away from the distal end, however, they appear closer to the circumference of the germline, with the change in distribution starting at the transition zone and finishing as the nuclei enter the third stage of prophase in meiosis. At the transition zone, the germline inner actin assumes a more cylindrical structure, becoming a hollow cylinder as it reaches the pachytene.The second layer of actin covers the inner layer, giving shape to the germline. This cylinder within a cylinder actin structure disappears toward the oocyte region, at which point the actin appears as thick fibers covering the oocytes. In the spermatheca, the actin also forms into thick bundles of fiber, although these fibers appear to be packed more closely together than in the oocyte region.Three-dimensional rendering of the proximal end of the germline, as demonstrated, reveals an average of 151 sperm in each spermatheca. Once mastered, this analysis can be completed in 10 minutes per germline. While attempting this procedure, it is important to remember to define the analysis parameters according to the magnification of the objective used to visualize the germline in your experiment.After watching this video, you should have a good understanding of how to perform an automatic analysis of a germline and to study cytoskeletal structure and to score the number of the nuclei within the germline.

Research

JoVE Journal

Developmental Biology

Computational Analysis of the Caenorhabditis elegans Germline to Study the Distribution of Nuclei, Proteins, and the Cytoskeleton

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